[Bioc-devel] New Package Submission Deadline for Bioc Release 3.12

[Shepherd, Lori]

The final day to submit new packages to the Bioconductor contributions tracker 
to have a shot at being included in the upcoming 3.12 release is Friday October 
2nd.

Please note: submission by this date does not guarantee it will be included - 
the package must undergo an official review and be accepted by Wednesday 
October 21st.

https://github.com/Bioconductor/Contributions


Submissions after Friday October 2nd and those that are not accepted by October 
21th will still be able to be in Bioconductor but will be included in the 
development branch until the 3.13 release next Spring.


Please see the release schedule for other important deadlines
http://bioconductor.org/developers/release-schedule/


Thanks you



Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


This email message may contain legally privileged and/or confidential 
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Re: [Bioc-devel] [EXTERNAL]Re: Update R package I developed which has been released by bioconductor

[Shepherd, Lori]

The remote set up you have is correct.  Based on your previous email and your 
new email to bioc-devel it looks like the issue is your access 
credentials/public key  and activating your git credentials account so you can 
manage keys.


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Xiaowen Chen 
Sent: Thursday, September 24, 2020 10:04 PM
To: Shepherd, Lori ; bioc-devel@r-project.org 

Subject: Re: [EXTERNAL]Re: Update R package I developed which has been released 
by bioconductor


By the way, when I performed �git remote -v�

It is different with yours, I have a �.git� for upstream



origin https://github.com/TheJacksonLaboratory/epihet.git (fetch)

origin https://github.com/TheJacksonLaboratory/epihet.git (push)

upstream g...@git.bioconductor.org:packages/epihet.git (fetch)

upstream g...@git.bioconductor.org:packages/epihet.git (push)



Is it right?

Best,

Xiaowen



From: "Shepherd, Lori" 
Date: Monday, September 21, 2020 at 9:22 AM
To: Xiaowen Chen , "bioc-devel@r-project.org" 

Subject: [EXTERNAL]Re: Update R package I developed which has been released by 
bioconductor



Bioconductor would not have your package on github.  Bioconductor has your 
repository in a git server.   If you already have a clone of your github 
repository you could follow the instructions here to add the remote to the 
Bioconductor repository you referenced here:

http://bioconductor.org/developers/how-to/git/sync-existing-repositories/<http://secure-web.cisco.com/1CGgZFviZNHf_PzBZoDIbYfrWRtCAwE3cXN_Br4oaRqMG09TfgkuIPaaxMorCSWOA2I-xG9LPFz8HvmW0DJCUsryRqjDpMlCCP8YGR-HE6UHUyiBMtcTmAA0Hv_au5qFFBiqwEtqSc9J3USTWIxrc2P3gDVByHH5nd1KeU-vuxvjj0iZWdcn6vjPhFCKcPkoYhIm8P5XMBNhJ9DFKM75lukyg2L4We-JZRzv--Rty7SvM78FRQOJ_2eTDHZeFm35Jr4nNl9tWOsEAUQNqBYKSxN4FmxewdWNw66l2EV-6qsKNUzbO1QV8_cEUZTvco2jt/http%3A%2F%2Fbioconductor.org%2Fdevelopers%2Fhow-to%2Fgit%2Fsync-existing-repositories%2F>



so :

git clone  

cd epihet





Make sure you do the

git fetch --all

git pull upstream master before making any changes!! This will make sure you 
get the release version bumps the core team performed and that everything is 
up-to-date with our version of your repository at git.bioconductor.org



Once you add the remote upstream if you do git remote -v

origin should point to your github

upstream should point to Bioconductor

It would be something similar to



origin 
https://github.com/https://secure-web.cisco.com/1jto4PqGAETGWWrZg1lJy8YTYiLxiUl6gMitOiLT-D9gFgHHJkw_50iAKfQD_Y8E-yvcvsQstFNjcCTuG0KbQi7vAxa3T_mSjpQJyFClUmFsBZrjmkvqRRxT7EXwChsNl-Hey6xDhuuoav2gXJqN8ogSDyK5oa3ZuPgiYMyctBxAd8NlrTcgj9CztmC__ziIZOaq4GKOHK8zzkngrqfKqbd9UqMtEVhpy93WVveVYXbzNZT72inuxFJSEAfyaD_pGEreCH1Ve-6JSCfxspTiqV9518XeNfXDIYzL_wVd_qG3nYj9_Xy0Kiop6kFuVXh5-/https%3A%2F%2Fgithub.com%2F%253cYour>
 github> .git (fetch)

origin 
https://github.com/https://secure-web.cisco.com/1jto4PqGAETGWWrZg1lJy8YTYiLxiUl6gMitOiLT-D9gFgHHJkw_50iAKfQD_Y8E-yvcvsQstFNjcCTuG0KbQi7vAxa3T_mSjpQJyFClUmFsBZrjmkvqRRxT7EXwChsNl-Hey6xDhuuoav2gXJqN8ogSDyK5oa3ZuPgiYMyctBxAd8NlrTcgj9CztmC__ziIZOaq4GKOHK8zzkngrqfKqbd9UqMtEVhpy93WVveVYXbzNZT72inuxFJSEAfyaD_pGEreCH1Ve-6JSCfxspTiqV9518XeNfXDIYzL_wVd_qG3nYj9_Xy0Kiop6kFuVXh5-/https%3A%2F%2Fgithub.com%2F%253cYour>
 github>.git (push)

upstream g...@git.bioconductor.org:packages/epihet (fetch)

upstream g...@git.bioconductor.org:packages/epihet (push)





So when you push changes:



git push origin master

would update YOUR github

it is saying git push  to the origin which is your github on the master branch



To update on Bioconductor

git push upstream master

it is saying git push changes to the upstream with is the bioconductor remote 
master branch (devel)



Make sure the version number has a version bump!  Our version is at 1.5.0  so 
you would have to bump the z of version x.y.z for it to register on 
Bioconductor (>=  1.5.1  )



Hope that helps clarify.





Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263



From: Bioc-devel  on behalf of Xiaowen Chen 

Sent: Monday, September 21, 2020 8:57 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] Update R package I developed which has been released by 
bioconductor



Hi,
I submit R package called epihet on 2018. It has been accepted and released on 
Bioconductor.
Recently, we received the reviewers� comments about the corresponding paper for 
epihet, and the reviewer need us to add more parameters for some function in 
epihet,
Could you tell me what I should do step-by-step? Now I know the link

  1.  
http

Re: [Bioc-devel] Extensive updates to DiffBind: help reviewing docs and/or beta testing?

[Shepherd, Lori]

Hello,

Others may chime in with their opinions as well but my own thoughts...

I see no reason not to post on the support.bioconductor.org site to request 
some beta testing users.  I suggest using the "NEWS Event" for post type also 
explaining / informing of some of the big /extensive changes to the package.  
Similarly when the changes are formally released you can post on the support 
channel but I would either use  "News Event" or "Tutorial" as Post Type rather 
than a Question.

At release time we do include all changes listed in the NEWS files of packages. 
 Please make sure the NEWS file is up-to-date and properly formatted and it 
will also be included there.
Example release announcement from Bioc 3.11 of collated NEWS files:

http://bioconductor.org/news/bioc_3_11_release/

 If this could potentially impact package that depend, import, suggest your 
package I might also suggest personally reaching out to those package 
maintainers to see if they also wanted to beta test and to make sure their 
packages still function as intended  (I think currently there are two packages 
based on DiffBind landing page ChIPQC, vulcan)

https://www.bioconductor.org/packages/devel/bioc/html/DiffBind.html

Cheers,



Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Rory Stark 

Sent: Tuesday, September 22, 2020 6:06 PM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] Extensive updates to DiffBind: help reviewing docs and/or 
beta testing?

I've checked in extensive updates to the DiffBind ChIP/ATAC analysis package to 
reflect current best practices. I'm looking for help/advice in the following 
areas:

  1.  Reviewing the documentation (particularly the updated vignette), and/or 
beta-testing the code by running analyses on real data, if anyone on this list 
is interested. Is there any reason I shouldn't also make this request in the 
form of a question on the Bioconductor support forum?
  2.  Advice regarding the best way to inform users of the updates when the 
package is released next month. I don't really see announcements of package 
updates in any specific place. Is it appropriate to post it as a "question" on 
the support site, or is there a better forum?

The main updates are in the areas of modelling (full generalized designs and 
contrasts enabled), analysis (more standardized use of the underlying edgeR and 
DESeq2 packages), normalization (many new options, including background, 
offsets, and spike-ins, with an extended vignette section on this topic), and 
the automatic application of blacklists (and generation of experiment-specific 
greylists from control reads).

Feel free to contact me directly with questions/comments regarding the package.

Cheers-
Rory

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This email message may contain legally privileged and/or confidential 
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recipient(s), you are hereby notified that any disclosure, copying, 
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Re: [Bioc-devel] BiocCheckGitClone error

[Shepherd, Lori]

Yes.  Go ahead and submit the package to the tracker.  We can investigate this 
further with your assigned reviewer.  Sorry for the inconvenience.

Cheers,


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Emilie Secherre 
Sent: Wednesday, September 23, 2020 3:35 AM
To: Shepherd, Lori 
Cc: bioc-devel@r-project.org 
Subject: Re: [Bioc-devel] BiocCheckGitClone error

I still couldn't fix the issue, therefore is that allowed to just don't push 
the .Rproj file in github ?
Thanks in advance for your answer
Emilie

[https://secure-web.cisco.com/1HQT4avzpKVe6j7PuRRxrsuWMDf9cWUZuvWvcmpy-Hm9ylUZcF1ZK9nij0XmQseltPyNpiVmy97v-prEItcNCrEAqe9fIjUDyu0csq6FZafOd080slA_qK4RzvNTFpksPzhjCbqJXkoQCSo1LZBF77jZxj3MjR8FCoZMJJ4U34udEfaunOUDkSlbg8LQPaGHtHgwcnYoVrpHPwzErSn4gBD2ViioFX0Ih7UCTGBvlWD1s5570xDsW6bkezIp2St53vPw6zUrY7552Hb1Flo43oOYZU90q15k8vJV2UjMlfP9FzDiX9wEkI4CumAgAmcQw/https%3A%2F%2Fipmcdn.avast.com%2Fimages%2Ficons%2Ficon-envelope-tick-round-orange-animated-no-repeat-v1.gif]<https://secure-web.cisco.com/17l9BTXu1ngxN75bEPvs7hsonthCqIcSnKrCD9HCnP5tOgrGU5-zej7v0522uC4i4IlpHOf0dxvuBmjmp-mYGyLhOYm6G5dz0qxy97sD-4hkfK2s7jtNVPTC8-M2oeFhjkSXd0EDiTJId30qyV1gokBTajOy93gX-6Bx39Ot39ZeuXxBgVHHsd1p6GI31OoRT8s04vOXupH16uslqopreYCdf-PEpBNdUHVb1lVMIgzxxZxnYLAVPcKf5JD52Ft_kBpHjxgPSJW0_dLWw7IckfVXudVlCvf5Jb6tYp5WEqaRZ72fBgYDr_He-ocy8agax/https%3A%2F%2Fwww.avast.com%2Fsig-email%3Futm_medium%3Demail%26utm_source%3Dlink%26utm_campaign%3Dsig-email%26utm_content%3Dwebmail>
Garanti sans virus. 
www.avast.com<https://secure-web.cisco.com/17l9BTXu1ngxN75bEPvs7hsonthCqIcSnKrCD9HCnP5tOgrGU5-zej7v0522uC4i4IlpHOf0dxvuBmjmp-mYGyLhOYm6G5dz0qxy97sD-4hkfK2s7jtNVPTC8-M2oeFhjkSXd0EDiTJId30qyV1gokBTajOy93gX-6Bx39Ot39ZeuXxBgVHHsd1p6GI31OoRT8s04vOXupH16uslqopreYCdf-PEpBNdUHVb1lVMIgzxxZxnYLAVPcKf5JD52Ft_kBpHjxgPSJW0_dLWw7IckfVXudVlCvf5Jb6tYp5WEqaRZ72fBgYDr_He-ocy8agax/https%3A%2F%2Fwww.avast.com%2Fsig-email%3Futm_medium%3Demail%26utm_source%3Dlink%26utm_campaign%3Dsig-email%26utm_content%3Dwebmail>

Le mar. 22 sept. 2020 � 15:36, Emilie Secherre 
mailto:emiseche...@gmail.com>> a �crit :
I pushed famat.Rproj after .gitignore was created and pushed with "famat.Rproj" 
in it. That's why i don't understand why famat.Rproj is still in the clone 
folder.

[https://secure-web.cisco.com/1HQT4avzpKVe6j7PuRRxrsuWMDf9cWUZuvWvcmpy-Hm9ylUZcF1ZK9nij0XmQseltPyNpiVmy97v-prEItcNCrEAqe9fIjUDyu0csq6FZafOd080slA_qK4RzvNTFpksPzhjCbqJXkoQCSo1LZBF77jZxj3MjR8FCoZMJJ4U34udEfaunOUDkSlbg8LQPaGHtHgwcnYoVrpHPwzErSn4gBD2ViioFX0Ih7UCTGBvlWD1s5570xDsW6bkezIp2St53vPw6zUrY7552Hb1Flo43oOYZU90q15k8vJV2UjMlfP9FzDiX9wEkI4CumAgAmcQw/https%3A%2F%2Fipmcdn.avast.com%2Fimages%2Ficons%2Ficon-envelope-tick-round-orange-animated-no-repeat-v1.gif]<https://secure-web.cisco.com/17l9BTXu1ngxN75bEPvs7hsonthCqIcSnKrCD9HCnP5tOgrGU5-zej7v0522uC4i4IlpHOf0dxvuBmjmp-mYGyLhOYm6G5dz0qxy97sD-4hkfK2s7jtNVPTC8-M2oeFhjkSXd0EDiTJId30qyV1gokBTajOy93gX-6Bx39Ot39ZeuXxBgVHHsd1p6GI31OoRT8s04vOXupH16uslqopreYCdf-PEpBNdUHVb1lVMIgzxxZxnYLAVPcKf5JD52Ft_kBpHjxgPSJW0_dLWw7IckfVXudVlCvf5Jb6tYp5WEqaRZ72fBgYDr_He-ocy8agax/https%3A%2F%2Fwww.avast.com%2Fsig-email%3Futm_medium%3Demail%26utm_source%3Dlink%26utm_campaign%3Dsig-email%26utm_content%3Dwebmail>
Garanti sans virus. 
www.avast.com<https://secure-web.cisco.com/17l9BTXu1ngxN75bEPvs7hsonthCqIcSnKrCD9HCnP5tOgrGU5-zej7v0522uC4i4IlpHOf0dxvuBmjmp-mYGyLhOYm6G5dz0qxy97sD-4hkfK2s7jtNVPTC8-M2oeFhjkSXd0EDiTJId30qyV1gokBTajOy93gX-6Bx39Ot39ZeuXxBgVHHsd1p6GI31OoRT8s04vOXupH16uslqopreYCdf-PEpBNdUHVb1lVMIgzxxZxnYLAVPcKf5JD52Ft_kBpHjxgPSJW0_dLWw7IckfVXudVlCvf5Jb6tYp5WEqaRZ72fBgYDr_He-ocy8agax/https%3A%2F%2Fwww.avast.com%2Fsig-email%3Futm_medium%3Demail%26utm_source%3Dlink%26utm_campaign%3Dsig-email%26utm_content%3Dwebmail>

Le mar. 22 sept. 2020 � 15:32, Shepherd, Lori 
mailto:lori.sheph...@roswellpark.org>> a �crit :
So I think the file probably got pushed up before you added it to .gitignore.  
So you would probably want to git rm the files,  commit, and push.  Then you 
could add them back in after and if they were still listed in the .gitignore 
then they would be ignored.


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Emilie Secherre mailto:emiseche...@gmail.com>>
Sent: Tuesday, September 22, 2020 9:04 AM
To: Shepherd, Lori 
Cc: bioc-devel@r-project.org<mailto:bioc-devel@r-project.org> 
mailto:bioc-devel@r-project.org>>
Subject: Re: [Bioc-devel] BiocCheckGitClone error

This time I used Git clone folder. Though, when I push famat package in github, 
.gitignore file isn't uploaded, so I created a .gitignore file in the github 
repository with "famat.Rproj&quo

Re: [Bioc-devel] BiocCheckGitClone error

[Shepherd, Lori]

So I think the file probably got pushed up before you added it to .gitignore.  
So you would probably want to git rm the files,  commit, and push.  Then you 
could add them back in after and if they were still listed in the .gitignore 
then they would be ignored.


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Emilie Secherre 
Sent: Tuesday, September 22, 2020 9:04 AM
To: Shepherd, Lori 
Cc: bioc-devel@r-project.org 
Subject: Re: [Bioc-devel] BiocCheckGitClone error

This time I used Git clone folder. Though, when I push famat package in github, 
.gitignore file isn't uploaded, so I created a .gitignore file in the github 
repository with "famat.Rproj" in it before pushing the whole package. 
Unfortunately, the "famat.Rproj" file is still in the git clone folder...

[https://secure-web.cisco.com/14HlJ6pYPmc3ca4y-t8kMrtl9__nsZZIVdh1FyubkHtI_uHav7g8NmQ3g-Ddrj8crOerXSz7-BGWmj25QldqKh3CziRw4-vIC05u5I75Qo3f0daNrBjyscENAIKQkhC87QNrfNSTXCTnRjEpzGPHtVFS6uzyXWChEq5nFnl-74b4Fcg092PiTaoGdd1X_Rg4D9CpCcT2XMQv7sIH2ep_u3gbh6cOAd_ELgRxwS30KMyWcEqRLglF7qSBH_7DOghdgZbaD1ZGO_eexhcDLj3Vq46ylckVe1nX6YLAESP1vV1hUpZ7guAhahUlHcW-7w6iM/https%3A%2F%2Fipmcdn.avast.com%2Fimages%2Ficons%2Ficon-envelope-tick-round-orange-animated-no-repeat-v1.gif]<https://secure-web.cisco.com/1kUcjeK1l5uJLWUgk1BEPSSsClwf6nXlSgM5k14zf32z1bnZJmqgWRn1b1BpkEBSNysDnSMiukeI70FhY3w7_9VXHSZxuSFyPsoZOCeYdt6XZmvRyG1y-kHEda2Ffe3Vy6uhqWccL_pE3Ru9s5EQyoBoVuNEs56AUlsD4cWsBjcfXiCDL6EBRbgmOIwR9l9iRR6VAMTQ5o8azDl8DAocIGa6H7VwNFbowLLmnLuTIUqMKK0TiEcIPataXipooaiyDu95bM1X0bo-7BHtGzt2UocrIT9TTtSxudid7Dk4nuBjLFCRbpxuVJYLfsEwA0-hU/https%3A%2F%2Fwww.avast.com%2Fsig-email%3Futm_medium%3Demail%26utm_source%3Dlink%26utm_campaign%3Dsig-email%26utm_content%3Dwebmail>
Garanti sans virus. 
www.avast.com<https://secure-web.cisco.com/1kUcjeK1l5uJLWUgk1BEPSSsClwf6nXlSgM5k14zf32z1bnZJmqgWRn1b1BpkEBSNysDnSMiukeI70FhY3w7_9VXHSZxuSFyPsoZOCeYdt6XZmvRyG1y-kHEda2Ffe3Vy6uhqWccL_pE3Ru9s5EQyoBoVuNEs56AUlsD4cWsBjcfXiCDL6EBRbgmOIwR9l9iRR6VAMTQ5o8azDl8DAocIGa6H7VwNFbowLLmnLuTIUqMKK0TiEcIPataXipooaiyDu95bM1X0bo-7BHtGzt2UocrIT9TTtSxudid7Dk4nuBjLFCRbpxuVJYLfsEwA0-hU/https%3A%2F%2Fwww.avast.com%2Fsig-email%3Futm_medium%3Demail%26utm_source%3Dlink%26utm_campaign%3Dsig-email%26utm_content%3Dwebmail>

Le mar. 22 sept. 2020 � 14:12, Shepherd, Lori 
mailto:lori.sheph...@roswellpark.org>> a �crit :
We run BiocCheckGitClone on a raw clone of the github directory.   If you are 
running it locally and had .gitignored those files before pushing to github 
then you should be okay.   A way to test this would be to do a git clone  of 
your github repository, in a different, temporary location to see if those 
files are still present when you do a git clone and running BiocCheckGitClone 
on that temporary cloned copy.

Cheers


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel 
mailto:bioc-devel-boun...@r-project.org>> on 
behalf of Emilie Secherre mailto:emiseche...@gmail.com>>
Sent: Tuesday, September 22, 2020 4:57 AM
To: bioc-devel@r-project.org<mailto:bioc-devel@r-project.org> 
mailto:bioc-devel@r-project.org>>
Subject: [Bioc-devel] BiocCheckGitClone error

Hello,

When i run R CMD and BiocCheck, i get no error or warnings. But, when
running BiocCheckGitClone, i'm getting this error :
System files found that should not be tracked : famat.Rproj, .Rhistory
The issue is that both files are in .gitignore, but this error isn't
removed... I'm using BiocCheckGitClone on the same file as BiocCheck.

Thank you in advance for your answer,

Emilie Secherre

<https://secure-web.cisco.com/1lwre-aHHcRizwgWLTysqlxTkQiybIA-Ps00M-PLKpqFVzJ64aTPySscIJyAnB8wINYl6Wsd_ltPJc8U5_1kHh6b6TDxaWvrB9i-FIKc_zu3ZOWI2irLvOWfyB-xEN1-NQq2ZiloDniTzfDEFtTRs87pcEz0oTQNyG5GtwQXpC3M3F2Eox3UixhBzpARysKMIYCbPbVuSmVxzchWnD4j4KgrxbcxPs61hCx0H-GoRXd7K_0oiIFq1wIg4YUAEP_66v4VUR3_ajkfABp01qcaJCnIjKHswCiAKb9Ta_tQTbiTb93glCt883z5FmK3T0pGo/https%3A%2F%2Fwww.avast.com%2Fsig-email%3Futm_medium%3Demail%26utm_source%3Dlink%26utm_campaign%3Dsig-email%26utm_content%3Dwebmail>
Garanti
sans virus. 
http://secure-web.cisco.com/1dpic_w7RKEppZqqs_Yss0WOlzxlFcgXQS9dTNgAck28Z4H--TRKKnEOu7DkBkYh4uI1v2iDQWoPnb-1lZuxZkxly8iOjadcs_GtP6slHhaA0r3px5xJX0Lyh_eBLQwJLOqvbP3wmQ0uTRem2-wSPhpNzqvnVu1nwNBcDWzN8gievsPXOUg1C0kxueCoPAU-irC58E9JwH1EJtFZINi4UZCHKD5cHwpoMNs5MZHQw4vBH8jyo2TuuuL3K8KeKTxTsGEi11Q2oky72N-x6851KYx7Qb4h2YVlZFKW8Z-SfbBB36f-nlMcb2MT8MhCEKwvT/http%3A%2F%2Fwww.avast.com
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Re: [Bioc-devel] Bioconductor package DegNorm

[Shepherd, Lori]

We do not see any changes in the version on Bioconductor  git.bioconductor.org. 
 You need to push the changes to that location not your github location and 
there needs to be a valid version bump for the changes to propagate.

Firstly,  please check your remotes
git remote -v

upstream should point to git.bioconductor.org
upstream  g...@git.bioconductor.org:packages/DegNorm

The instructions you sent that you followed were for maintaining a 
Bioconductor-only repository for an existing package.  This would be if you did 
not have a github repository of your own or only wanted to use the 
git.bioconductor.org version.  If this is not the case please refer to

https://bioconductor.org/developers/how-to/git/sync-existing-repositories/

These instructions would allow you to keep pointers to both a personal github  
and the bioconductor official repository.

make sure there are no errors when you
git pull upstream master

and/or no errors when trying to push changes up:
git push upstream master


If there are and it says something about public keys:
Did you follow the instructions for initilizing your git credentials when the 
package was accepted
https://github.com/Bioconductor/Contributions/issues/1491#issuecomment-637138209

Cheers,


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Jiping Wang 
Sent: Tuesday, September 22, 2020 8:48 AM
To: Shepherd, Lori 
Cc: bioc-devel@r-project.org 
Subject: Re: [Bioc-devel] Bioconductor package DegNorm

Hi Lori,

   I have made changes to some of the R functions a few months ago, also I have 
changed version etc (recently
fixed a few bugs). But I noticed in the current Bioconductor version, such 
changed have never been included. Could you advise what happened? Or anything 
additional should I do? I believed I followed steps in the following.
Thanks.

jiping

https://secure-web.cisco.com/1C78sfLYvvhE9fnuPonlmLQohdaSv4_KuRnc8mKA4EZauqXZ2sarLLn6Nq2bwi5YanH8qClEyO0YZ6R7js8DLFny1IDlHiFhN6o0QuIxKYYeEb5Gn0od_wEtSKembRmYmefR-zKOWccVhCpfMCjluJRLSNz5DYwMG1fIr06DCG0yjsRFcj5wcNNMRTrN9pMAxsY18Bh-182Qe52J2vgS5HITGNAlqIr2VPj2TkidmkclTH5ByuO68nNfG4tH5WjqfjFa5I6hp6Ex7Pca_rKjjBKZdYjyEX86zW0qacVHr8OhHilbCFNMqciPumMPQqfyDvM-n7aOMexDEWhIIkJJCSQ/https%3A%2F%2Fbioconductor.org%2Fdevelopers%2Fhow-to%2Fgit%2Fmaintain-bioc-only%2F

On 9/2/20, 12:29 PM, "Bioc-devel on behalf of Jiping Wang" 
 wrote:

Hi Lori,

  I hope I have fixed all bugs. I have pushed all changed to github. Thanks 
for help.

Best,
jiping

    From: "Shepherd, Lori" 
Date: Wednesday, September 2, 2020 at 9:40 AM
To: jiping/wang User 
Subject: Bioconductor package DegNorm

Hello Package Maintainer,

The Bioconductor Team would like to notify you that your package is 
currently
failing on the devel 3.12 version of Bioconductor, and has been for an 
extended
period of time.  Please fix your package to R CMD build and R CMD check 
cleanly
immediately to avoid deprecation of your package. While devel is a place to
experiment with new features, we expect packages to build and check cleanly 
in a
reasonable time period and not stay broken for any extended period of time. 
If
you are having trouble or have any further questions please do not hesitate 
to
reach out to the developers mailing list at bioc-devel@r-project.org

We appreciate your attention to this matter. The package has been failing 
since 06/29/20

Cheers


https://secure-web.cisco.com/1Gu6p5E755WRiodhYC0LQ1Wj0EDIL2NGK6Iv20B_ZZkDNzRm670rMz9xHbEYGCVLuVUHHYj26wP8fuBf8BPjwfLfvOIY72aowjnoYc_IfFUcp8F7GccSbJ5S-0bnKw9SIV8q_1hQFzA_GRFtPFRPOddJSL0yAUWDu6B6uPYsvolsgei4cbq1myEH5fLoNrvrjeLrr9ByKsT3k69VStgs5IJLF7QLGgP8wk36a2SXGFzvNq-_1DaQzubh0P8u3jNPiGQkpSR3h_DR8Q8TBLpiEgrBVLOmqF-fEZOOPPCrsDeEJR0dokBTtwu6Go_JvKB1Po9My4GLqxMjNJgy1zYGsjA/https%3A%2F%2Furldefense.com%2Fv3%2F__http%3A%2F%2Fbioconductor.org%2FcheckResults%2Fdevel%2Fbioc-LATEST%2FDegNorm__%3B%21%21Dq0X2DkFhyF93HkjWTBQKhk%21Fj9WnIAbw3NfGYpF-gcbNWKpL-EdvTmxq2BMLQVvyYgs3mA01UtyJ84W8D1TNLHHTmtBAA%24



Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

This email message may contain legally privileged and/or confidential 
information. If you are not the intended recipient(s), or the employee or agent 
responsible for the delivery of this message to the intended recipient(s), you 
are hereby notified that any disclosure, copying, distribution, or use of this 
email message is prohibited. If you have received this message in error, please 
notify the sender immediately by e-mail and delete this email message from your 
computer. Thank you.

   

Re: [Bioc-devel] BiocCheckGitClone error

[Shepherd, Lori]

We run BiocCheckGitClone on a raw clone of the github directory.   If you are 
running it locally and had .gitignored those files before pushing to github 
then you should be okay.   A way to test this would be to do a git clone​  of 
your github repository, in a different, temporary location to see if those 
files are still present when you do a git clone and running BiocCheckGitClone 
on that temporary cloned copy.

Cheers


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Emilie 
Secherre 
Sent: Tuesday, September 22, 2020 4:57 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] BiocCheckGitClone error

Hello,

When i run R CMD and BiocCheck, i get no error or warnings. But, when
running BiocCheckGitClone, i'm getting this error :
System files found that should not be tracked : famat.Rproj, .Rhistory
The issue is that both files are in .gitignore, but this error isn't
removed... I'm using BiocCheckGitClone on the same file as BiocCheck.

Thank you in advance for your answer,

Emilie Secherre


Garanti
sans virus. 
http://secure-web.cisco.com/1dpic_w7RKEppZqqs_Yss0WOlzxlFcgXQS9dTNgAck28Z4H--TRKKnEOu7DkBkYh4uI1v2iDQWoPnb-1lZuxZkxly8iOjadcs_GtP6slHhaA0r3px5xJX0Lyh_eBLQwJLOqvbP3wmQ0uTRem2-wSPhpNzqvnVu1nwNBcDWzN8gievsPXOUg1C0kxueCoPAU-irC58E9JwH1EJtFZINi4UZCHKD5cHwpoMNs5MZHQw4vBH8jyo2TuuuL3K8KeKTxTsGEi11Q2oky72N-x6851KYx7Qb4h2YVlZFKW8Z-SfbBB36f-nlMcb2MT8MhCEKwvT/http%3A%2F%2Fwww.avast.com

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Re: [Bioc-devel] Update R package I developed which has been released by bioconductor

[Shepherd, Lori]

Bioconductor would not have your package on github.  Bioconductor has your 
repository in a git server.   If you already have a clone of your github 
repository you could follow the instructions here to add the remote to the 
Bioconductor repository you referenced here:
http://bioconductor.org/developers/how-to/git/sync-existing-repositories/

so :
git clone  
cd epihet


Make sure you do the
git fetch --all
git pull upstream master before making any changes!! This will make sure you 
get the release version bumps the core team performed and that everything is 
up-to-date with our version of your repository at git.bioconductor.org

Once you add the remote upstream if you do git remote -v
origin should point to your github
upstream should point to Bioconductor
It would be something similar to

origin https://github.com/ .git (fetch)
origin https://github.com/.git (push)
upstream g...@git.bioconductor.org:packages/epihet (fetch)
upstream g...@git.bioconductor.org:packages/epihet (push)


So when you push changes:

git push origin master
would update YOUR github
it is saying git push  to the origin which is your github on the master branch

To update on Bioconductor
git push upstream master
it is saying git push changes to the upstream with is the bioconductor remote 
master branch (devel)

Make sure the version number has a version bump!  Our version is at 1.5.0  so 
you would have to bump the z of version x.y.z for it to register on 
Bioconductor (>=  1.5.1  )

Hope that helps clarify.




Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Xiaowen Chen 

Sent: Monday, September 21, 2020 8:57 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] Update R package I developed which has been released by 
bioconductor

Hi,
I submit R package called epihet on 2018. It has been accepted and released on 
Bioconductor.
Recently, we received the reviewers� comments about the corresponding paper for 
epihet, and the reviewer need us to add more parameters for some function in 
epihet,
Could you tell me what I should do step-by-step? Now I know the link

  1.  
http://secure-web.cisco.com/1-EVvVLIafjMbq01E8DqEQNgmvkKvvnjD-0pOAg6fnFQJZO7UJhpm74hsFevQdnOceH8Ueh2BWTT9kb9bsdL13IqIS93SOktOTaRvzl88vZQIjyKpVvpYcasFBguMZ539EF4nnf-yJhgY9ZqzCEecd6Lt5PcT0r6hY6iwYo-kRFbGTZgQvUYbiv4RVLCB0aMNRwNiL_faHaysCM-N9aMnkF0QCtDVuYHDOpwzG0F5eCLtvMhWpKTH29P3I5RfQgzRralE_Wz3O-tYENZrRrhyzlXMEbSEmVj6BtcGZ5p0YdkUaFJ_5NswJT984xe0R4_R/http%3A%2F%2Fbioconductor.org%2Fdevelopers%2Fhow-to%2Fgit%2Fsync-existing-repositories%2F
 for sync an existing GitHub repository with Bioconductor
  2.  
http://secure-web.cisco.com/1a15GjCpVQyP3eF8WecbERPx8u0-Q3oUVwuRg9flwlizP3Dc6jfSdhF4CRMxd0I4M7S6UAfWCIbVnl67rKj6PsgIKMl5dppsGvqDKq8rf66Cm3qOq2JthrZCWEmdK4xZxV60M5gelNAIlZgVx1Q4HRDN_N4xilgDKIOy5WaMqWYc-57D0HIplyKyzL7xcmCZRnrdmYTfuxIAtS9KhxTHXcp1dfY6CZmW00wMdYPUWfUCkFjSe4_DancgDyMQkmB6EZ4S-PO5qKEdtIAkAEscewyygalAfrQEpiFigAz2iRvFjnDKvTOw5mBH4gvd0eGkb/http%3A%2F%2Fbioconductor.org%2Fdevelopers%2Fhow-to%2Fgit%2Fbug-fix-in-release-and-devel%2F
 for fix bugs in devel and release
but I still not sure which github repository I need to git clone on my local 
machine, my own github or Bioconductor github, but I did not found my package 
�epihet� on Bioconductor github

Thank you.
Best,
Xiaowen

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agent responsible for the delivery of this message to the intended 
recipient(s), you are hereby notified that any disclosure, copying, 
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Re: [Bioc-devel] Few questions of maintaining a new bioconductor package

[Shepherd, Lori]

In Addition to Nitesh's comments:

Please do not push the version to 1.0.0 yourself.  This will be done at the 
time of release by the core team.  Continue to increment z of verion x.y.z.   
For example 0.99.5.

For now,  you have to wait for a nightly build to view the results of the 
build/check.
http://bioconductor.org/checkResults/devel/bioc-LATEST/TimiRGeN/

Information on timing of build report and how long from push to viewing is 
summarized at the top of this page:
http://bioconductor.org/developers/how-to/troubleshoot-build-report/
Remember new builds will only register with a valid version bump.


You could always create a temporary directory and try checking the code out 
from git.bioconductor.org to see if the changes got successfully pushed to the 
server.  Or check out the RSS feed

Cheers,


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Krutik Patel 
(PGR) 
Sent: Friday, September 18, 2020 5:01 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] Few questions of maintaining a new bioconductor package

Dear Bioconductor team,

I've recently had my package, TimiRGeN, accepted into bioconductor and have a 
few questions on the maintenance side of things.

1) I am ready to push a newer version of the package. Will I have to set the 
version to 1.0.0 now? Currently it is version 0.99.4158.

2) Once pushed, how can I check if the build has been successful? Will I have 
to wait and see if it has passed the nightly builds on build/checkResults? Or 
is there a faster method.

3) I would like to set up a new SSH key and use this to maintain my package. To 
do this I will need to activate my account on Bioconductor Git Credentials, but 
I do not remember setting up a password for this.

Any help in these matters would be great.

Best,
Krutik

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Re: [Bioc-devel] Packagebuilder skips building of MsCoreUtils package

[Shepherd, Lori]

This seems to have resolved on today's build report.


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Rainer 
Johannes 
Sent: Tuesday, September 15, 2020 3:52 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] Packagebuilder skips building of MsCoreUtils package

dear all,

seems that the BioC package builder does not build the MsCoreUtils package even 
after we bumped the version. The last change date listed in the BioC 3.12 check 
results is "2020-06-23 06:08:43 -0400" and version 1.1.3 is listed, but in the 
BioC git we have already version 1.1.5. Please let us know if we have 
mis-configured something so that we can fix that.

thanks, jo


Johannes Rainer, PhD
Eurac Research

Institute for Biomedicine
Via Galvani 31, I-39100 Bolzano, Italy
M +39 327 4075490
T +39 0471 055 491
email: johannes.rai...@eurac.edu
github: jorainer
twitter: jo_rainer

Legal Seat
Viale Druso 1, I-39100 Bolzano, Italy
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If you receive this transmission by error, please notify the author immediately 
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Re: [Bioc-devel] "length(url) == 1 is not TRUE" error for vignette only on build system

[Shepherd, Lori]

To follow up on this:

Please check the package code for adding/accessing resources in the netDx 
package.  If the BiocFileCache options were used correctly there should not 
have been multiple entries added to the builders cache as Martin demonstrated 
below.

Once the package has been updated to ensure duplicate entries will not be 
added, we can clean up the builders.  The package code should be adjusted first 
to ensure that users will not encounter the same situation.



Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Martin Morgan 

Sent: Friday, September 11, 2020 6:22 PM
To: Pages, Herve ; Shraddha Pai 
Cc: bioc-devel@r-project.org 
Subject: Re: [Bioc-devel] "length(url) == 1 is not TRUE" error for vignette 
only on build system

bfcquery() just searches the cache, so if you've created two resources that 
match the name then you end up with two rids

> xx = bfcnew(bfc, "foo")
> bfcquery(bfc, "foo", "rname")
# A tibble: 1 x 10
  rid   rname create_time access_time rpath rtype fpath last_modified_t� etag
 
1 BFC3  foo   2020-09-11� 2020-09-11� /Use� rela� 64ea�   NA NA
# � with 1 more variable: expires 
> xx = bfcnew(bfc, "foo_bar")
> bfcquery(bfc, "foo", "rname")
# A tibble: 2 x 10
  rid   rname create_time access_time rpath rtype fpath last_modified_t� etag
 
1 BFC3  foo   2020-09-11� 2020-09-11� /Use� rela� 64ea�   NA NA
2 BFC4  foo_� 2020-09-11� 2020-09-11� /Use� rela� 64ea�   NA NA
# � with 1 more variable: expires 

and even

> xx = bfcnew(bfc, "foo_bar")
> bfcquery(bfc, "foo", "rname")
# A tibble: 3 x 10
  rid   rname create_time access_time rpath rtype fpath last_modified_t� etag
 
1 BFC3  foo   2020-09-11� 2020-09-11� /Use� rela� 64ea�   NA NA
2 BFC4  foo_� 2020-09-11� 2020-09-11� /Use� rela� 64ea�   NA NA
3 BFC5  foo_� 2020-09-11� 2020-09-11� /Use� rela� 64ea�   NA NA
# � with 1 more variable: expires 

If the cache is under netDx control, then you can be careful about creating new 
resources by checking first whether the resource exists, as outlined in 
http://secure-web.cisco.com/1t9-aFwD7wK-0S-MuqPB5uIzT5hQ2gyAD8KMGooS3HThd0k45RZ-frPKl-6Yl2EwZFFcmutTlgEODe0vTjmGHdvrtnhcf5beUQTSS3KiUAl4eWVWv4m3kjsTCUxTVQ2Ll5cGeus1QPlv2osdgHIycOGo6WKDjPqb6PoCxqWOMpEB_x8cSenUxF2N0OkDSEKuwlgJzHwqGjVOwqZQ_odXuqKEnKXz5moLlJO0XSz5XXkTj4kTGwtMAjqKAk_tR8DujPGfYr6Cc70ReKMZUWNVIOc4JgCOAmkILBW94Rp0x_3CX-8DEDeaRhlrgoM7MxkqHGyB0UxHyCXGepxXY196Uglz7WmH1uY02-XQsQ_6e8og/http%3A%2F%2Fbioconductor.org%2Fpackages%2Fdevel%2Fbioc%2Fvignettes%2FBiocFileCache%2Finst%2Fdoc%2FBiocFileCache.html%23cache-to-manage-package-data

If one is managing internet resources, just  use bfcadd

> bfc <- BiocFileCache()
> path <- bfcrpath(bfc, url)
adding rname 
'https://secure-web.cisco.com/1lUwUbgjSoXsv6f7JfdXhRG2f7_ISpNGSvQkNDjD3wQSEEMkTAVHfopgsowEo1GgsXrbByzyoKcAqYa3Kw2bxocuFRTwCIF5UxwWY7fw_FCeNByJcX4L4A9pGyPD1Il4OWJRoYewqI9SOxbFsK6XqqYQmOxhzALdAwDrJw1cOOpppzIIoz5unFJOO2Ihuca8QuIswQZGQqxSBXbeuu8WxSl9QoenolmV7PHovZu_sUMd1DYSflBtliuDz8hRJHSdp-N4wLsvl5GZXxTcJH4ZruhecvOJPR7aGrHCRLZln3wWoMKctL_Oc2xnUYu0ZYrCrVD5MQ8Wf7fgFEl7RPTt5RbTMxrbLO0zXxZZaEwhL5AU/https%3A%2F%2Fbioconductor.org%2Findex.html'
  |==| 100%

> path <- bfcrpath(bfc, url)
>

where the first time 'url' is used (as a unique key) the resource is downloaded 
to the cache; the second time it is simply accessed from the cache.

It might be necessary to manually 'clean up' the builders

Martin


On 9/11/20, 4:10 PM, "Bioc-devel on behalf of Pages, Herve" 
 wrote:

I'm not a BiocFileCache expert, sorry. You will probably get better help
by opening a BiocFileCache issue on GitHub.

Cheers,
H.


On 9/11/20 12:00, Shraddha Pai wrote:
> Hi Herve,
> Sorry - hit shortcut to "send" by mistake.
>
> This is the code snippet that got cut off:
> if (length(rid)>1) {
> x <- as.POSIXct(rid_rec$last_modified_time)
> y <- order(x,decreasing=TRUE)
> rid <- rid[y[1]]
> }
>
> Overkill? I could just take rid[1] but that would not be methodical.
>
> Will file issue once you confirm that the problem is that there should
> be a unique rid associated with each rname.
>
> Thanks again - appreciate it,
> Shraddha
>
> On Fri, Sep 11, 2020 at 2:57 PM Shraddha Pai  > wrote:
>
> Hi Herve,
> Thank you for pinpointing this.
> Just so I'm clear: rid should not have two IDs correct?
> For each rname, the cache should only have a unique ID, right? Or is
> that not the case?
>
> To get the package to build I will take the 

Re: [Bioc-devel] Vignette examples

[Shepherd, Lori]

Did you export the function in the package?



Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Emilie 
Secherre 
Sent: Thursday, September 10, 2020 10:38 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] Vignette examples

Hello,



I'm currently making a bioconductor package. When i'm running R CMD check,
all the examples i used in function vignettes have one issue : could not
find function "mypckgfunction". Is there a way to fix this issue ? The
examples work perfectly when i'm using them in a R script, and are used in
unit tests without any warning, it's just about examples in vignettes...



Thank you in advance for your answer,

Emilie Secherre

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Re: [Bioc-devel] Build issues under macOS

[Shepherd, Lori]

I believe the issue has been resolved.

CellaRepertorium and BayesSpace also have been manually rerun so you should 
have (or shortly have) accurate build reports on your open submission.

Cheers


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Shepherd, Lori 

Sent: Wednesday, September 9, 2020 11:29 AM
To: McDavid, Andrew ; 
bioc-devel@r-project.org ; mst...@fredhutch.org 

Subject: Re: [Bioc-devel] Build issues under macOS

Thanks everyone.  I'm looking into the Single Package Builder issues with the 
build bin and hopefully will have a solution uploaded soon.



Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of McDavid, 
Andrew 
Sent: Wednesday, September 9, 2020 11:26 AM
To: bioc-devel@r-project.org ; mst...@fredhutch.org 

Subject: Re: [Bioc-devel] Build issues under macOS

FWIW I am getting the same error in my builds on merida1 for a package that is 
under review:
http://secure-web.cisco.com/1fi0cAc90qwsj_0fchhD0YC4uiLHQd0o4HYR5eLE3tx2LPSw-Z6bzsHUh9GORoSnthoiawosT0tgXA49TjW2iE9qNJJqCOburi1VJCCXkJ0wzP9uxDkH6LztUpfySrdCbtBAy2zLo-7sL5waSK4sqWBOnh-P598vNN5kyAWmdFy4xudqD-4_8H5VaCpgDa37lG422UiagbjAWLxSRuBZKS4j4-24rb6gNs61RPbPo_1OsybmZ3CkZnf7kYXNTP8lanOlmNLx-rx5-gFA7Uzgk2TELzqx8fph3Z_TkW3uZNaI9axgwVtwLbExTcC1qp9BRhV807F3Zy4MzUv_7hz2IZQ/http%3A%2F%2Fbioconductor.org%2Fspb_reports%2FCellaRepertorium_buildreport_20200908175926.html%23merida1_buildbin_anchor

Similar to Matt, I have Rcpp code, but no fortran code so I am perplexed why 
there is any linking to gfortran happening in the first place, what 
install_name_tool is trying to do to the .so, and how I could attempt to 
reproduce this issue locally to investigate it myself.

Andrew McDavid
Biostatistics and Computational Biology
Office: SRB 4.206 Ph: 585.275.5983

On Sep 9, 2020, at 6:00 AM, 
bioc-devel-requ...@r-project.org<mailto:bioc-devel-requ...@r-project.org> wrote:

Date: Wed, 9 Sep 2020 01:03:10 +
From: "Stone, Matt" mailto:mst...@fredhutch.org>>
To: "bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>" 
mailto:bioc-devel@r-project.org>>
Subject: [Bioc-devel] Build issues under macOS
Message-ID: 
<294fbff9-0972-4f77-8b8c-1b8e5a7f5...@fredhutch.org<mailto:294fbff9-0972-4f77-8b8c-1b8e5a7f5...@fredhutch.org>>
Content-Type: text/plain; charset="utf-8"

Hi,

I've begun the submission of a new package [1], but I'm encountering some 
errors in the automated build under macOS on merida1 and would greatly 
appreciate any assistance.

I've currently tried to build twice, once upon initial submission and once 
after updating the DESCRIPTION to remove a redundant Maintainer field. I'm a 
bit confused that each build failed with different errors, as the only 
difference between the two was the removal of the Maintainer field.

In the first build [2], the binary build failed because the installer could not 
link to the fortran libraries. I have previously encountered a similar issue on 
my own macbook and was able to work around it by installing gfortran directly 
[3] rather than through homebrew. I have this noted in the package's README, 
but is there a better solution to ensure compatibility in more environments, 
including merida1?

In the second build [4], the check failed because the package was 
uninstallable, and the binary build failed because edgeR could not be found. 
I'm assuming the latter is the cause of the former error. edgeR is an indirect 
dependency via scran; is it necessary to make it an explicit import?

Before submission, I set up the BiocCheck github action supported by r-lib [5], 
and was able to build the package and run a mostly clean (minus a few NOTEs) 
check/BiocCheck under Ubuntu, Windows, and macOS. Is anyone familiar with the 
distinction between the environments on merida1 and the docker image in this 
workflow? I'd be happy to help update the latter to be consistent with merida1.

Thank you!

Matt


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This email message may contain legally privileged and/or confidential 
information.  If you are not

Re: [Bioc-devel] Single Package Builder Updates

[Shepherd, Lori]

Updates are complete.  There should be no further interruption


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Shepherd, Lori 

Sent: Wednesday, September 9, 2020 12:40 PM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] Single Package Builder Updates

There have been some bugs reported for the MacOS Single Package Builder. We 
will begin running some tests and updates shortly which may result in some 
downtime or unexpected ERROR's when trying to trigger build reports.  We 
appreciate your understanding and hope to have the issue resolved shortly.

Cheers,


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


This email message may contain legally privileged and/or confidential 
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recipient(s), you are hereby notified that any disclosure, copying, 
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this message in error, please notify the sender immediately by e-mail and 
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[Bioc-devel] Single Package Builder Updates

[Shepherd, Lori]

There have been some bugs reported for the MacOS Single Package Builder. We 
will begin running some tests and updates shortly which may result in some 
downtime or unexpected ERROR's when trying to trigger build reports.  We 
appreciate your understanding and hope to have the issue resolved shortly.

Cheers,


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


This email message may contain legally privileged and/or confidential 
information.  If you are not the intended recipient(s), or the employee or 
agent responsible for the delivery of this message to the intended 
recipient(s), you are hereby notified that any disclosure, copying, 
distribution, or use of this email message is prohibited.  If you have received 
this message in error, please notify the sender immediately by e-mail and 
delete this email message from your computer. Thank you.
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Re: [Bioc-devel] Build issues under macOS

[Shepherd, Lori]

Thanks everyone.  I'm looking into the Single Package Builder issues with the 
build bin and hopefully will have a solution uploaded soon.



Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of McDavid, 
Andrew 
Sent: Wednesday, September 9, 2020 11:26 AM
To: bioc-devel@r-project.org ; mst...@fredhutch.org 

Subject: Re: [Bioc-devel] Build issues under macOS

FWIW I am getting the same error in my builds on merida1 for a package that is 
under review:
http://secure-web.cisco.com/1fi0cAc90qwsj_0fchhD0YC4uiLHQd0o4HYR5eLE3tx2LPSw-Z6bzsHUh9GORoSnthoiawosT0tgXA49TjW2iE9qNJJqCOburi1VJCCXkJ0wzP9uxDkH6LztUpfySrdCbtBAy2zLo-7sL5waSK4sqWBOnh-P598vNN5kyAWmdFy4xudqD-4_8H5VaCpgDa37lG422UiagbjAWLxSRuBZKS4j4-24rb6gNs61RPbPo_1OsybmZ3CkZnf7kYXNTP8lanOlmNLx-rx5-gFA7Uzgk2TELzqx8fph3Z_TkW3uZNaI9axgwVtwLbExTcC1qp9BRhV807F3Zy4MzUv_7hz2IZQ/http%3A%2F%2Fbioconductor.org%2Fspb_reports%2FCellaRepertorium_buildreport_20200908175926.html%23merida1_buildbin_anchor

Similar to Matt, I have Rcpp code, but no fortran code so I am perplexed why 
there is any linking to gfortran happening in the first place, what 
install_name_tool is trying to do to the .so, and how I could attempt to 
reproduce this issue locally to investigate it myself.

Andrew McDavid
Biostatistics and Computational Biology
Office: SRB 4.206 Ph: 585.275.5983

On Sep 9, 2020, at 6:00 AM, 
bioc-devel-requ...@r-project.org wrote:

Date: Wed, 9 Sep 2020 01:03:10 +
From: "Stone, Matt" mailto:mst...@fredhutch.org>>
To: "bioc-devel@r-project.org" 
mailto:bioc-devel@r-project.org>>
Subject: [Bioc-devel] Build issues under macOS
Message-ID: 
<294fbff9-0972-4f77-8b8c-1b8e5a7f5...@fredhutch.org>
Content-Type: text/plain; charset="utf-8"

Hi,

I've begun the submission of a new package [1], but I'm encountering some 
errors in the automated build under macOS on merida1 and would greatly 
appreciate any assistance.

I've currently tried to build twice, once upon initial submission and once 
after updating the DESCRIPTION to remove a redundant Maintainer field. I'm a 
bit confused that each build failed with different errors, as the only 
difference between the two was the removal of the Maintainer field.

In the first build [2], the binary build failed because the installer could not 
link to the fortran libraries. I have previously encountered a similar issue on 
my own macbook and was able to work around it by installing gfortran directly 
[3] rather than through homebrew. I have this noted in the package's README, 
but is there a better solution to ensure compatibility in more environments, 
including merida1?

In the second build [4], the check failed because the package was 
uninstallable, and the binary build failed because edgeR could not be found. 
I'm assuming the latter is the cause of the former error. edgeR is an indirect 
dependency via scran; is it necessary to make it an explicit import?

Before submission, I set up the BiocCheck github action supported by r-lib [5], 
and was able to build the package and run a mostly clean (minus a few NOTEs) 
check/BiocCheck under Ubuntu, Windows, and macOS. Is anyone familiar with the 
distinction between the environments on merida1 and the docker image in this 
workflow? I'd be happy to help update the latter to be consistent with merida1.

Thank you!

Matt


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[Bioc-devel] Bioconductor Release 3.12 Schedule Posted

[Shepherd, Lori]

The Bioconductor Release 3.12 Schedule has been posted and is tentatively 
scheduled for October 28th. Important deadlines can be found on the website and 
will be posted here and on the bioc-devel at r-project.org mailing list. As a 
quick summary:

October 2: New package submission deadline (packages will still need to pass 
the formal review process to be included). Package submitted after this date 
are not guaranteed to be reviewed; they will be reviewed time pending.

October 13 Current Release 3.11 Freeze. No changes will be accepted to the 
Bioconductor 3.11 branch after this date.

October 21 No API changes to devel 3.12. Also, newly submitted packages need to 
be accepted by this date to be included in the release

October 23 Deadline for packages to be passing R CMD install/build/check.

October 27 Devel 3.12 branch is frozen to create release branch.

October 28 Release Bioconductor 3.12





Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


This email message may contain legally privileged and/or confidential 
information.  If you are not the intended recipient(s), or the employee or 
agent responsible for the delivery of this message to the intended 
recipient(s), you are hereby notified that any disclosure, copying, 
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Re: [Bioc-devel] Hotfix rejected by git

[Shepherd, Lori]

Yes I can see the updates 1.17.1  on the master branch on git.bioconductor.org. 
 We are looking into the RSS git ERROR.

We only allow corrections to the current release (RELEASE_3_11) and devel 
(master) branches.  We do not allow updates to past releases for legacy and 
reproducibility.

Cheers,


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Spivakov, 
Mikhail 
Sent: Tuesday, September 8, 2020 7:22 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] Hotfix rejected by git

Hello!

We�ve identified a small bug in our Chicago package that we�ve updated on the 
master branch and now wanted to update retrospectively in releases 3.9, 3.10 
and 3.11.

I initially updated and pushed just the master branch, and got this:

$ git push


remote: fatal: this operation must be run in a work tree

remote: ERROR:root:Exception: Command '['git', 'rev-parse', '--show-toplevel']' 
returned non-zero exit status 128

remote: ERROR:root:local variable 'package_name' referenced before assignment

remote: Note: failed to update RSS feed;git repository updated successfully.

To g...@git.bioconductor.org:packages/Chicago

   05d4c19..73223a0  master -> master

>From the above I presumed that the issues with RSS update were not critical, 
>and that the git repo itself was updated successfully. Please correct me if 
>I�m wrong�

I then switched to the corresponding release branches, backpropagated the 
changes from master using $ git cherry-pick and, after some initial rejects due 
to illegal version numbering, managed to push RELEASE_3_11 successfully. 
However, I�m still getting the changes into RELEASE_3_9 and RELEASE_3_10 
rejected for reasons that do not seem to be related to version numbering:

remote: FATAL: W refs/heads/RELEASE_3_10 packages/Chicago m.spivakov DENIED by 
fallthru
remote: error: hook declined to update refs/heads/RELEASE_3_10
remote: FATAL: W refs/heads/RELEASE_3_9 packages/Chicago m.spivakov DENIED by 
fallthru
remote: error: hook declined to update refs/heads/RELEASE_3_9
remote: fatal: this operation must be run in a work tree
remote: ERROR:root:Exception: Command '['git', 'rev-parse', '--show-toplevel']' 
returned non-zero exit status 128
remote: ERROR:root:local variable 'package_name' referenced before assignment
remote: Note: failed to update RSS feed;git repository updated successfully.
To g...@git.bioconductor.org:packages/Chicago
   9658bab..73bfc0a  RELEASE_3_11 -> RELEASE_3_11
 ! [remote rejected] RELEASE_3_10 -> RELEASE_3_10 (hook declined)
 ! [remote rejected] RELEASE_3_9 -> RELEASE_3_9 (hook declined)
error: failed to push some refs to 'g...@git.bioconductor.org:packages/Chicago'

I would very much appreciate any advice on how to fix this.

Thanks so much,
Mikhail


--
Mikhail Spivakov, PhD
Group Leader and Honorary Senior Lecturer (Associate Professor)
MRC London Institute of Clinical Sciences
Imperial College Faculty of Medicine
Hammersmith Hospital Campus
Du Cane Road
London W12 0NN

http://secure-web.cisco.com/1U822-uvoL9om08hwQO041V4JXFHowXUFi7YivT8ac5MmHwuMQ9e1Q_dzOj_KxgfdBUW5rtuFYCsadFAQ3RDO1s-AF2X6Gte7-lOuT4sTKbcfLHPm1ZdUtj0hQonw3kKtHRRSMsOmP9kmAXiyLus_lsUgfBn4BNrRtlxWAiwLTSj1YZO3MNRj1PfIheRS00LWVoko5gxhXFycg4YpReoX1KSvlC9qXYbxcCOq05HOmVHsvwSNifKqp0VpuEcxb7YVUPYTNazSqz52SbXEhM2JZgnfmOBHEyCUdBA_8oFxO3i4426E1oG5nlT9vm1JIZf8/http%3A%2F%2Fwww.FunctionalGeneControl.group

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[Bioc-devel] List of Deprecated Packages for Bioc3.12

[Shepherd, Lori]

Please see the support site post for the current list of deprecated packages 
for release 3.12.  These packages will be removed from Bioc3.13.

It should be noted, we did try to reach out to these package maintainers 
multiple times and they were either unresponsive or had emails bounce. We 
encourage anyone that is familiar with a package maintainer on this list to 
reach out to them and notify them directly. Packages can be un-deprecated if a 
maintainer fixes the package to build/check cleanly before the next release and 
requests un-deprecation on the bioc-devel@r-project.org mailing list.

https://support.bioconductor.org/p/133699/

Thank you


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


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Re: [Bioc-devel] BiocViews error during build on macOS

[Shepherd, Lori]

This looks like an intermittent ERROR that probably occurred at the unlucky 
time of when we would try to reinstall the package biocViews.  I'll kick off a 
manual build of your package in review to see if it clears up.  If it does not 
we will investigate further on our side and you can ignore the ERROR for now. 
Your reviewer is aware.

Cheers,





Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Carlos A. 
Catania (AKA Harpo) 
Sent: Tuesday, September 1, 2020 5:34 PM
To: bioc-devel 
Subject: [Bioc-devel] BiocViews error during build on macOS

Hello,

We are in the process of submitting a package to Bioc.

https://secure-web.cisco.com/15Snq7v_EFkYcPIz3RQ2kfvSfZOk1C2QmvWw65Hf8sM59g0qlzhbK0qS4lnbC9OhwzGT4Q92BxDQURPdYf_EGuwqXN-urigjeEJYVLV3oMqr5Dfn7_wPqWDGeo1gefrFG1vMUz0_JDmIAwkdmKYCnFvkc_LGOfVB9K8k_Uah4IJZ326bGJrV0Av3ESmE42uyBCNfXAMLg5INXcqXXaqGhd8S2nu136Im1sRvAzttVCWDL-0LXpCWg_rvckPjNTfKPY3PPwPkhTsexmfgJHwlX3ekjjX5-0Ptqx6zT26s7uOD8esoydr65LdrlBECZZpEMiv122eNnNd3YxtD1VQ7gxg/https%3A%2F%2Fgithub.com%2Fharpomaxx%2FGSgalgoR

After bumping a push to trigger a new build, the bioc-issue-bot
reported an unknown ERROR in merida1 host running macOS.

Error: package or namespace load failed for BiocCheck in
loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 there is no package called biocViews
Execution halted

Windows and Linux platform did not report the error.
Since we don't have access to macOS, we are not sure how to proceed. Could
you please point to some information
on how to deal with the ERROR?
Bests,

Carlos A. Catania (AKA Harpo)

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Re: [Bioc-devel] Request package deprecation

[Shepherd, Lori]

Thank you for letting us know.  I will begin the deprecation process for the 
package. Thank you for your contributions.


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Crispin Miller 

Sent: Thursday, August 27, 2020 5:27 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] Request package deprecation

Hi there,
I�ve moved email address since creation of this package but I would like to 
request deprecation and End of Life for the package: simpleaffy
It�s been superseded and is out of date.
Best wishes,
Crispin Miller


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Re: [Bioc-devel] New package Vignette

[Shepherd, Lori]

Thank you for reaching out.  Since the package just became available please 
allow a few days for everything to populate on the builders and landing pages.
We will keep an eye on it and if it is still not appearing by next week our 
team will follow up with an investigation.

Thank you


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of ELENI ADAM 

Sent: Friday, August 21, 2020 11:17 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] New package Vignette

Dear Bioconductor team,

Our package (hummingbird) got accepted some days ago and yesterday the
'landing page' was created at:
https://secure-web.cisco.com/1ZLSyM1lwdlsFukP5L08iJsZkpAAfve-r-DbZZgm6xRFra40h83Jtaq3pxcAtLerBiCF1Y4FdZTpYezKqaMhrLyFbebPAhODXrGAPxtgu3ayOSSoCFzasItaWAm0Vjuio1NAl8aZbW8A2BYyLKh1ushyraAy4NqqW-uHGgxVcxzvkjTkENn9Kb4k1i19biCd5FSqCTCy_4IN1KU_bKAmZ5jfB9UZDM9YljLLaoKMHZtvD0R8njJu3XsEd_HoSybWjf0a9dTKvdIyqv49z1jIEnIL0yg_zFhRis9hBTfZhIUWLPuPhLVDfwsQn82ag440x0ewwbY4owPL26VZji1U10A/https%3A%2F%2Fbioconductor.org%2Fpackages%2Fhummingbird
But unfortunately, there is no file under the "Documentation" section. The
package has a vignette, but it is not appearing there.

How can I place the vignette on the webpage so that the users can see it
before downloading the package?

Thank you,
Eleni Adam
*PhD Candidate in CS*
*Old Dominion University*
*Norfolk, VA, USA*

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Re: [Bioc-devel] [Bioconductor/Contributions] New package: preciseTAD (#1553)

[Shepherd, Lori]

Hello,

Thank you for your inquiry and we are sorry for any delays.  We try to review 
packages within 2-3 weeks.  Your reviewer is aware and should be in contact 
soon.

Cheers,


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Spiro 
Stilianoudakis 
Sent: Saturday, August 15, 2020 3:39 PM
To: bioc-devel@r-project.org 
Cc: Mikhail Dozmorov 
Subject: Re: [Bioc-devel] [Bioconductor/Contributions] New package: preciseTAD 
(#1553)

Hi all,

I am checking up on a package that I have submitted to bioconductor. Last
update I was given was that it had passed all checks without errors or
warning. If you could let me know if or when it will be reviewed I would
greatly appreciate it!

Package name: preciseTAD
Issue #: 1553
Best,

Spiro Stilianoudakis
PhD Candidate | Department of Biostatistics
Virginia Commonwealth University

On Tue, Jul 28, 2020 at 12:31 AM bioc-issue-bot 
wrote:

> Dear Package contributor,
>
> This is the automated single package builder at bioconductor.org.
>
> Your package has been built on Linux, Mac, and Windows.
>
> Congratulations! The package built without errors or warnings
> on all platforms.
>
> Please see the build report
> 
> for more details. This link will be active
> for 21 days.
>
> * Remember: *if you submitted your package after July 7th, 2020,
> when making changes to your repository push to
> g...@git.bioconductor.org:packages/preciseTAD to trigger a new build.
> A quick tutorial for setting up remotes and pushing to upstream can be
> found here
> .
>
> �
> You are receiving this because you were mentioned.
> Reply to this email directly, view it on GitHub
> ,
> or unsubscribe
> 
> .
>

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[Bioc-devel] Fw: MultiAssayExperiment not found in docker devel image

[Shepherd, Lori]

Marcel or Nitesh?  This was sent to the issue bot.




Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Joseph Gerrein 
Sent: Tuesday, July 28, 2020 11:03 AM
To: bioc-issue-...@bioconductor.org 
Cc: Jerry (Zhijun) Tang ; Lala Motlhabi 
Subject: MultiAssayExperiment not found in docker devel image

Dear bioconductor team,

Hello! I would like to use MultiAssayExperiment in a preloaded bioconductor 
Docker container that does not require any package installations.  I loaded the 
docker devel image and also the Docker release 3_11 image (from 
https://hub.docker.com/r/bioconductor/bioconductor_docker/tags)
 into Docker desktop on my Windows machine. I wanted to use the 
MultiAssayExperiment and also SummarizedExperiment, but when I tried to load 
them using the library function they were not found. Are these docker images 
preloaded with MultiAssayExperiment?  Do you have any Docker images preloaded 
with MultiAssayExperiment that are well maintained and/or supported?

I loaded the docker image from the MultiAssayExperiment's/TCGA bioconductor 
2020 workshop and I was able to load MultiAssayExperiment using the library 
function � 
https://hub.docker.com/r/mr148/multiassayworkshop
 - Is this container reliable and good to use in general for working with 
SummarizedExperiment and MultiAssayExperiment in bioconductor?


Thanks!

Joe


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Re: [Bioc-devel] Bioc-issue-bot not acknowledging a submitted package

[Shepherd, Lori]

Could you try closing the issue and reopening a new issue. But before opening 
could you please changing the name of the repository.

Your github repository location is

HPAStainR_package

But the package DESCRIPTION names the package is  HPAStainR.

The repository and DESCRIPTION Package name must match and this is a strong 
requirement for when it is introduced into the daily build system.  I'm sorry 
the automatic process did not give you this ERROR message; It should have and I 
will investigate more into why that was the case.

Cheers,



Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Tim 
Nieuwenhuis 
Sent: Tuesday, July 28, 2020 4:01 PM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] Bioc-issue-bot not acknowledging a submitted package

Hello bioc-devel list,

I submitted a package seven days ago called 
HPAStainR
 and the bioc-issue-bot never commented on it. Is there something wrong with my 
issue submission that prevented the bot from acknowledging the package? Is this 
a fixable issue or do I need to resubmit? Also, if this is not the right place 
to ask this question, where should I?

Best regards,
Tim Nieuwenhuis
3rd Year Graduate Student
Human Genetics
Halushka Laboratory
Johns Hopkins University SOM


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Re: [Bioc-devel] networkBMA package

[Shepherd, Lori]

We will not update the CITATION file for you.  You will have to push it up 
after we get the credentials issue straightened out.

The email associated with your credentials account seems to be
ka...@u.washington.edu .  Please try logging in with that email to add ssh keys 
to your account.

Cheers,




Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Ka Yee Yeung 

Sent: Sunday, July 26, 2020 6:52 PM
To: bioc-devel@r-project.org 
Cc: Adrian E Raftery 
Subject: [Bioc-devel] networkBMA package

Hi,

I'm the maintainer of the "networkBMA" package.  My package has the following 
message on the 3.11 release page:
"Important note to the maintainer of the networkBMA package: An error occured 
while trying to generate the citation from the CITATION file."

The corrected and updated CITATION file is attached. Could you please replace 
the CITATION file in the latest release?

Also, I tried to set up the Bioconductor Git Credentials", but got the 
following error message when I entered my email,
"ka...@uw.edu is not associated with a maintainer of a Bioconductor package. 
Please check the spelling or contact bioc-devel@r-project.org for help."

Could you add me?

Thank you,
Ka Yee Yeung
Professor, University of Washington Tacoma

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Re: [Bioc-devel] New version in tscR doesn't trigger new build

[Shepherd, Lori]

Please read the top of this page for timing.  It can take up to 36-48 hours to 
appear on the build report depending on when you pushed your changes
http://bioconductor.org/developers/how-to/troubleshoot-build-report/

Based on the information you provided I would expect to see the changes on 
today's report that post approximately 1300 EST

Cheers


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Fernando P�rez 
Sanz 
Sent: Friday, July 17, 2020 2:09 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] New version in tscR doesn't trigger new build

Hello, bioconductor,

Yesterday around 9.00 am,  I made changes in tscR package to fix a
dependency bug  with another package.

I made :

 >git push upstream RELEASE_3_11
 >git push origin RELEASE_3_11

having changed the version in DESCRIPTION from 1.0.0 to 1.0.1, but it
doesn't seem to have triggered the new build check,
because last build report show check version 1.0.0.

If you clone repository

 >git clone g...@git.bioconductor.org:packages/tscR

the version in master branch is 1.1.1 and in RELEASE_3_11 branch, is 1.0.1.

Can someone help me, please?

Regards

Fenando

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Re: [Bioc-devel] Triggering a new build

[Shepherd, Lori]

Thank you for your inquiry.  We have experienced some issues adding credentials 
for new packages.  We are investigating and should have a solution shortly.  We 
will comment on your open issue on the tracker when the issue is resolved.  We 
apologize for any inconvenience this has caused.

Cheers,


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Spiro 
Stilianoudakis 
Sent: Thursday, July 16, 2020 10:37 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] Triggering a new build

Hello Bioconductor,

I submitted a new package titled preciseTAD, for review. There were errors
in the build results. I have addressed them and I went through the steps to
add a remote pointing to g...@git.bioconductor.org:packages/preciseTAD. I
successfully pushed the results upstream, but it doesn't seem to have
triggered a new build check. Can someone help or let me know what the
appropriate steps might be for triggering a new build?

Issue: #1553

Best,

Spiro Stilianoudakis

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[Bioc-devel] New Package Submission Workflow Updates!

[Shepherd, Lori]

Hello Bioconductor Development Community,

The team has made a significant change to the single package builder process 
for submitting new packages to Bioconductor.

Previously, when submitting a new package, the process was to submit on github, 
add a webhook for interactive building on version bump, acceptance, addition to 
the git.bioconductor.org repository system, and addition to the daily builder 
manifest.

Now upon submission of your package to github, the preapproval process will 
involve immediately adding packages to git.bioconductor.org. Subsequent builds 
of the package during the review process will be triggered by a version bump 
and push to the upstream repository at g...@git.bioconductor.org:packages/. Upon acceptance your package will be added to the daily builder 
manifest for official inclusion in Bioconductor.


The webhook will be deactivated and no longer trigger builds during the review 
process.
Any package that was previously submitted (Before July 7th, 2020) will not have 
to worry about the new workflow. You can continue your new package review as 
you have been and we will deactivate your webhook once you are through the 
submission process.
This will only affect packages newly submitted.

Please ask any questions or concerns you may have.

Thank you
Lori Shepherd on behalf of the Core Team



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Re: [Bioc-devel] Unable to replicate Windows build error on new package.

[Shepherd, Lori]

Your reviewer should be aware to ignore the error and will review your package 
shortly.

Cheers


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Erik Christensen 
Sent: Tuesday, July 7, 2020 3:10 PM
To: Shepherd, Lori ; bioc-devel@r-project.org 

Subject: Re: [Bioc-devel] Unable to replicate Windows build error on new 
package.

Thanks,

Do I need to bump the version or do anything to trigger a rebuild or just wait 
for review now?


--

Erik Christensen mailto:echr...@uwo.ca>>

-Original Message-
From: "Shepherd, Lori" 
mailto:%22Shepherd,%20lori%22%20%3clori.sheph...@roswellpark.org%3e>>
To: Erik Christensen 
mailto:erik%20christensen%20%3cechr...@uwo.ca%3e>>, 
bioc-devel@r-project.org 
mailto:%22bioc-de...@r-project.org%22%20%3cbioc-de...@r-project.org%3e>>
Subject: Re: [Bioc-devel] Unable to replicate Windows build error on new 
package.
Date: Mon, 06 Jul 2020 11:56:49 +

Please ignore the build bin ERROR.  I think this is an issue on the 
Bioconductor build system rather than directly related to your package.


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Erik 
Christensen 
Sent: Friday, July 3, 2020 4:39 PM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] Unable to replicate Windows build error on new package.

Hi,

I'm working on a new R package 
(https://secure-web.cisco.com/1HFmLtrnT-HzI71X6sTuc9lAzhWM5lqF6PVrvPG22uGJQ6qshZL6PR6Me8GyEEZ2jjOcVzxmleHFajMBY7Bsfbi9WOEra50LcQj-wHINOt3_vsxO5Jak5M-WWZOZPSKD1yLCGYgI8tAUMBUN4gTuhZ2XHAhvzhqMAZ-aLyL_Yktw-mtQPnMhh_P1V2x1vytIErFrJfUhS0pchwLBiWBzXjFSQHsBKtyULnKTpmLadc_-6INJ9cs9f7TCsDGjlEsfxalQxXoMgPVVqe0mcIqP2n3_a12ssip5U57a9QXImssNUY3LUAQb3xMOybkkNQqN_PRtKBu8Kl02VXmYAUucRBA/https%3A%2F%2Fgithub.com%2Fshooshtarilab%2FTMExplorer)
 and don't quite understand the build error I'm getting. I'm able to build the 
binary package without problems on my Windows install (I'm primarily a Linux 
dev) but the Bioconductor build system fails.

Here is a link to the build report: 
http://secure-web.cisco.com/1wu17svsUuFvP8L1S81mY0Gcj-x0keg5i7w30tL03XB1VhAvG334oGtc4DefhDqvqCFxS9MWXaVtJnuGNqYOmqTayhjkWmwH7ZY8rb8Z_rl8n8i9KWL6U2oTMYPjwNKESb-sgZoQ2waoUvFrAIx4zp_3Jqa9Rbrwqg_fzpwTkZSfV2yn9MQThig1wkKXYiAcvlDw34RyYjBDKt8XrIW0CmmpBSxindCwBJIlrD9nbOSciI_Lkb5rIrzU7II4muU1vEY5hGgufnH8euwo9VB0rqsgrXHP2NLbbxoAP5U9AHG-_5PFz7tdqm5kayxJ4nPf6BNm-j8dey4tl2JM4Q8QXYWhMnPZuHRZhaP1Vz8CqbqQ/http%3A%2F%2Fbioconductor.org%2Fspb_reports%2FTMExplorer_buildreport_20200703160041.html%23tokay1_buildbin_anchor

How should I interpret this error so I can fix the package?

--

Erik Christensen 
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email message is prohibited. If you have received this message in error, please 
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Re: [Bioc-devel] Unable to replicate Windows build error on new package.

[Shepherd, Lori]

Please ignore the build bin ERROR.  I think this is an issue on the 
Bioconductor build system rather than directly related to your package.


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Erik 
Christensen 
Sent: Friday, July 3, 2020 4:39 PM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] Unable to replicate Windows build error on new package.

Hi,

I'm working on a new R package 
(https://secure-web.cisco.com/1HFmLtrnT-HzI71X6sTuc9lAzhWM5lqF6PVrvPG22uGJQ6qshZL6PR6Me8GyEEZ2jjOcVzxmleHFajMBY7Bsfbi9WOEra50LcQj-wHINOt3_vsxO5Jak5M-WWZOZPSKD1yLCGYgI8tAUMBUN4gTuhZ2XHAhvzhqMAZ-aLyL_Yktw-mtQPnMhh_P1V2x1vytIErFrJfUhS0pchwLBiWBzXjFSQHsBKtyULnKTpmLadc_-6INJ9cs9f7TCsDGjlEsfxalQxXoMgPVVqe0mcIqP2n3_a12ssip5U57a9QXImssNUY3LUAQb3xMOybkkNQqN_PRtKBu8Kl02VXmYAUucRBA/https%3A%2F%2Fgithub.com%2Fshooshtarilab%2FTMExplorer)
 and don't quite understand the build error I'm getting. I'm able to build the 
binary package without problems on my Windows install (I'm primarily a Linux 
dev) but the Bioconductor build system fails.

Here is a link to the build report: 
http://secure-web.cisco.com/1wu17svsUuFvP8L1S81mY0Gcj-x0keg5i7w30tL03XB1VhAvG334oGtc4DefhDqvqCFxS9MWXaVtJnuGNqYOmqTayhjkWmwH7ZY8rb8Z_rl8n8i9KWL6U2oTMYPjwNKESb-sgZoQ2waoUvFrAIx4zp_3Jqa9Rbrwqg_fzpwTkZSfV2yn9MQThig1wkKXYiAcvlDw34RyYjBDKt8XrIW0CmmpBSxindCwBJIlrD9nbOSciI_Lkb5rIrzU7II4muU1vEY5hGgufnH8euwo9VB0rqsgrXHP2NLbbxoAP5U9AHG-_5PFz7tdqm5kayxJ4nPf6BNm-j8dey4tl2JM4Q8QXYWhMnPZuHRZhaP1Vz8CqbqQ/http%3A%2F%2Fbioconductor.org%2Fspb_reports%2FTMExplorer_buildreport_20200703160041.html%23tokay1_buildbin_anchor

How should I interpret this error so I can fix the package?

--

Erik Christensen 
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[Bioc-devel] single package builder updates

[Shepherd, Lori]

Hello,

We will be performing some updates on the single package builder for new 
submissions today June 30.  There will be a period of downtime while we run the 
updates.  During this time packages on the tracker will not receive automatic 
builds.  We apologize for any inconvenience and appreciate your patience.

Cheers,


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


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Re: [Bioc-devel] Passing BiocCheck with roxygen2 tags.

[Shepherd, Lori]

I think it's looking for details on the return value for the functions.  I 
believe the correct syntax is @return  to add a return value section in roxygen


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Erik 
Christensen 
Sent: Thursday, June 25, 2020 11:24 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] Passing BiocCheck with roxygen2 tags.

Hello,

Is there a way to add the value section in man pages using roxygen tags? I
am currently using "@section Value: ..." but this fails biocheck with

"WARNING: Add non-empty \value sections to the following...{{dropped:23}}

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Re: [Bioc-devel] Package mantenence QSutils

[Shepherd, Lori]

I see your commit on the Bioconductor git.bioconductor server.  Your update 
however did not include a version bump.  Without a version bump the builder 
does not recognize any changes.   Please bump the version of the package to 
1.7.1

For What Its Worth -- Please only use Authors@R  and remove Maintainer field.  
Having Authors@R with a 'cre'  is sufficient.

Cheers,


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of guerrero 
murillo, mercedes 
Sent: Tuesday, June 23, 2020 4:58 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] Package mantenence QSutils

Good morning (in spain) to whom it might concern,


I'm Mercedes Guerrero, mantainer of the package 
QSutils
 . Recently I've noticed that there is an error in the name of one author of 
the package. I would like to change it, and I followed the "Push to GitHub and 
Bioconductor 
repositories"
 to change the problem. I see the update in the GitHub page where I uploaded 
the package 
(Here)
 (Author correction commit), but I can't see any difference in the Bioconductor 
page. It is normal? There is something that I have to do to change the citation 
error?


Thanks in advance,


Mercedes.


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Re: [Bioc-devel] Bioconductor package MEAT not updating

[Shepherd, Lori]

There is a RELEASE_3_11 branch and a master (devel 3.12) branch.  You pushed to 
the master (devel)  branch which has been updated to 1.1.0

http://bioconductor.org/packages/3.12/bioc/html/MEAT.html



To push to release you would have to follow the instructions found here:

https://bioconductor.org/developers/how-to/git/bug-fix-in-release-and-devel/

using RELEASE_3_11

We only recommend updating release if it is a bug fix.


Cheers,



Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Sarah Voisin 

Sent: Tuesday, June 23, 2020 5:12 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] Bioconductor package MEAT not updating

Hi,

I have been trying to update my package MEAT following these instructions:
https://secure-web.cisco.com/1P-BkLhd9kn3m4aeE_m5b5HJNKEIchsuOWjb1cKqqL8fTgieJfTx8LkpCpaedqYj8hMl4_HF5FxleldBAIY82HhDA2WA_1SHWT1sgFqlLI7aifjl1kM7TjCeeqkucHZjiv_g9ZUgxL08JRMDRWYuV_trzzsVXdqXJvVgPaZJnfBTeAlndEsYravIxR02yk1S6Q2NDCbL5LBl54_uTJ-SW1htHPdibubFBPhLmzGzBG9K6I-3w_LRgA8eLe8FJ8DvcXbkLHLp9w_4MLXLR_1lkZKHumgkUUqsXvJuoivdeN2UXzPwy2lWbChKwMy5749nlo4EMSgvWR1kJmGqmb5m1RJkGFFngKLm3U2EkzLfyiTc/https%3A%2F%2Fbioconductor.org%2Fdevelopers%2Fhow-to%2Fgit%2Fpush-to-github-bioc%2F

While github has been updated (and version has been bumped to 1.1.0),
Bioconductor hasn't (
https://secure-web.cisco.com/1NtPavk6Wn6xxWMKqEKofI6Xjvb7Q6ZWdj246gEpoKHQahkofCgYRcz5QO7UipLcf_KnvpbSVx0wPhL6c1HdoXjo1sY7xt4GJTwgQh5mGBkY9YH1UguuEd_XpPeo9CZCeJODMHDEVRfcyEbGTIqxJJVt94nBkG-mdz0apw5-OSQcDW8JS8gGkGSub_5xgZokJe3COzp9z7Enu0ZWgrnLnLTQD6agOTH4Tam7uN1HkBngc3sE9clvoAKU7jPRySw4vZhCB2e75L5AX9v3iZcFdhwOiiBdROfu1z5vfGWtngrJ9mhBxNG8GniZgxfylV54qr1ZlmziPHHMeW-A-z5mJhC1EmU2cWRgMgmucQJvFk1M/https%3A%2F%2Fbioconductor.org%2Fpackages%2Frelease%2Fbioc%2Fhtml%2FMEAT.html)

Is there something I did wrong?
I am quite new to package development as this is my first package, so
please bear with my ignorance!

Kind regards,

*Sarah Voisin*
*Senior Lecturer*
Institute for Health and Sport (IHES)
Victoria University, Footscray Park Campus, VIC 3011 Australia
*Email*: sarah.voisin.ae...@gmail.com
*Office phone*: +61 3 9919 5744

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Re: [Bioc-devel] Bioconductor package devel site not updating

[Shepherd, Lori]

It was the issue on the Bioconductor side.  If you look at the page now it 
looks like everything is updated.  Let us know if anything does not appear 
correct.


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Hoffman, Gabriel 
Sent: Friday, June 19, 2020 8:00 AM
To: Shepherd, Lori ; bioc-devel@r-project.org 

Subject: Re: Bioconductor package devel site not updating


Hi Lori,

Thanks for your help.  It looks like you found the issue, but here is my 
original message.  (I�m not sure why it didn�t go through)



Best,

Gabriel



Hi,

I maintain the variancePartition package and I recently posted an update 
v1.19.4 to the development branch (BioC 3.12).  The build was successful: 
http://bioconductor.org/packages/devel/bioc/html/variancePartition.html<http://secure-web.cisco.com/1OyTHHUsZY3VsP1fPtVX8zsmeaxZcZkgT8ylIH3E8VUQs2-13amHCQjt8X7-Zo2zmICuxJuG_9r9phDTlNEIoLti5Hu_nRc3dWHIfhbgq1wjR_uLwbBhfx2l2q-vR8SYyAwrK0wvHdIVZO5AHH8XGP7RUPBfT05KePvVn_wX0OwqLoW-nwEqMXKg08U4i0_hOWAWqJUJOqNbYipgR_vxbvSgKpohxTM_64q_pnAkqGtMgUsn-SpF06xhG3Oy-LwwSjZiaZuI7nEj5-qx7g-KK7wdBV-Rmv6-vwEWiBBWP0qLfKwoBDvVu4K1LV4L4pvu1t1d_gyc1hDS11y28qD1ie_cXE-MYiIcgn4cnf4yCtvo/http%3A%2F%2Fbioconductor.org%2Fpackages%2Fdevel%2Fbioc%2Fhtml%2FvariancePartition.html>
 . The vignettes and manual were correctly updated to this version.



My issue is that the webpage did not update.  It is still on v1.19.1.  This 
causes three problems.

  1.  The link to download the source package doesn�t work because it points to 
variancePartition_1.19.1.tar.gz.
  2.  I added a new vignette.  I can load it if I specify the URL directly 
(http://bioconductor.org/packages/devel/bioc/vignettes/variancePartition/inst/doc/FAQ.html<http://secure-web.cisco.com/1-lncMzHuEQWU3uOX8U2aV8WN_8s3cg8q-DPxUJyabGmvYdqkGtL0X70arCoDTXeeHE_s61kRE6Am5KeqMo-PxdJJs4rDtuO2hlrfHME_u0G_Lv7lYFhYlAIDJ2xGdCWbGNkquZrklX5dx4LHz0QYbSEN2MfbSCyAbbS0a-lUCQRQbeU8204wNugf6a5ly87OcgPQoJmsoXU1mJmhVKT5y4ezUtf9YS7Hj0p6Wf1A2MYtGx1cGqhJhHFGlsegve4nZGN6cPVSAo0xWNdcDebJMw4GrDg79meNCyMtkotsbmBar-KlthZiv043CpoPlwA3sbD_iGzxpDgs4ZiidJXtPy3iiH2DWOjljkvWlctzkt4/http%3A%2F%2Fbioconductor.org%2Fpackages%2Fdevel%2Fbioc%2Fvignettes%2FvariancePartition%2Finst%2Fdoc%2FFAQ.html>)
 but the webpage doesn�t link to it because the page is the old version.
  3.  This version makes some changes requested by reviewers, and I need the 
webpage to update before I can resubmit my manuscript.



My question is: Is the issue with the webpage on Bioconductor�s side, or is it 
an issue with my package?



(I get the old page on multiple browsers and multiple machines, so it isn�t a 
caching issue)



Thanks

Gabriel







From: "Shepherd, Lori" 
Date: Friday, June 19, 2020 at 7:08 AM
To: "Hoffman, Gabriel" , "bioc-devel@r-project.org" 

Subject: Re: Bioconductor package devel site not updating



USE CAUTION: External Message.

Hello,



The message you sent appears blank.  So I'll take my best guess at what you are 
referring to:



Please see this post indicating that we are having trouble with our website and 
are in process of fixing it.  We have located the issue and pushed a fix and 
once applied the landing pages should generate properly.



https://stat.ethz.ch/pipermail/bioc-devel/2020-June/016923.html<https://secure-web.cisco.com/1Ry8QVshv1h8LZw09yFl2sSqlNV0dhUCNDOLFBIZTAnbhs9ohcFLwUlHM_d1jttdUiO1XzVsuZRy3aYzg0wFCvGCjef8-D0gfQMzP7Aj_0HqUKI4PyRhRU3FdQF9OyC9gczcLT2IDdOztuMhppoWDJyfLfbuRNbwCBPZnvPMzERKd_Bxnmm8gYnL0DgC-SaRZnjebeitKrDIOvjNNmc3P1xzYqn4fH2E6gwiUFNc3rBIbo_gFFq89aB_tv2OirJJMVxcLxuLNGKGLZ-LDkkj7wmqPhKapmgc8ljU7Ck53LLK2ROBfii9_uQYJq9uJIK-Smr2N9m1nbpoDiYUP0rJdWg/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__stat.ethz.ch_pipermail_bioc-2Ddevel_2020-2DJune_016923.html%26d%3DDwMFAw%26c%3DshNJtf5dKgNcPZ6Yh64b-A%26r%3DKdYcmw5SdXylMrTGSuNVkNJulowod64k0PTDC5BHZkk%26m%3D-WIBPVmkz719yBNTRf_Ycqugpy7a70f6i0rKzBKUTv0%26s%3DTPQSupVoQleHsY2i_4PnuwGoD6SEj8hXd5_XXfMQRUo%26e%3D>





Please check the build reports for the version numbers that are being used to 
build the package.



http://bioconductor.org/checkResults/<https://secure-web.cisco.com/10fUrbyz6IHKb3XRo880qoYQ3tghmrxRCvh9-T2Rwo6iqjQc2UhdBv-h0LS7nRIvqq3JGzMS7gfRamf3HPA7al2pacr4YOp1SHAqZjzuwlwpIJqaiJlio8Z0FzXzvUa3D5XSGxp6gxF6BQ1epRzgXiOTffoyXJ_LOsvB_9Tm3Gxh0zr3NnNrgeHT3IiZQzYvH8c2dIR6MQr8IaKvH7dSkpYveqTIGJRUA3TkBwk6MymEoHA3jWI_XPD2MekEyBF21Qqz_BTqnvYLDhCg0LZY8ECZId3WgfbCYMJfCNlUNjDkrNUZZU8IJz-3UVHNQsE9eq-u4JPSbG0UlN8Y0CUewUw/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttp-3A__bioconductor.org_checkResults_%26d%3DDwMFAw%26c%3DshNJtf5dKgNcPZ6Yh64b-A%26r%3DKdYcmw5SdXylMrTGSuNVkNJulowod64k0PTDC5BHZkk%26m%3D-WIBPVmkz719yBNTRf_Ycqugpy7a70f6i0rKzBKUTv0%26s%3DZmdgkn_PDLzCRnp0ONOkhaPVueqyb_pq7tnbpF0kfm4%26e%3D>



Keeping

Re: [Bioc-devel] lipidr: Unable to reproduce error (possibly from S4Vectors)

[Shepherd, Lori]

I reinstalled iheatmap yesterday and it should be reflected in today's 
(Mondays) report.

Cheers,


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Ahmed Mohamed 
Sent: Monday, June 22, 2020 2:18 AM
To: Martin Morgan 
Cc: Vincent Carey ; Herv� Pag�s 
; bioc-devel ; Shepherd, Lori 

Subject: Re: [Bioc-devel] lipidr: Unable to reproduce error (possibly from 
S4Vectors)

Excellent catch Martin.
I was able to confirm the issue using the script below (on Bioc-Devel Docker). 
The issue was also resolved by simply reinstalling iheatmapr. It would be great 
if iheatmapr is reinstalled manually on the devel build systems.

remove.packages(c("iheatmapr", "S4Vectors"))
devtools::install_github("Bioconductor/S4Vectors", 
ref="e8dffc0157f2c4779fce3c85e5ef601bb0a35d33")
install.packages("iheatmapr")
packageVersion("S4Vectors")
# "0.27.0"
packageVersion("iheatmapr")
# "0.4.12"
library(lipidr)
library(iheatmapr)
example("iheatmap")
# Runs successfully

## Update S4Vector
rm(list = ls())
rstudioapi::restartSession()
devtools::install_github("Bioconductor/S4Vectors")
packageVersion("S4Vectors")
# "0.27.12"

library(iheatmapr)
example("iheatmap")
# Error in .wrap_in_length_one_list_like_object(value, name, x) :
#   failed to coerce 'list(value)' to a IheatmapPlots object of length 1

## Reinstall iheatmapr
rm(list = ls())
rstudioapi::restartSession()
install.packages("iheatmapr")
library(iheatmapr)
example("iheatmap")
# Runs successfully


Cheers.
Ahmed.

On Thu, 18 Jun 2020 at 00:52, Martin Morgan 
mailto:mtmorgan.b...@gmail.com>> wrote:
You can see package versions on the build system from

  
https://bioconductor.org/checkResults/devel/bioc-LATEST/index.html<https://secure-web.cisco.com/1HWo5rIWA1m5ihxjEdHQES7eiiUCH5lqvmKOON4J2Nm8lJSd6ncmMQs2_hUktt5pXPTp1smrU6cKa4190T7elc944QS2Ydfuvp0t0c29VorU11a_JwrxBfbADYAfJGX5CDQJNzcBds5IVb_Ltdmsg7t8Ld_JyXp3M7L7uW2MvmMMnH8ci3Phnzvw_iaOi0u9G-l54dBJQI5av1sYcF-XB-chvqVtJ_doIbdWZgo0cQbvpDTl4qwhMSI3-T5j57ghQcQiG5qiGemiudrobXzA6XqKDpvteiE2tnv1JEegc1WaEKcl6RRjDDR3DXUQOSDD-iwfdcr_fKL4y8BIfVSxVcfA9foqFw5ODRUoVPtzsaS0/https%3A%2F%2Fbioconductor.org%2FcheckResults%2Fdevel%2Fbioc-LATEST%2Findex.html>

clicking on 'installed pkgs' link in the center top table. iheatmapr is at 
version 0.4.12.

I think what is happening is like 
https://support.bioconductor.org/p/131689/#131695<https://secure-web.cisco.com/1CwyVIg3N8SoBBwdD_FZCiSutr81swQb4KYpE6AXzbu-D36e_5eSxfAEMhJSyL-J7KoruFV35JklCfpumYnw_PV4SpILT4B7wuZtuwXsxnWJYFdapO9ukunWgWn39PwtvG1o5zkiJjv1wwLOio-63U40zo3qPGplTSe3XQN4LtamopYmUBwTYsEewP58hJ4qna2-BpptSChUQo998UFg55JhNHe8ejCjdB1IvVvZSikJx2zpcqfEQZ-kvLK_NcASuHZk8jVRxH9LtAiCXae2enWAZvaXxUDc-_0Oiov8GTnMdglDnbpl2KouhuA9_2xdNAvcsZwWynXeOmu0sJhz8GA/https%3A%2F%2Fsupport.bioconductor.org%2Fp%2F131689%2F%23131695>
 where S4Vector method has been changed but packages that use it have a methods 
table that is cached when the package is installed.

So there are no errors if you do a new install of packages (like on CI or the 
docker) but not if the iheatmapr package has already been installed (as I guess 
on the build system).

This means that the only way to reproduce this would be to install a previous 
version of S4Vectors, then install iheatmapr to capture the old methods table, 
then install the current version of S4Vectors. But at the end of the day the 
solution is (a) for iheatmapr to be updated on the build systems and ideally 
(b) for iheatmapr to bump it's version. A version bump would be trivial if it 
were a Bioconductor package, but could be problematic for CRAN. I did bcc the 
maintainer.

I don't think you should work around this (e.g., by disabling the example) 
because, at least if it were me, I'd forget to reenable this and hence end up 
with less extensive testing of my package (and the overall Bioconductor 
ecosystem).

Maybe @Herv� Pag�s will chime in; my diagnosis could be wrong.

Martin

On 6/17/20, 6:56 AM, "Bioc-devel on behalf of Ahmed Mohamed" 
mailto:bioc-devel-boun...@r-project.org> on 
behalf of moha...@kuicr.kyoto-u.ac.jp<mailto:moha...@kuicr.kyoto-u.ac.jp>> 
wrote:

Thanks Vincent.

I would like to debug the error, but I still cannot reproduce it.
SessionInfo, below, shows update to date versions! My Travis build also
works, with Bioc Devel and iheapmapr 0.4.12 (

https://travis-ci.org/github/ahmohamed/lipidr/jobs/696329028#L2718<https://secure-web.cisco.com/1If8yOo3b_xBYYwzpHg-c7ZSLnTAhugHgmCjgkxTHiPbgSmK-eSNwegV5ae_l5VcGUe0rds-f7dFKtbjP7jCW1gpaFTioG1RhvwHy1xdrRWcQt-RqbT5PGC_IDlLdsQe132vjO1GjpChUt_K8tweNVhePXGcHlTmc_KOfzswdP_0X9YEmStFcons03ZGXW-lRS3oObzAeqSeuMiqJwarP6pM87LZPguM8Z

Re: [Bioc-devel] Problem installing sesameData on locked down server

[Shepherd, Lori]

It is our understanding that for servers there is normally one main node that 
has internet access while the other server nodes do not and that all nodes 
would have access to some shared drive/space.  We suggest asking your IT team 
to download the resources you need for analysis to the shared space.  There are 
functions in ExpeirmentHub, as you've explored, that could allow IT to download 
them to a specific location (by using setExperimentHubOption("CACHE", 
)  or by using environment variables EXPERIMENT_HUB_CACHE ).  If IT 
is able to download for you, then you could change the cache location also to 
where ever that shared drive is and use localhub=TRUE to access the already 
download resources.



Looking at your original email more closely,  uploading a cache directly might 
not work because of the hard coded local file paths.  The underlying caching 
mechanism in ExperimentHub and AnnotationHub is BiocFileCache.  We implemented 
an exportbfc function but I don't think we ever implemented it in the Hubs.  I 
will look into implementing this in the hubs but it may take some time.


What I can suggest trying in the meantime is working through something like the 
following:

# locally
library(ExperimentHub)
eh = ExperimentHub()

# download the sesameData files using experimenthub so they are in your local 
cache

bfc = BiocFileCache(getExperimentHubOption("CACHE"))

exportbfc(bfc, outputFile="ExperimentHub.tar", outputMethod="tar")
# you could also use zip
exportbfc(bfc, outputFile="ExperimentHub.zip", outputMethod="zip")


You can then try uploading this file to  the server,  untar or unzip and then 
try pointing to use that location on the server with 
setExperimentHubOption("CACHE", )


Hope this helps.


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Schneper, Lisa M. 
Sent: Wednesday, June 17, 2020 10:08 AM
To: Shepherd, Lori ; bioc-devel@r-project.org 

Subject: Re: Problem installing sesameData on locked down server

Dear Lori,

Thank you very much. I checked with our IT team and the server doesn't allow 
this traffic out for security reasons. Is there a way to create a local 
directory that has the information that the program is looking for and point 
the proxy there?

Thank you,

Lisa

From: Shepherd, Lori 
Sent: Wednesday, June 17, 2020 8:23 AM
To: Schneper, Lisa M. ; bioc-devel@r-project.org 

Subject: Re: Problem installing sesameData on locked down server

If the institution is behind a proxy there is a different ExperimentHub (and 
AnnotationHub) option for setting the proxy.

try:
setExperimentHubOption("PROXY",  )




Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Schneper, Lisa 
M. 
Sent: Tuesday, June 16, 2020 6:05 PM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] Problem installing sesameData on locked down server

Hi,

I would like to use the SeSAMe package to analyze methylation data that we've 
generated. Unfortunately, I'm having difficulty installing the sesameData 
package on our server. The server does not access the internet due to security. 
 I think I've installed all the dependencies. I was able to download the cache 
using a version of R on my local computer and tried to put the downloaded files 
on the server.

I'm getting an error b/c ExperimentHub Caching can't connect to the server and 
can't figure out how to fix it (or if it is possible):

> setExperimentHubOption("CACHE","/home/geneticData/R-3.6.2/library/CACHE/ExperimentHub/")

> library(AnnotationHub)

> setAnnotationHubOption("CACHE","/home/geneticData/R-3.6.2/library/CACHE/AnnotationHub/")

> setExperimentHubOption("LOCAL",TRUE)

> setAnnotationHubOption("LOCAL",TRUE)

> library(sesameData)

Loading sesameData.

ExperimentHub Caching causes a warning:

URL 
'https://secure-web.cisco.com/1QG4CRZR1UJL2pjbyFBDtIKGCM9boQZgRQNA9uuIfL7QL5omF1je_lr4TopC9SabxnI2MLq_kTv5GemLFqTJg1NCuoSOWkSNLxBZ7DwK2RMZY5V0CPEwbef9xO0RV0kvTpDf0z59UZWsq2Ib4kNFhV4a6D5POCywJGgV4F_s1xSWbghThfdStnIBx3dTXPavNBfdeEkWH3ZSsRdj8sg2bbDIN8jiuA3oW54IrOi6AXYvxG5GpZcfi6t0fJTeKnwMLzVXPlv-0jP9kHaqiSjLOPRukH9w4IusNozuFnU-wcBB3sd8CkvL-R70_ftObQE_G87aDJl-DPwh7ckLPvJ4JMObL9wOdIMsMW6fnfG0rcSI/https%3A%2F%2Fbioconductor.org%2Fconfig.yaml':
 status was 'Couldn't connect to server'Warning message:

In message(cond, appendLF = TRUE) :

  additional arguments ignored in message()


This is my sessionInfo()


> sessionInfo()

R version 3.6.2 (2019-12-12)

Platform: x86_64-pc-linux-gnu (64-bit)

Re: [Bioc-devel] Bioconductor package devel site not updating

[Shepherd, Lori]

Hello,

The message you sent appears blank.  So I'll take my best guess at what you are 
referring to:

Please see this post indicating that we are having trouble with our website and 
are in process of fixing it.  We have located the issue and pushed a fix and 
once applied the landing pages should generate properly.

https://stat.ethz.ch/pipermail/bioc-devel/2020-June/016923.html


Please check the build reports for the version numbers that are being used to 
build the package.

http://bioconductor.org/checkResults/

Keeping in mind there can be up to a 48 hour delay to see the results as 
described here:

http://bioconductor.org/developers/how-to/troubleshoot-build-report/




If none of these applied to your issue, please provide more detail on what 
package you maintain and specifics on what you are experiencing.

Thank you.



Cheers,



Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Hoffman, 
Gabriel 
Sent: Thursday, June 18, 2020 9:37 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] Bioconductor package devel site not updating


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Bioc-devel@r-project.org mailing list
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Re: [Bioc-devel] updating package on the development version

[Shepherd, Lori]

Please see this post indicating that we are having trouble with our website and 
are in process of fixing it.  We have located the issue and pushed a fix and 
once applied the landing pages should generate properly.

https://stat.ethz.ch/pipermail/bioc-devel/2020-June/016923.html


Please check the build reports for the version numbers that are being used to 
build the package.

http://bioconductor.org/checkResults/

Keeping in mind there can be up to a 48 hour delay to see the results as 
described here:

http://bioconductor.org/developers/how-to/troubleshoot-build-report/

Cheers,



Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Dwivedi, 
Bhakti 
Sent: Thursday, June 18, 2020 4:24 PM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] updating package on the development version

Hi,

I am trying to update previous release of my package (GISPA) on the development 
version.

I pushed the changes and new release GISPA 1.13.1 following 
https://secure-web.cisco.com/16G6QGHF8mpcsjsZBAAOMWj_a4_z0hmCZlj_TnB4TkGbw3lcmQkHHEjOqoyzLjoOMRn1aXjkTjb5avdzEYK8TvzOinzWcd9qWMiZtKViQYb59qlnna0b2zm1kpo9g5N-CAfehjdWj1aJjXXzU0Hr8DFvi9egMpJ8mJfKVtjZIxiNHpmVpAVpylYQTaAhqJ00j8m4g_-g32S9NI3JBhD0t4AqG-FOe6_XBx_MtqxawqmeCbMmzb7ACMy2fDyMtMWJN_8CFfp0MxJHYuURFn_zJFFrA_8OC5MS263jFlJ4tkGIjjP4i3l23Pk98aN0pleohwwTq6H5r4yXwIUIJZ1UtYixHkMKeMzfgh7Mx2jvPXCs/https%3A%2F%2Fbioconductor.org%2Fdevelopers%2Fhow-to%2Fgit%2Fsync-existing-repositories%2F

But, I do not see the change on the bioconductor development version 
http://secure-web.cisco.com/1BfCJ7lm3FxR9215Gg0wJ4F_f-OUbGZlfSX7Ht1DBVyLt-CZZV-KC00A6xzrjCgeuhtuBWXSLpVmnjtVS2OXstGp5uPIT9ZrzhInLClCHaban0Vu4Cgjcat6pKhyv0_mkXT3BDemwUsYEc-n5Ci7Hg5ZyWVJNiFi8RXqmJZ7jivCEJbsbmPLkns3Aqlvm7sIpUsbyrHU_3sZB9ThrXyRAg1i6MYujiums1jeOJyKkH8xJ8rzlg4SZosumRATLEpNxRcqx0vJYGendXkAFaOLdducAMIKK1cFguQP3GuBIZGWXXTBajVSvf3AtXUEkgCGHMX_okMSo4UDIdulKBzh1bxvq1SjHw4IhYlMYjTUg9KI/http%3A%2F%2Fbioconductor.org%2Fpackages%2Fdevel%2Fbioc%2Fhtml%2FGISPA.html.
 Where can I view the changes and make sure it passed all the checks?

Regards,
Bhakti





This e-mail message (including any attachments) is for t...{{dropped:23}}

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Re: [Bioc-devel] Website Not Updating

[Shepherd, Lori]

No this has nothing to do with your package.  We located the issue already.  
But thank you for your concern.


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Chengyang.Ji12 
Sent: Thursday, June 18, 2020 9:11 PM
To: Shepherd, Lori ; bioc-devel@r-project.org 

Subject: RE: [Bioc-devel] Website Not Updating


Hi,



I added �Phylogenetics� and �SNP� to BiocViews of my package sitePath in both 
release and develop version. Wonder if that�s causing the problem. Because 
�Phylogenetics� is a legit BiocViews so far as I know but was never used 
before. And changing BiocViews is not �bug fix� update which might break the 
webpage rendering?



Just want to help you pinpoint the cause and if it is really me, what do I do 
to help fix it.



Best,

Chengyang



Sent from 
Mail<https://secure-web.cisco.com/1bod6Qs4eIy48hnZ5RYZIeCH3mAL7jAcJ8kYAkDZ4TXKxiagcweUBhVTkZNqI65qROJFe2pUoWSxTMION1ShNb90Pc__7BuK6jKymd5s1t_1MmOSb3TZdEZ9iZQeKX0en-4x240sXMZCKrPSkpx4OQJ6hkff5ts9pocdbId2e1CXHZfAG8-fIh4E0rXwk-gEGfJq78TPkrIpw4XMGaVKsNUrVxnD9JPr7pzwwgrssG3VX9dPbcbBOvP1u3I2ousRta7-CdqMDvSrClWY1A8NdN2PsdZh1P2h0v8HlGJXZJwpbRyVfeYMCrMbsIwyALcY9vPNsJWIBRp_10Ub9aOUcaQ/https%3A%2F%2Fgo.microsoft.com%2Ffwlink%2F%3FLinkId%3D550986>
 for Windows 10



From: Shepherd, Lori<mailto:lori.sheph...@roswellpark.org>
Sent: 18 June 2020 22:02
To: bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>
Subject: [Bioc-devel] Website Not Updating



Hello All,

It was brought to our attention that our website was not updating over the last 
few days.  You may see outdated or missing package landing pages.  We are 
working on a fix that should be implemented by the end of the day today.

Cheers,


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


This email message may contain legally privileged and/or confidential 
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[Bioc-devel] Website Not Updating

[Shepherd, Lori]

Hello All,

It was brought to our attention that our website was not updating over the last 
few days.  You may see outdated or missing package landing pages.  We are 
working on a fix that should be implemented by the end of the day today.

Cheers,


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


This email message may contain legally privileged and/or confidential 
information.  If you are not the intended recipient(s), or the employee or 
agent responsible for the delivery of this message to the intended 
recipient(s), you are hereby notified that any disclosure, copying, 
distribution, or use of this email message is prohibited.  If you have received 
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Re: [Bioc-devel] Updates to Single Package Builder for submitting new packages

[Shepherd, Lori]

We are done with the updates.  If anyone has any issues submitting a new 
package to the tracker please let us know.

We updated the single package builder to now require that ssh keys are added to 
a github account since we utilize the ssh keys for access to maintaining your 
package once accepted into Bioconductor.

Cheers,


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Shepherd, Lori 

Sent: Wednesday, June 17, 2020 9:34 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] Updates to Single Package Builder for submitting new 
packages

Hello all,

We are working on some updates to the Single package builder used for 
submitting new packages.  This shouldn't affect any packages already in the 
submission queue only new incoming packages being submitted.  The update should 
not take long and we will announce when we are finished.


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


This email message may contain legally privileged and/or confidential 
information.  If you are not the intended recipient(s), or the employee or 
agent responsible for the delivery of this message to the intended 
recipient(s), you are hereby notified that any disclosure, copying, 
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this message in error, please notify the sender immediately by e-mail and 
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[Bioc-devel] Updates to Single Package Builder for submitting new packages

[Shepherd, Lori]

Hello all,

We are working on some updates to the Single package builder used for 
submitting new packages.  This shouldn't affect any packages already in the 
submission queue only new incoming packages being submitted.  The update should 
not take long and we will announce when we are finished.


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


This email message may contain legally privileged and/or confidential 
information.  If you are not the intended recipient(s), or the employee or 
agent responsible for the delivery of this message to the intended 
recipient(s), you are hereby notified that any disclosure, copying, 
distribution, or use of this email message is prohibited.  If you have received 
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Re: [Bioc-devel] Problem installing sesameData on locked down server

[Shepherd, Lori]

If the institution is behind a proxy there is a different ExperimentHub (and 
AnnotationHub) option for setting the proxy.

try:
setExperimentHubOption("PROXY",  )




Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Schneper, Lisa 
M. 
Sent: Tuesday, June 16, 2020 6:05 PM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] Problem installing sesameData on locked down server

Hi,

I would like to use the SeSAMe package to analyze methylation data that we've 
generated. Unfortunately, I'm having difficulty installing the sesameData 
package on our server. The server does not access the internet due to security. 
 I think I've installed all the dependencies. I was able to download the cache 
using a version of R on my local computer and tried to put the downloaded files 
on the server.

I'm getting an error b/c ExperimentHub Caching can't connect to the server and 
can't figure out how to fix it (or if it is possible):

> setExperimentHubOption("CACHE","/home/geneticData/R-3.6.2/library/CACHE/ExperimentHub/")

> library(AnnotationHub)

> setAnnotationHubOption("CACHE","/home/geneticData/R-3.6.2/library/CACHE/AnnotationHub/")

> setExperimentHubOption("LOCAL",TRUE)

> setAnnotationHubOption("LOCAL",TRUE)

> library(sesameData)

Loading sesameData.

ExperimentHub Caching causes a warning:

URL 
'https://secure-web.cisco.com/1QG4CRZR1UJL2pjbyFBDtIKGCM9boQZgRQNA9uuIfL7QL5omF1je_lr4TopC9SabxnI2MLq_kTv5GemLFqTJg1NCuoSOWkSNLxBZ7DwK2RMZY5V0CPEwbef9xO0RV0kvTpDf0z59UZWsq2Ib4kNFhV4a6D5POCywJGgV4F_s1xSWbghThfdStnIBx3dTXPavNBfdeEkWH3ZSsRdj8sg2bbDIN8jiuA3oW54IrOi6AXYvxG5GpZcfi6t0fJTeKnwMLzVXPlv-0jP9kHaqiSjLOPRukH9w4IusNozuFnU-wcBB3sd8CkvL-R70_ftObQE_G87aDJl-DPwh7ckLPvJ4JMObL9wOdIMsMW6fnfG0rcSI/https%3A%2F%2Fbioconductor.org%2Fconfig.yaml':
 status was 'Couldn't connect to server'Warning message:

In message(cond, appendLF = TRUE) :

  additional arguments ignored in message()


This is my sessionInfo()


> sessionInfo()

R version 3.6.2 (2019-12-12)

Platform: x86_64-pc-linux-gnu (64-bit)

Running under: Springdale Linux 7.8 (Verona)


Matrix products: default

BLAS:   /home/geneticData/R-3.6.2/lib/libRblas.so

LAPACK: /home/geneticData/R-3.6.2/lib/libRlapack.so


locale:

 [1] LC_CTYPE=en_US.UTF-8   LC_NUMERIC=C

 [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8

 [5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8

 [7] LC_PAPER=en_US.UTF-8   LC_NAME=C

 [9] LC_ADDRESS=C   LC_TELEPHONE=C

[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C


attached base packages:

[1] parallel  stats graphics  grDevices utils datasets  methods

[8] base


other attached packages:

[1] curl_4.3 sesameData_1.4.0 ExperimentHub_1.12.0

[4] AnnotationHub_2.18.0 BiocFileCache_1.10.2 dbplyr_1.4.3

[7] BiocGenerics_0.32.0


loaded via a namespace (and not attached):

 [1] Rcpp_1.0.3pillar_1.4.3

 [3] compiler_3.6.2BiocManager_1.30.10

 [5] later_1.0.0   digest_0.6.23

 [7] bit_1.1-15.2  RSQLite_2.2.0

 [9] memoise_1.1.0 lifecycle_0.2.0

[11] tibble_3.0.1  pkgconfig_2.0.3

[13] rlang_0.4.5   shiny_1.4.0.2

[15] DBI_1.1.0 yaml_2.2.1

[17] fastmap_1.0.1 dplyr_0.8.5

[19] httr_1.4.1IRanges_2.20.2

[21] S4Vectors_0.24.4  vctrs_0.2.4

[23] rappdirs_0.3.1stats4_3.6.2

[25] bit64_0.9-7   tidyselect_1.0.0

[27] Biobase_2.46.0glue_1.3.1

[29] R6_2.4.1  AnnotationDbi_1.48.0

[31] purrr_0.3.4   blob_1.2.1

[33] magrittr_1.5  promises_1.1.0

[35] ellipsis_0.3.0htmltools_0.4.0

[37] assertthat_0.2.1  mime_0.9

[39] interactiveDisplayBase_1.26.0 xtable_1.8-4

[41] httpuv_1.5.2  crayon_1.3.4

[43] BiocVersion_3.10.1

Here are the list of files in my CACHE:


> list.files("/home/geneticData/R-3.6.2/library/CACHE/ExperimentHub/")

 [1] "656b10a5788d_1673"

 [2] "656b13963d2e_1682"

 [3] "656b14d8873b_1681"

 [4] "656b1539427_1684"

 [5] "656b16238d1f_1685"

 [6] "656b21dde7c0_1670"

 [7] "656b27f30d6e_1667"

 [8] "656b2ce156bc_1679"

 [9] "656b2d083cf2_1664"

[10] "656b321fe953_1677"

[11] "656b38d6e1d7_1688"

[12] "656b4124fa1e_1675"

[13] "656b45f6c53f_1668"

[14] "656b4c0fcefb_1669"

[15] "656b4d0f61da_1678"

[16] "656b4ef9a36a_experimenthub.sqlite3"

[17] "656b50445f74_1687"

[18] "656b5ac899f2_1666"

[19] "656b5f8d7984_1674"

[20] "656b62a0e8fb_1676"

[21] "656b6757aca7_656b6757aca7_hub_index.rds"

[22] "656b675d174f_1672"

[23] "656b6c8aa10d_1683"

[24] "656b6f99ff9e_1671"

[25] "656b77d94af6_1665"

[26] "656b7805f993_1686"

[27] "656b7e0567a8_1680"

[28] "BiocFileCache.sqlite"

If I try 

Re: [Bioc-devel] fatal: 'upstream/RELEASE_3_11' is not a commit and a branch 'RELEASE_3_11' cannot be created from it

[Shepherd, Lori]

If you git clone the git.bioconductor.org repository for your package in a 
different folder location you would be able to see the copy and commits we have 
on our server (I understand not very convenient)

There is a delay from commits to updates on the building reports and landing 
page.  It is discussed at the top of the page and has been answered numerous 
times on the mailing list

http://bioconductor.org/developers/how-to/troubleshoot-build-report/

We are in the process of potentially expanding the submission process tracker 
building on commit to the daily builder.  There is still no time period on when 
that would be available as it has just started being explored.

Cheers,


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bhagwat, Aditya 
Sent: Friday, June 12, 2020 11:33 AM
To: Shepherd, Lori ; bioc-devel@r-project.org 

Subject: RE: [Bioc-devel] fatal: 'upstream/RELEASE_3_11' is not a commit and a 
branch 'RELEASE_3_11' cannot be created from it


Thankyou Lori,



Is there a way to get a visual overview of recent commits at 
https://git.bioconductor.org/packages/multicrispr<https://secure-web.cisco.com/1DzTC21Xsa01UK-VZkKk4yvwj_VU6qp85rqzcKCvvPMtm2vah4-NZjCAOKXcKftajD-J_w4XNYR6kLkwlc3GHf2OiIPJgqZyL75sZ8VqF0VU14xhmRORFhrGnYF9LaVvgeCdpIHt6nYIpOP1Iqtm4SxSlQZxBPes6PuXMj0O8IKEzoYniEDKV8i0Om9zJq0V6MZ5t82_OwcYqQlomckoYFnPfegBOQTE0zImOFpX4OVb7EbkBxnsULFIX__s_wylxcSctW2sWmwOs1YzSytASDL87V2RYWBOBRZ6vrGyj7WCe3ucom8SmlnU_D9whWOO34I4eG4ErtNZIravWIuPUXw/https%3A%2F%2Fgit.bioconductor.org%2Fpackages%2Fmulticrispr>?
 (as in e.g. github)

Asking because I cannot see recent commits (pushed to upstream successfully 
yesterday) reflected in build 
reports<https://secure-web.cisco.com/1jJOzEyoW2u-3tHDFcgIXdMcB7kOXmu9Nm8ZW3YJPv38b7AL5FKIwuPDG-mk-VK2RdohHNb094i-Jw69AJKUHMEPRCwSDJc3epGdu1oXfs3y1pB4y9EIq5qq64scEvOXk4qo434vvfrRlgLpROeZnAVed-P0lE-Wg3VADtxGOEomvwrpyClTfASKZR3hzSGuZI7oP522KScMh4MwjaWXtAvFU6AX54GaGDPWsBy2-LvKJhkK5MXA88qDQPAps3DTlT9OOx3QBU3Vn-K3rD4-PosS7lXJ7JkrlXfSzmnMzctmZx8fpRukHIFeC7zo7VIE1D3-7SqwQriVj90ow34NVGW2G_s4ro-fKJSxtqlNzak8/https%3A%2F%2Fbioconductor.org%2FcheckResults%2F3.12%2Fbioc-LATEST%2F>
 or landing 
page<https://secure-web.cisco.com/1A2W_b5ZAOGQ8Ht9ZFzC1E_hGsPYkaraU-OYX5DQLKHG1CDSVVsO3z1RrEZifTEa7Be45ASdmCX4DLcPoH3dlRN9kF-SCtD1Cqzd1h74rL-bm97PldOPsCjm_QrIhfwXtWbjmgjCOqdc4z_LYwHKcUQXizoM8Twn_0y0mvBIg_kXlp9AzxF31kdHa33NPA-VVAAk1VuF1yJWS2bFMg_LU51SXt24BoFVNmtsGKIyWbU5C2UB1yLcTq5EvalNJzI7eBgOwPDLObUy0W8SYa5A24zf3N6GDwchPgOXL5EOhsK-_W4VZnHnQFeNr82ysGdn38SUlyqrf_UwczMyBW5nC6ARU77Kgfl72pViMawG0aok/https%3A%2F%2Fbioconductor.org%2Fpackages%2Fdevel%2Fbioc%2Fhtml%2Fmulticrispr.html>.

A related question: the CI/CD feature during package submission (master branch 
push to github triggers build attempt on the BioC servers) was actually very 
useful, but I can understand that you don�t provide this for accepted packages 
to keep the load on your servers manageable.

What CI/CD setup would you recommend (from the perspective of being maximally 
relevant for BioC).



Travis?



Thank you for helping!



Aditya



____

From: Shepherd, Lori [lori.sheph...@roswellpark.org]
Sent: Thursday, June 11, 2020 6:18 PM
To: Bhagwat, Aditya; bioc-devel@r-project.org
Subject: Re: [Bioc-devel] fatal: 'upstream/RELEASE_3_11' is not a commit and a 
branch 'RELEASE_3_11' cannot be created from it

Newly accepted packages are added into devel only.  They will be a release 
branch as soon as the next scheduled Bioconductor release occurs.



Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263



From: Bioc-devel  on behalf of Bhagwat, 
Aditya 
Sent: Thursday, June 11, 2020 12:15 PM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] fatal: 'upstream/RELEASE_3_11' is not a commit and a 
branch 'RELEASE_3_11' cannot be created from it



Dear Bioc Core,

Thank you for accepting multicrispr on 
BioC<https://secure-web.cisco.com/1Y5aHfpLYwxVOA6Cj3bxEVuenqe6D8K2mYcqfAmwz6Fi6eyzj9ZL85VY2H0PZrFkpkFbO_w5JIWkUIDUjYSFPRsOWFmm_pDVgAJBRmO1uCb9LgJF5mh_FUnj2zUAPVJbk9HPy9BzwWn8pHCQOyHp9T_xfBrl1tFAkt7ZrYGptTyl0u1HYKnjYTmc-l5OjWQoyG3bIOTfYV1lc_cNItl7XwfDdyx4NkyoksEKEZfvA_2PlrkF8te0_49BJxVw47JVUK1Tjj-F-nuVxx2gAF3nDoPiQl1f5bOcc1zKgTYrgh1x2so6QfUHbqu_M7rEFHBQ9OFgeC30W0bOLRd4YEfu5XA/https%3A%2F%2Fgithub.com%2FBioconductor%2FContributions%2Fissues%2F1486>.
I was going through the instructions on how to sync existing 
repositories<https://secure-web.cisco.com/1Xe9o5uhiFHsFKbmSBGQuqpBQbV-hql0tIGwW7TBNOQyRT67-xND5I-TSMoVXC2pXrgYxNb-5-sPbt5rOOjgawuDHJv7Y7yJFhVBV51tIj9xSy4Nk-GlEPEtV_1RG79MZbJ5d7LZ82dFp-BZmzP

Re: [Bioc-devel] netDx: Build errors despite code working in BioC docker

[Shepherd, Lori]

Sorry my mistake.


Looking at the devel branch -- it looks like accessing the ensembl archives is 
the issue in biomart. Ensembl/biomart connectivity is known to be spotty.  I 
believe caching is already implemented in the biomart backend and you could 
verify with the maintainer but if not caching when its a successfully download 
would be beneficial.  Is there a reasoning for using an archived version 
instead of a current version?


For release -  I'm sorry for the confusion, I copied the link wrong.  404 still 
does indicate a file not found. It is odd as I can also test locally and do not 
run into ERRORs.  I can try and hop on the builders next week to try and dig a 
little further into why/what cannot be found.




Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Shraddha Pai 
Sent: Friday, June 12, 2020 10:32 AM
To: Bioc-devel ; Shepherd, Lori 

Subject: Fwd: [Bioc-devel] netDx: Build errors despite code working in BioC 
docker

Forgot to cc the group.
Also, this is the correct link:
http://download.baderlab.org/netDx/supporting_data/refGene.hg18.bed<http://secure-web.cisco.com/1BG3zQjrC4UXZnY6W31nyWRYP1FitXbJGL62ML_BhhL94zaaIolEoaxXzHx5QjIRwzDUCauCke2kWQfkC9xdmncnnubfy7pIvU6jLQT462RVSpcpiw2ZIh68sCagt1kcDudQdEiqUiA0Nw1FE8FPCBMBwTgmx55qgSV24LG0lr4VqmMudk3NVjXEsUJcNou9G7U5yhVdBv8Kxv1l8vG_b_7cj_NNDXONQY6UmchPoRhO3gbppmkmxZvlDyHhGMECwR4oEs29KyTblmT6FvTZnU_wocFiiOMxvizuQY_iFxODZhuGKE7olnWNkR1GpT7_zVxdsSSjy_rdAaHo8SgdSBg/http%3A%2F%2Fdownload.baderlab.org%2FnetDx%2Fsupporting_data%2FrefGene.hg18.bed>

Hosting it on our end isn't an issue.
S



-- Forwarded message -
From: Shraddha Pai 
mailto:shraddhapai.ne...@gmail.com>>
Date: Fri, Jun 12, 2020 at 10:24 AM
Subject: Re: [Bioc-devel] netDx: Build errors despite code working in BioC 
docker
To: Shepherd, Lori 
mailto:lori.sheph...@roswellpark.org>>


Hi Lori,
Which line number and file did you find the above link in?
I'm looking at both the RELEASE_3_11 and master, within the 
Predict_CaseControl_from_CNV.Rmd file.
In all instances, the link to refGene.hg18.bed appears to be correct.

I did find that the bed on the server was rw_r__r__ so I used a chmod 755 it. 
That shouldn't affect the situation because the file was world-readable before.

Thanks,S

On Fri, Jun 12, 2020 at 8:30 AM Shepherd, Lori 
mailto:lori.sheph...@roswellpark.org>> wrote:
A 404 ERROR generally has to do with accessing web resources.  I looked at your 
vignette and it appears that this link

http://baderlab.org/netDx/supporting_data/refGene.hg18.bed<http://secure-web.cisco.com/1TP-zIIaBfWsvlmHEcSZvDlHiwO38Y1zaiQ2rt1cYpD7qKJyqAfq-48yQLNYkGyiGHapd5n2sXvCBW6Or3qpzoiQ3as-2so5egDRF5T4fA5351kAA9e5xkLH-K6xynbenplj_we7KO2bPVjeegaUmsWEzLgtr9BcQt8dQ_E-8LPPzsdumv9DEe2KQV6cn6wJXpXqi-ci6kzrm22BUdcqtcAY4JJxgZJEdLytmx9CaglTrVxITe29gEl1Fp_IsbUWdyHzt4Z4Pt8N4AOvN5XKIZFdBrzEieLx1WauItREZd5n_HpBCAYOT7yS_g378F03ZqGgxvgUA5AUgJ5wN_NYEaA/http%3A%2F%2Fbaderlab.org%2FnetDx%2Fsupporting_data%2FrefGene.hg18.bed>

Does not exist.  Resources accessed by Bioconductor should be publically 
available.  If that location is not publicly accessibly the data can not live 
there.  If you need a place to host public data I suggest the Bioconductor 
AnnotationHub or ExperimentHub.

Cheers,


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel 
mailto:bioc-devel-boun...@r-project.org>> on 
behalf of Shraddha Pai 
mailto:shraddhapai.ne...@gmail.com>>
Sent: Thursday, June 11, 2020 5:44 PM
To: Bioc-devel mailto:bioc-devel@r-project.org>>
Subject: [Bioc-devel] netDx: Build errors despite code working in BioC docker

Hello BioC community,
I have been trying unsuccessfully for a week now to update both release and
dev branches of the netDx packages but am still getting build errors.

Today I got a build error for the release branch:
https://secure-web.cisco.com/1THF9VgEAVqGQdkK1Gugz4M1qdnd051bge4D5IxMpTOYv7mZRSDvQ6IvmsvcQh1Xc_5N7u-du_uMo645h6ZiSLuahMPE8xmFMVQyP7fFZw1BCFsNSQ-LpfMzPNn51l9ZaRS1GefMdVgHpBF5L_eeMMhA3K9scm2Lyys7bxR20xQ0BKySUiiRU8U_ES7bGMwu0mTaiuP0UcUbkCQ_tS-7BobJM5G4SFviHdd9ERzDGnqEXiRusVhrCr8uOIgPtgBxqSEF3gUbIHVoySNk1x8DonZ1veWjoE-7Of61xe1TyPqJJGDTWpuiQteFCOsGbdu0Om64XyDyr7slE9kQ-zwuaJd8hlSVw4FNOFn0iRiKlS7Y/https%3A%2F%2Fbioconductor.org%2FcheckResults%2F3.11%2Fbioc-LATEST%2FnetDx%2Fmalbec2-buildsrc.html

I tried to reproduce the error in the following way:
1. I have a BioC docker that runs R 4.0.0 and Biobase 2.48.0 (from
sessionInfo()).
2. I ran a fresh "git clone" to get the latest netDx. "git clone
https://secure-web.cisco.com/1fKSTDcaThEf6GEuD3oF4OvI_QkP6aAAEwSW5STRXbQgyROz5rzyoCW93NMHjn

Re: [Bioc-devel] netDx: Build errors despite code working in BioC docker

[Shepherd, Lori]

A 404 ERROR generally has to do with accessing web resources.  I looked at your 
vignette and it appears that this link

http://baderlab.org/netDx/supporting_data/refGene.hg18.bed

Does not exist.  Resources accessed by Bioconductor should be publically 
available.  If that location is not publicly accessibly the data can not live 
there.  If you need a place to host public data I suggest the Bioconductor 
AnnotationHub or ExperimentHub.

Cheers,


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Shraddha Pai 

Sent: Thursday, June 11, 2020 5:44 PM
To: Bioc-devel 
Subject: [Bioc-devel] netDx: Build errors despite code working in BioC docker

Hello BioC community,
I have been trying unsuccessfully for a week now to update both release and
dev branches of the netDx packages but am still getting build errors.

Today I got a build error for the release branch:
https://secure-web.cisco.com/1THF9VgEAVqGQdkK1Gugz4M1qdnd051bge4D5IxMpTOYv7mZRSDvQ6IvmsvcQh1Xc_5N7u-du_uMo645h6ZiSLuahMPE8xmFMVQyP7fFZw1BCFsNSQ-LpfMzPNn51l9ZaRS1GefMdVgHpBF5L_eeMMhA3K9scm2Lyys7bxR20xQ0BKySUiiRU8U_ES7bGMwu0mTaiuP0UcUbkCQ_tS-7BobJM5G4SFviHdd9ERzDGnqEXiRusVhrCr8uOIgPtgBxqSEF3gUbIHVoySNk1x8DonZ1veWjoE-7Of61xe1TyPqJJGDTWpuiQteFCOsGbdu0Om64XyDyr7slE9kQ-zwuaJd8hlSVw4FNOFn0iRiKlS7Y/https%3A%2F%2Fbioconductor.org%2FcheckResults%2F3.11%2Fbioc-LATEST%2FnetDx%2Fmalbec2-buildsrc.html

I tried to reproduce the error in the following way:
1. I have a BioC docker that runs R 4.0.0 and Biobase 2.48.0 (from
sessionInfo()).
2. I ran a fresh "git clone" to get the latest netDx. "git clone
https://secure-web.cisco.com/1fKSTDcaThEf6GEuD3oF4OvI_QkP6aAAEwSW5STRXbQgyROz5rzyoCW93NMHjnzEDFLHsvAalFQhFtr_Qg5ojG18B_csfChJwfgjFgej58_bvHymqRBn0PDIjsPSRfCREsqZ19SiqWzH_-c3hH_jOVpSMMBfc3jhhiAvlbuIMTeUdq6OfxlQA8H8ZWUZsznD8yS9mqZHBM_3rAHRimO_e5brMo6KMqErI1O4-so2EAr8vHWw_oEOltZLrSrnXi8B4tkLXevvJbWh8J3Bg7_IX6Pq7U_Pbmp23PTXoWWUq4UkTuKSG9S2HPgnlpbTKn7YZjryXf9c_0SImb9sX8QL64a16OvdA4oHV65xhjXS9EdY/https%3A%2F%2Fgit.bioconductor.org%2Fpackages%2FnetDx;
 , after the URL on the build
page above.
3. Switched to release branch "git checkout RELEASE_3_11"
4. Reinstalled netDx "R CMD INSTALL netDx" and confirmed using
sessionInfo(); netDx_1.0.1
5. Set up Renvirons as mentioned on the build page and launched R also as
suggested there, after declaring the corresponding variable.
6. The offending vignette is "Predict_CaseControl_from_CNV.Rmd". So I first
ran "knitr::purl("Predict_CaseControl_from_CNV.Rmd") , and then removed the
suppressMessages() around the offending function call,
"buildPredictor_sparseGenetic()".
7. Ran "source("Predict_CaseControl_from_CNV.R"). And it ran through
successfully.

What am I missing? Is it that the snapshot date it from June 10  but the
build page is from June 11 so I need to wait for the changes to kick in?

I'm also getting errors with the devel branch, so will probably separately
write about that (sigh).

Thanks,Shraddha

--
Shraddha Pai, PhD
http://secure-web.cisco.com/1XEZzaW2WII993HXVeWrJ29xC3iDjrN9p69iNANpk3heRN8fWRR0p-M3N2r-u0OoD0VH--V2nOw3ZtHGaBNPtVQIQFrt3suXwzgnH9narseMShrzX5tpvqAEYKJqatOEiJVLHqeZVrUgDzN9H_KK0cG2EPyojWkIQq7-4EjPtqAwXtTKe8wi_hY7tGkAwMjXiEiq-qgmN7z7b9Xc4jvBMPxTqIlMR68FZh1v6OVUgfEe280siYp9MZhguNZvMLMFVFuJ42yS8b0XYDuBEkO-b_hFsSGVf9KyQBS8g_RJNC6kSwagJRfvKZCXjeNdH4zkb3zJwFUJa7NIE2MCtKsw32xIad_FirzU9WTKcm2B8G0c/http%3A%2F%2Fshraddhapai.com
 ; @spaiglass on Twitter
Post-doctoral Fellow, 
http://secure-web.cisco.com/1RDoqupc8w03I66baJG97_eAlkJmwNqizjNkPfKrKecjRu1y1jue9yQ50WHGmOWYeP7HrqYdqk3QKnY4ZJPoBcBf_Iy_r4XEEW72jGp6we6RFtyds_DrcKy8w0jSHm3f-h1Fb-qR87slJm8nf48CSUUo9_PANDSg8vBf_2D_jRq94w7Sx8lr-L1PWGAQzUGNzvgqr77N7g_zJ_XrdeAGRu23UbveleW1s2v5ACNmI5kwAfij0vOjcmNT65ExAU67PuLbOKcGz4O-tsrBn2JUXc-XOQSRZO5UlbKy7g8eE0keWVn8m5gOmUtld-5POFuJjySDWX500OUfcZKQz3DgCWQ/http%3A%2F%2Fbaderlab.org
The Donnelly Centre for Cellular and Biomolecular Research
University of Toronto

[[alternative HTML version deleted]]

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Re: [Bioc-devel] fatal: 'upstream/RELEASE_3_11' is not a commit and a branch 'RELEASE_3_11' cannot be created from it

[Shepherd, Lori]

Yes what you described is correct and why the ERROR is occurring.  So at the 
next Bioconductor release (3.12) you will have a  RELEASE_3_12 branch that 
Bioconductor will created for Bioc 3.12 commits  and the master branch will 
continue to link to our devel branch.

Cheers,


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bhagwat, Aditya 
Sent: Thursday, June 11, 2020 3:07 PM
To: Shepherd, Lori ; bioc-devel@r-project.org 

Subject: RE: [Bioc-devel] fatal: 'upstream/RELEASE_3_11' is not a commit and a 
branch 'RELEASE_3_11' cannot be created from it

Thankyou Lori, Nitesh,

So you are saying is that

  *   upstream/RELEASE_*_* is created from your end with the next BioC release.
  *   The git error message arises because upstream/RELEASE_3_11 does not exist 
to copy the contents of (locally created) RELEASE_3_11 into.

The points under 
http://bioconductor.org/developers/how-to/git/faq/<http://secure-web.cisco.com/1jV03DzbYYI4ojCV090DnNjqLbd4WnU6ykMByn7ZvEc4pjDZ3pZfU9O7PCwT0JiwxzaaLJGR1MYGDAlCp8w2VSiOAbz_QRBUg_9GA3LQAXlIvPipEiGYuTYFRgIKO2cqNLAMgX6Pd92odRIvV-TPX1J2ehnqXTmw1pw4GxI3WwxwEWzFSkUZ1ICrmzNObBXH9ulKRyTQOubGzgi18XC9ctn8ZO8LOVM9TZtMibXR_tmKsHRw9R44-248lV8l79HJN-ZRphPBbZVKKsN9ep-Ez5CpzpunH4NeAM4vBdOuXKwy7XVtfty-tyJLDZnW1MQVuFsccT6asME-j9roYs-PLyCC-ZdGt7gl5NIH5d4FjOJc/http%3A%2F%2Fbioconductor.org%2Fdevelopers%2Fhow-to%2Fgit%2Ffaq%2F>
 #14 did work for me, but the above explanation makes sense.

Thanks!

Aditya


____
From: Shepherd, Lori [lori.sheph...@roswellpark.org]
Sent: Thursday, June 11, 2020 6:18 PM
To: Bhagwat, Aditya; bioc-devel@r-project.org
Subject: Re: [Bioc-devel] fatal: 'upstream/RELEASE_3_11' is not a commit and a 
branch 'RELEASE_3_11' cannot be created from it

Newly accepted packages are added into devel only.  They will be a release 
branch as soon as the next scheduled Bioconductor release occurs.


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Bhagwat, 
Aditya 
Sent: Thursday, June 11, 2020 12:15 PM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] fatal: 'upstream/RELEASE_3_11' is not a commit and a 
branch 'RELEASE_3_11' cannot be created from it

Dear Bioc Core,

Thank you for accepting multicrispr on 
BioC<https://secure-web.cisco.com/1Y5aHfpLYwxVOA6Cj3bxEVuenqe6D8K2mYcqfAmwz6Fi6eyzj9ZL85VY2H0PZrFkpkFbO_w5JIWkUIDUjYSFPRsOWFmm_pDVgAJBRmO1uCb9LgJF5mh_FUnj2zUAPVJbk9HPy9BzwWn8pHCQOyHp9T_xfBrl1tFAkt7ZrYGptTyl0u1HYKnjYTmc-l5OjWQoyG3bIOTfYV1lc_cNItl7XwfDdyx4NkyoksEKEZfvA_2PlrkF8te0_49BJxVw47JVUK1Tjj-F-nuVxx2gAF3nDoPiQl1f5bOcc1zKgTYrgh1x2so6QfUHbqu_M7rEFHBQ9OFgeC30W0bOLRd4YEfu5XA/https%3A%2F%2Fgithub.com%2FBioconductor%2FContributions%2Fissues%2F1486>.
I was going through the instructions on how to sync existing 
repositories<https://secure-web.cisco.com/1Xe9o5uhiFHsFKbmSBGQuqpBQbV-hql0tIGwW7TBNOQyRT67-xND5I-TSMoVXC2pXrgYxNb-5-sPbt5rOOjgawuDHJv7Y7yJFhVBV51tIj9xSy4Nk-GlEPEtV_1RG79MZbJ5d7LZ82dFp-BZmzPwrjKRAib7x8vphKaRW4qc_q6EIPMOrs282w4JaJxxRd-Jsxi6X_gw41rihMwaTa84WG62bi5im6SkX3hoyYq6qwitZdOiUeNN9FYJHB_VREnXcM16haB2xWae5BwiJJdtuP3Y1T-wW9L0HnO14_bhkOd794PH_lDa0cdICiv2NVJVoaSyYZK93SX5T2wpON1FgO_xhi1D5Z45H163FH75DerE/https%3A%2F%2Fbioconductor.org%2Fdevelopers%2Fhow-to%2Fgit%2Fsync-existing-repositories%2F>.
All instructions up to point 9 work.

Point 10, however fails, when creating the release branch:
$ git checkout -b RELEASE_3_11 upstream/RELEASE_3_11
fatal: 'upstream/RELEASE_3_11' is not a commit and a branch 'RELEASE_3_11' 
cannot be created  from it

I wonder what I am doing wrong (seems like it should be something trivial, but 
I am not seeing it).

Thank you for helping!

Aditya

[[alternative HTML version deleted]]

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responsible for the delivery of this message to the intended recipient(s), you 
are hereby notified that any disclosure, copying, distribution, or use of this 
email message is prohibited. If you have received this message in error, please 
notify the sender immediately by e-mail 

Re: [Bioc-devel] fatal: 'upstream/RELEASE_3_11' is not a commit and a branch 'RELEASE_3_11' cannot be created from it

[Shepherd, Lori]

Newly accepted packages are added into devel only.  They will be a release 
branch as soon as the next scheduled Bioconductor release occurs.


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Bhagwat, 
Aditya 
Sent: Thursday, June 11, 2020 12:15 PM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] fatal: 'upstream/RELEASE_3_11' is not a commit and a 
branch 'RELEASE_3_11' cannot be created from it

Dear Bioc Core,

Thank you for accepting multicrispr on 
BioC.
I was going through the instructions on how to sync existing 
repositories.
All instructions up to point 9 work.

Point 10, however fails, when creating the release branch:
$ git checkout -b RELEASE_3_11 upstream/RELEASE_3_11
fatal: 'upstream/RELEASE_3_11' is not a commit and a branch 'RELEASE_3_11' 
cannot be created  from it

I wonder what I am doing wrong (seems like it should be something trivial, but 
I am not seeing it).

Thank you for helping!

Aditya

[[alternative HTML version deleted]]

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this message in error, please notify the sender immediately by e-mail and 
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Re: [Bioc-devel] FEM package update and release

[Shepherd, Lori]

FEM was deprecated before the last release as shown in the release build report.

http://bioconductor.org/checkResults/release/bioc-LATEST/FEM/

FEM will not be undeprecated and added to devel (master)  until after it is 
building in the RELEASE_3_11 branch.

The package has been broken for over four months and the email that was listed 
in the DESCRIPTION of the package was undeliverable to all our attempts to 
reach out to fix the package which is consistent with our deprecation policy.

Please make all necessary changes to the RELEASE_3_11 branch on 
git.bioconductor.org  and email us when the package is building cleanly to 
start the undeprecation process.

Cheers,



Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Zhen Yang 

Sent: Wednesday, June 10, 2020 3:40 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] FEM package update and release

Dear Biocondcutor admins:

This is Zhen Yang, the maintainer of the Bioconductor package of "FEM" 
(https://secure-web.cisco.com/1AAfYhbwS6z55CClXAtYY-ZpNArZ365NvI4ZtwAC0U6FER4aRYb2YprsZcMsuj9uyCMOQVim04nZytrwOMV-DvIQZzNegp5HkkJp-11XMsk58BTUvJCi02Zzr16sRJdQECiWbAqjes4F8kLxO-1J97B8Dl9Qt8piuH8kiF5hfgTPHzRnNXTiQszYt2Bevbpt5XcxXFv7zc7ZCVKnr0ucw9k-cefLfF5u2JWWy8TLB_OHbmhHE5q0CxOSf0H86cd-MUbTRuEb0El7db3J2lUz49xyOP9V2N78__57YFyTXHUHvwMsGpfGK3T0_UOL4Co2jotw99BtuL7ZzrcVwy6JUwonoPOdbDLc1agjoPb69ScA/https%3A%2F%2Fbioconductor.org%2Fpackages%2Frelease%2Fbioc%2Fhtml%2FFEM.html),
 We have recently made some update for this package, and I have submitted it to 
the Github 
(https://secure-web.cisco.com/1SD1Iq4XRcJ7UFUmOpaAJMKpqnCLnTs8iOx65OWgL2yg5BA2bqtQQMn9TNq-OV0-Bcw2cgHr3A6IWvQS-xgMxrZdMYfJh25ga4tmle3C9h3Ryj5ZI0b5cC6iu0-3EzQbFC7LZILgSW39kt5LYWrZOr3KzLG744NiA8s6XzwaVkurXTK9z92RVaAFt7-8ehfbqs43UiUPClw7v797nGJffg5KQp8bK_0cHJg_IcqElQmGumc2sUnfiOGXZkVXnizHfZ-MP2t4-VPa4J59S25SkFN3i9Iy2kOJyMVzmhBdoJU1j5225bXh-DBkA30-L5dmDhGoCny2Q9a-y
 SF9HfNDZaA/https%3A%2F%2Fgithub.com%2Fzyangx%2FFEM) and BioC last week, It 
seems Code in Github have got updated but not in BioC. We checked page of 
devel-version for FEM but nothing in:

https://secure-web.cisco.com/1SVs8qoRBfmGALIg1QPuNi-DFJZu42jp_tNtu835yLRemUgN9_J5rP17KRl7bLWyWlhna3YK3TPWgeqLPsQ_YlF6FKDYyQ-s4QRPXdzVgIsCErT9zCh3mVofzc2y0dN6ErS-U_-6WL0wJHuuX-S3mo3EEKsvwuwQwtVfgV6A15vzLATSoWanHj0xGCkS40WIcmPZU6EZYL7x1cDvDYFY74cF3Cq7jOmmITZu5KmBE7P3ARkswL4PCM20H_PmVBHzjxvV6kC6tdL2zSxMFjGFwduvmMvaDB9H1jOfbdNFJRHKpFzSvHsZ7zanXFEpvsDatuLyc3j11Bvc7HjH4TNGUWTomp4KRRNVwiYVKcpkQros/https%3A%2F%2Fbioconductor.org%2Fpackages%2Fdevel%2Fbioc%2Fhtml%2FFEM.html

I would like to ask is there anything I should do after I push my code to BioC 
and how long it would take to release the devel-version?

Thanks a lot and best wishes!

Zhen Yang
Fudan University

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[Bioc-devel] List of Deprecated Packages for Bioc 3.12

[Shepherd, Lori]

The Bioconductor Team is continuing to identify packages that will be 
deprecated in the next release to allow for the Bioconductor community to 
respond accordingly. The list will be updated monthly. This is the current list 
of deprecated packages for Bioc 3.12 :



Maintainer requested deprecation:

Software:

CGEN
DESeq: please see DESeq2
chimera
flowFit
flowSpy
netReg
metaseqR: please see metaseqR2
MPFE
OGSA
prada
PWMEnrich
rTANDEM
scsR
shinyTANDEM
spotSegmentation


Unresponsive/not-maintained packages:

Software:


adaptest
ArrayTV
BioNet
BioSeqClass
CHARGE
CNVtools
CorMut
flowType
flowVS
focalCall
FourCSeq
gage
GeneOverlap
GenRank
GOFunction
ImpulseDE
ImpulseDE2
joda
JunctionSeq
LINC
Logolas
MAIT
Mirsynergy
MotIV
NarrowPeaks
netbenchmark
NOISeq
omicade4
omicRexposome
OmicsMarkeR
pathprint
PathwaySplice
PGSEA
plrs
Prize
reb
Roleswitch
safe
sampleClassifier
sigaR
signet
Starr



Experiment Data Package:

FunciSNP.data
mitoODEdata
Mulder2012
PWMEnrich.Dmelanogaster.background
PWMEnrich.Hsapiens.background
PWMEnrich.Mmusculus.background
RNAinteractMAPK
RnaSeqSampleSizeData




It should be noted, we did try to reach out to these package maintainers 
multiple times and they were either unresponsive or had emails bounce. We 
encourage anyone that is familiar with a package maintainer on this list to 
reach out to them and notify them directly. Packages can be un-deprecated if a 
maintainer fixes the package to build/check cleanly before the next release and 
requests un-deprecation on the bioc-devel@r-project.org mailing list.

We will be sending emails out to packages that have been broken across all 
platforms for an extended period of time as those are packages that are up for 
immediate deprecation if not corrected in a timely fashion.

Thank you


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


This email message may contain legally privileged and/or confidential 
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agent responsible for the delivery of this message to the intended 
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Re: [Bioc-devel] MotifDb missing some PWMs from FlyFactorSurvey database

[Shepherd, Lori]

Paul

  -  On the support site,  you can edit your profile and put package names as 
watchedtags.  When a person posts to the support site and tags with the package 
name you would then be emailed.   This assumes they tag the post correctly but 
also an option


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Paul Shannon 

Sent: Friday, June 5, 2020 1:12 PM
To: Nystrom, Spencer 
Cc: bioc-devel@r-project.org 
Subject: Re: [Bioc-devel] MotifDb missing some PWMs from FlyFactorSurvey 
database

Thanks, Spencer.  Sorry I missed the support posting - there�s no automatic 
forwarding from there to maintainers.

I�ll take a look at this later today, then post back to the support list, and 
we will get a fix in.

Thank you for pointing out the problem!

 - Paul

> On Jun 5, 2020, at 9:46 AM, Nystrom, Spencer  wrote:
>
> Hi,
>
> I've identified a few missing PWMs from the MotifDb package and would like to 
> help get them added. I posted on the support page but have not received a 
> response after 10 days, so messaging here instead (link to forum post: 
> https://secure-web.cisco.com/1TFAehHIfvF8C-fsHqKF9EZUlEaLQqYsIygNO_BAsoXZwv_Wu3u5B4wJVetP6b2oLhIIOFSZhhOumdKzED0ovgHBPNyPVtPXiHxRm8b66_DTxd3gOar2MNQ5l9qQH4_wqJMMJaxbnBCWUwAGnSDJO91ueABvVc6mU2FAghpGjUfBlWvlYMMhZzzmbgjYqsldl1Ta23cGowoJ3ncf7CeSKr6bKFMch5qHT0BqRq0t6Gi_b7w1KzlscAc0wC3Pxjq5gXX9vMchpSqTrtO3_MRw3Ojfo2wOimSuSsQL0RWe2mKIGnuSE0r8q7XSF0fsyFaH-DmeMbMdAxJok14mifZioaA/https%3A%2F%2Fsupport.bioconductor.org%2Fp%2F131312%2F).
>  Full details can be found in the support post, but in summary, there are a 
> small number of Drosophila transcription factors which do not have any 
> entries in MotifDb, meaning anyone using that database for their motif 
> analysis will not identify these factors as potential candidates. A .meme 
> format file ("flyFactor_Missing_Motifdb.meme") of these missing motifs along 
> with a reproducible script to identify these factors can be found at this 
> gist: 
> https://secure-web.cisco.com/1Hw4j-u2eWVf5hZXzqLZ4apPGgjUddOX5ixtNdTGwQZ4NPy_KaMZids5AaShi-S2meTRVKS9jM3cf2iEulIctx81-ZyEXDGgnDv79mSzGZG0QjWEwCoKwaCa8Eg2m1zL4AW14psIhbcmvxc36OZX77cPdvVBZBl0WIzqa0g6N2n6c75iPRS0Mi4k86awArVwZ6SMWbd9onXyqHQqqfNpEcQnilZw0UkOntlEVSBQWpNszEdDH6zw1gLuglq1F4JIJwa6onOYuveddTXIVT0r3veLCqhDXiDZIxFN9PmMrUUh9Xqiq2S2uRkK53JqfA-krBLQfCwo4agchyGpfqwWZOA/https%3A%2F%2Fgist.github.com%2Fsnystrom%2Fb7701858bec6bc4ce7758a7582422359.
>  I am happy to help curate any additional metadata required to get these 
> factors added to the database.
>
> Best,
>  -Spencer
>
>[[alternative HTML version deleted]]
>
> ___
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Re: [Bioc-devel] Bioconductor package tidybulk

[Shepherd, Lori]

The master branch is the development branch (Bioc 3.12) .  The version  of  
x.y.z   The y is always odd in devel  and even in release.  This is the very 
first section on the page you referenced.  
http://bioconductor.org/developers/how-to/version-numbering/

We do not jump full y versions in the middle of a release.

The current RELEASE_3_11  version is  1.0.0  =  the appropriate version bump on 
this branch is  1.0.1

The current master version is 1.1.0  = the appropriate version bump on this 
branch is  1.1.1


If you are unfamiliar with git and github branches I encourage you to read more 
documentation about it.  There are many helpful tutorials.
You can have as many branches on your local github repository as you like. We 
recommend creating unique branches for bioconductor releases to mimic our 
branch structure.   In general, and to make it less confusing we would highly 
recommend using the master branch as the development branch and link that to 
the master (development version) of Bioconductor.   This would be consistent 
and then you can following the guides and tutorials listed on the Bioconductor 
help pages

http://bioconductor.org/developers/how-to/git/


The release branch is designed to always be a stable branch and should only be 
updated for bug corrections.
The master branch should be for development and new features.



We will assume you ran the following to set up your remotes as recommended:
git remote add upstream g...@git.bioconductor.org:packages/tidybulk.git


if you do
git remote -v

you should see something similar:
origin   (fetch)
origin   (push)
upstream g...@git.bioconductor.org:packages/tidybulk.git (fetch)
upstream g...@git.bioconductor.org:packages/tidybulk.git (push)


To create and work on a release branch:

git fetch --all
# this gets all branches from all remotes


# The following would only need to be run once EVER!
git checkout -b RELEASE_3_11  upstream/RELEASE_3_11

# this says checkout  a branch (-b)  call it RELEASE_3_11  and have it 
copied/link to the code at  upstream/RELEASE_3_11 (the #bioconductor upstream 
remote branch of RELEASE_3_11)

After it is created, to switch to this branch on a daily basis you can simply:
git checkout RELEASE_3_11



git pull upstream RELEASE_3_11
# pulls changes from the upstream RELEASE_3_11 remote


# The following would only need to be run once EVER!   It creates a branch on 
your local github called RELEASE_3_11
git push -u origin RELEASE_3_11



Make your code changes to fix bugs! Make sure to do a valid version bump by 
bumping the  z  of version  x.y.z

git add 
git commit# give an informative commit message


git push upstream RELEASE_3_11
# This should push to the Bioconductor git repository

git push origin RELEASE_3_11
# This should push to your github local git repository


git checkout master
# Switch back to your master branch for development and code changes


If you are ever confused on what branch you are on you can do
git branch


To work on the devel master branch the commands would be similar to above but 
using master

git pull upstream master  # pulls from git bioconductor
git pull origin master# pull from your individual github

# make changes, commit changes

git push upstream master  # pushes to git Bioconductor
git push origin master   # push to your github


Hopefully that helped clarified and will get you started.



Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: stefano 
Sent: Thursday, June 4, 2020 12:56 AM
To: Shepherd, Lori 
Cc: bioc-devel@r-project.org 
Subject: Re: Bioconductor package tidybulk

Thanks Lori,

I have to questions

1)
I got versioning error


```

rstudio-1 267 % git push upstream master
Counting objects: 372, done.
Delta compression using up to 32 threads.
Compressing objects: 100% (276/276), done.
Writing objects: 100% (290/290), 1.13 MiB | 0 bytes/s, done.
Total 290 (delta 208), reused 21 (delta 13)
remote: Resolving deltas: 100% (208/208), completed with 41 local objects.
remote: Error: Illegal version bump from '1.1.0' to '1.2.1'. Check
remote: 
http://bioconductor.org/developers/how-to/version-numbering/<http://secure-web.cisco.com/1Juo69PrrnIOXU2DlRv55eEvQE69YG8gNnojLbxZZWpn2-BCpwQ95EvShTW84fzr36gEkai208agWd63Ju9NfDXE-J9WHITwNW8oj6a0nxd1bS_UtLog1j_kotLO3TRPxw6votAQ8BdaCk4PzIaCZRX2wTPTRQsHNIV1_U4F47Y3w5QyE-kq7njCZrhtOzxb6HxIn6mtY-Xgj7a3Wkas_WsiIDmeKI8MdDFgePj_CwYe7BMLtq680xbPHpzYD-KvS32jkv_R8yL5Bqf2xd1lUZxeJU7rCj4PTKVa0Q9JgSdl3ax7Ozze9-LxNvuOsmqKWWGorQqVctJQPHiJjwDlmPjmeCsjgtgODdtBWqLJ73s4/http%3A%2F%2Fbioconductor.org%2Fdevelopers%2Fhow-to%2Fversion-numbering%2F>
remote: for details
To g...@git.bioconductor.org:packages/tidybulk.git

```

Even reading the guide 
http://bioconductor.org/developers/how-to/version-numbering/<http://sec

Re: [Bioc-devel] Bioconductor package tidybulk

[Shepherd, Lori]

It will not be tested before integration.  We assume that all maintainers and R 
CMD build and R CMD check before submitting changes to Bioconductor.

You will need to have activated your git credentials account

https://git.bioconductor.org/BiocCredentials/login/?next=/BiocCredentials/

And follow the instructions for pushing to git.bioconductor.org.
We provide many help instruction files for different scenarios

http://bioconductor.org/developers/how-to/git/


You will most notably be interested in
Syncing to Bioconductor
http://bioconductor.org/developers/how-to/git/sync-existing-repositories/

and pushing fixes to release and devel
http://bioconductor.org/developers/how-to/git/bug-fix-in-release-and-devel/




Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: stefano 
Sent: Wednesday, June 3, 2020 4:29 AM
To: Shepherd, Lori ; bioc-devel@r-project.org 

Subject: Re: Bioconductor package tidybulk

Hello Again,

I would be happy to submit the github master with the patch tonight if you 
could please confirm the commit command. Will it be tested before integration I 
assume.

Thanks a lot!

Best wishes.

Stefano



Stefano Mangiola | Postdoctoral fellow

Papenfuss Laboratory

The Walter Eliza Hall Institute of Medical Research

+61 (0)466452544


Il giorno mer 3 giu 2020 alle ore 12:26 stefano 
mailto:mangiolastef...@gmail.com>> ha scritto:

Thanks Lori, (it seems outlook lost my sent email)



sorry I missed this. It's so strange, few days ago I checked at


https://www.bioconductor.org/packages/devel/bioc/html/tidybulk.html<https://secure-web.cisco.com/1ymalO2Wo2gRPT4USwKYJChnovSH3sx87LQTVbhEAL5rIc3rN6fxBVq0xvtPe8K_Q-R_eFRNkhIlQj7WO0ojRaWF_pEyWlhdIOd2PMRLmE2OPNqgY5f94zo8UYWUGdcvlZcVx8reWZ3HqP5ZigV5z6s1O1vpAhOg7Ilz6E1U3-x5Ew-CEeVKmnYZe96PicWrzG2pfFGcttYa35E5pwKrrGI-dm5Sy6FKZhrPJtO-Qm65EpKlgjJg-S1H0Dng6El9eZl79ifySj3rIrEtYwcVvsRCgOGmn5RqrxF4_1vKVJl7MF59rIRIHqt-OR9BXO6Ol7hNnQze5_Kl_SbkOEyd9h_FG7hn_MIzYBsitEyDD5-8/https%3A%2F%2Fwww.bioconductor.org%2Fpackages%2Fdevel%2Fbioc%2Fhtml%2Ftidybulk.html>


and the build was OK for devel and stable versions.


I have done the fix


commit d1fe5beb290765181e0ce377b890f453c62ea9da


Should I (?)


- integrate the commit to the tidybulk version present in Bioconductor, and push

- or push the update github repo


Could you point me to the resource tat states how to push to Bioconductor, so 
I'm sure I am doing the right thing.


Thanks alot.


Best wishes.

Stefano



Stefano Mangiola | Postdoctoral fellow

Papenfuss Laboratory

The Walter Eliza Hall Institute of Medical Research

+61 (0)466452544


Il giorno mer 3 giu 2020 alle ore 07:10 Shepherd, Lori 
mailto:lori.sheph...@roswellpark.org>> ha 
scritto:
Hello Package Maintainer,

The Bioconductor Team would like to notify you that your package is currently
failing on release and devel versions of Bioconductor and has been for an
extended period of time.  This is very problematic.  Please fix your package to
R CMD build and R CMD check cleanly immediately to avoid deprecation of your
package. If you are having trouble or have any further questions please reach
out to the developers mailing list at 
bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>


We appreciate your immediate attention to this matter.

Cheers

http://bioconductor.org/checkResults/devel/bioc-LATEST/tidybulk<http://secure-web.cisco.com/1V0Xuq_KL0x1Cl4QqzHrj1dnBRaQhCCuV-22PXesIk07DaPPjoJ3QsrSPROh_5cXbYpawIN5i2Nq1BZR_hLHXPuM6pjQ-3eMVQGnIfUDaGyUaM2r0OKlVcRHQal8uBYNnIvQH6S2oehrbakBF8VT50ga-chmesQYDXRVuPo_IWNS6IIR3LBhvBnY1hv5_raI9CsjS9fUpU-G09_CAyRyUA17JrLjrtMAT4Bxi5T0NN53kKg2ZP4Unsqwtr5Oix4WaXxRCKrMa0s77HeePZYvUAYnkfUYZCiYXuVsqmRytlG92KumBHz-0P1es_zBp5JVmqn-Y3mjMBOwl7Vy8Lx1o8anxo8xN9qChrHFrl14SjZQ/http%3A%2F%2Fbioconductor.org%2FcheckResults%2Fdevel%2Fbioc-LATEST%2Ftidybulk>
http://bioconductor.org/checkResults/release/bioc-LATEST/tidybulk<http://secure-web.cisco.com/1gjLzb1cWpFF_sHsM57h5yIYvuiIuFDLZmakncmleiFa_KJWoTiDpmLs9wxxenQRe9bjnc5MCunwT6ishis6WIailFEBNiwNXyJWEXo9_I4MXs7HnnVHP8L-aUJI9D52getJRFvo3Y1oau4z0D0sMu_33XBgwAkFIcpDb8aleVdkalFB6T0bdquwBcfn_pO0zBXW8UgXsoFB3_RvbY4sgsDnymfSGqVXlwELCaQ9euMvV9waafBekDjsrAOD5H7L_t2wd91GpDyI8LNZhIFPO1vmUtCO5BkFrYxJvEEoLmqNSftO5yyQ2UqMuB8OQeacnKOLGwd0V-6_USxeGmvqSxVi2BDpIV7ukHTLkFTScrn4/http%3A%2F%2Fbioconductor.org%2FcheckResults%2Frelease%2Fbioc-LATEST%2Ftidybulk>



Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

This email message may contain legally privileged and/or confidential 
information. If you are not the intended recipient(s), or the employee or agent 
responsible for the delivery of this message to the intended recipient(s), you 
are hereby notifie

Re: [Bioc-devel] Vignette Building Latex Errors on Windows Release Branch

[Shepherd, Lori]

The cslreferences problem seems to be caused by some recent changes to 
Pandoc/rmarkdown.  We downgraded pandoc on tokay2 to 2.7.3  which has remedied 
the error.

Cheers,


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Shepherd, Lori 

Sent: Tuesday, May 19, 2020 2:19 PM
To: Mike Smith ; bioc-devel 
Subject: Re: [Bioc-devel] Vignette Building Latex Errors on Windows Release 
Branch

Pandoc 2.9.2  appears to be installed on tokay2




Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Mike Smith 

Sent: Monday, May 18, 2020 11:49 AM
To: bioc-devel 
Subject: Re: [Bioc-devel] Vignette Building Latex Errors on Windows Release 
Branch

Reading around, it looks more likely this is an issue with pandoc than
LaTeX directly.  I guess it'd help to know what version of pandoc is
running on the build machine, I'm unable to recreate either using the
pandoc supplied with RStudio.

Mike

On Fri, 15 May 2020 at 21:09, Sergio Picart Armada 
wrote:

> Dear bioc devel,
>
> We are having the same problem with our package FELLA.
> Any help is appreciated!
>
> Best,
> Sergi
>
> Missatge de petr smirnov  del dia dv., 15 de maig
> 2020 a les 19:42:
>
> > I am having trouble reproducing some vignette build errors for our
> > PharmacoGx package on Windows (tokay2).
> >
> > The error is a Latex error:
> > LaTeX Error: Environment cslreferences undefined.
> >
> > It seems likely to be due to a missing dependency for the style file
> > we are using, however, I do not understand why it works on all other
> > build machines. tokay1 does not have the same error, and is building
> > the same vignette. Likewise, none of the other OS machines are missing
> > this dependency.
> >
> > I also tried to reproduce in a newly reinstalled Windows environment.
> > After installing R 4.0, Rtools, all the package dependencies, and:
> > knitr, knitcitations, rmarkdown, pander, and tinytex, the package
> > builds on the machine. As far as I can tell, all these packages are
> > also installed on tokay2.
> >
> > Does tokay2 use a different Latex distribution from what is installed
> > by tinytex ?
> >
> > --
> > Petr Smirnov
> >
> > psmirnov2...@gmail.com
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://secure-web.cisco.com/17Rs-rRez65-ZHN_w5_QwL2wfnrf3wMZOzqfA9zX5OlkaPU0QqfKdI_B_MysjDdF00kKgfUVbHHnXQ328VKiz11JRQwkhqVkKa5DLUs--4IklPLrfkGouPhpVQNwwZPu26zHSvzl8qTPiQ-WXqWXcqGOP0iwrN7BAuCalMN3ZIERZW0oSwSmCLEkpTYNGgWDmuGHNLCSVlGWoWol7JiSk-yBKmBAQiCgyyt6tTwByOZ-NQQOprjDkCkhStwmO69Z8UQMJUeZQG_ohCN7EC6kuCYVr5qsJ2fJWETk4zB5eZIIhXGx_7Etvw-6HTa3geJ2CboJOJiRMCOesr6jmL8hg1w/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel
> >
>
> [[alternative HTML version deleted]]
>
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[Bioc-devel] Single Package Builder for New Package Submission

[Shepherd, Lori]

Hello all,

We will be updating the Single Package Builder to run on the devel version of 
Bioconductor 3.12 over the new few days. During the update the Single Package 
Builder may experience intermittent down time. We apologize for any 
inconvenience this may cause and hope to keep downtime to a minimum.

Cheers



Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


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Re: [Bioc-devel] Vignette Building Latex Errors on Windows Release Branch

[Shepherd, Lori]

Pandoc 2.9.2  appears to be installed on tokay2




Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Mike Smith 

Sent: Monday, May 18, 2020 11:49 AM
To: bioc-devel 
Subject: Re: [Bioc-devel] Vignette Building Latex Errors on Windows Release 
Branch

Reading around, it looks more likely this is an issue with pandoc than
LaTeX directly.  I guess it'd help to know what version of pandoc is
running on the build machine, I'm unable to recreate either using the
pandoc supplied with RStudio.

Mike

On Fri, 15 May 2020 at 21:09, Sergio Picart Armada 
wrote:

> Dear bioc devel,
>
> We are having the same problem with our package FELLA.
> Any help is appreciated!
>
> Best,
> Sergi
>
> Missatge de petr smirnov  del dia dv., 15 de maig
> 2020 a les 19:42:
>
> > I am having trouble reproducing some vignette build errors for our
> > PharmacoGx package on Windows (tokay2).
> >
> > The error is a Latex error:
> > LaTeX Error: Environment cslreferences undefined.
> >
> > It seems likely to be due to a missing dependency for the style file
> > we are using, however, I do not understand why it works on all other
> > build machines. tokay1 does not have the same error, and is building
> > the same vignette. Likewise, none of the other OS machines are missing
> > this dependency.
> >
> > I also tried to reproduce in a newly reinstalled Windows environment.
> > After installing R 4.0, Rtools, all the package dependencies, and:
> > knitr, knitcitations, rmarkdown, pander, and tinytex, the package
> > builds on the machine. As far as I can tell, all these packages are
> > also installed on tokay2.
> >
> > Does tokay2 use a different Latex distribution from what is installed
> > by tinytex ?
> >
> > --
> > Petr Smirnov
> >
> > psmirnov2...@gmail.com
> >
> > ___
> > Bioc-devel@r-project.org mailing list
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Re: [Bioc-devel] Debugging not updated for coexnet package

[Shepherd, Lori]

There is lots of documentation on how to achieve this.

Most specifically for pushing changes to the RELEASE_3_11 branch following the 
documentation

http://bioconductor.org/developers/how-to/git/bug-fix-in-release-and-devel/




Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Juan David 
Henao Sanchez 
Sent: Wednesday, May 13, 2020 8:27 AM
To: Herv� Pag�s 
Cc: Bioc-devel 
Subject: Re: [Bioc-devel] Debugging not updated for coexnet package

Hi.

Thanks for your help solving this issue. Could you please let me know how I
can fix the bug in the specific BioC version (3.11). How could I push my
current updated code into this specific version?

Thanks in advance.

I am looking forward to hearing from you soon.

Kind regards,

Juan

El mi�., 13 may. 2020 a las 0:44, Herv� Pag�s ()
escribi�:

> Hi Juan,
>
> On 5/12/20 13:37, Juan David Henao Sanchez wrote:
> > Dear all.
> >
> > I received an error regarding my package coexnet when it is checking for
> > multiple platforms. I already fix the problem a couple of days ago and I
> > push the solution like:
> >
> > git push origin master
>
> Indeed the package is now green in Bioc devel (the master branch of your
> package):
>
>
> https://secure-web.cisco.com/1zTvATemlXuwTsvdpt1GSyrR7oj4jKLSuVCFqEK8Bx3Ts3it5bWxLbK1v3PpyD_6tfq4WU4gWj_NQ04_TtwsZ2hK4RQsb-OaJIfEqhlWqhD6O12vKs2OpFOneeTYwcf0V4rEAScnuJQSvkfhFu6XiJLVfp5clHpKPE1EsKf8KipCDobKaXsexUyjocrgN51GAGQyUzjRKX03jeDLkmjhR7wk3ahdNWrf3UvYx4-dY19Qdt7lZTttHHk2N0caKsMImcktvRxlq5dfS0L6exoFpzt5f20YD3bnbtBUbCt9lFkOyesNr6TTka0_KFQ7GxPOIJhSPRvI7azRnoJ4I0x7HwE5Vn9g88HymJootFjCrME8/https%3A%2F%2Fbioconductor.org%2FcheckResults%2F3.12%2Fbioc-LATEST%2F
>
> However, as I mentioned in the email I sent you off list, the package is
> still broken in BioC 3.11 (the current release):
>
>
> https://secure-web.cisco.com/1qrz9-Njh-eGNyUg0E4PSo3kL_kE0PXtuHFxkeHDzLaJzY-F0pVmXz4t8eicwDp4CoICG3raQcKmB5kpD0h_ml52ivByFLPamaHcJ3vbS3DPxCewObxoXpIHuTGaSX_vzYA6JNHbnyeqchCQIjAua-8Y059kj0VR-mFNAxgMpRILLsRKNHkWLBSTbwIBhLzO4Dob3xuefzyua_mOvJU1X7O-9fYoTxuJg6MFAVUiR4L1Gmy_5d2o1_Mq6woySFk0fxC9RgZizOBdxyEX8qhb0-PgF37R2CZ4b7IceNwZLgXZJ7HJ0vvuYIa4rsSqcg-3mq5uXGxAxq_UMcWJIKUTxFACVnqB6DnzBUzmA6zawbCI/https%3A%2F%2Fbioconductor.org%2FcheckResults%2F3.11%2Fbioc-LATEST%2F
>
> So you also need to fix the RELEASE_3_11 branch of your package.
>
> Best,
> H.
>
> >
> > However, I continue receiving the same error message and it is the same
> > previous version of my package.
> >
> > There is something additional I have to do to update my package?
> >
> > Thanks on advance,
> >
> > I look forward to hearing from you soon.
> >
> > Juan
> >
>
> --
> Herv� Pag�s
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpa...@fredhutch.org
> Phone:  (206) 667-5791
> Fax:(206) 667-1319
>


--
Juan David Henao
Magister in Bioinformatics
Universidad Nacional de Colombia

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Re: [Bioc-devel] BgeeCall package present twice

[Shepherd, Lori]

Yes looking at the links further it is a legacy version.

The one that resolves to a workflow page if you look closely is when 3.11 was 
in development phase

https://bioconductor.org/packages/release/workflows/html/BgeeCall.html


While the software page is the current release.

I'm not exactly sure why the development page still appears, this was 
surprising to me,  and is something I will try to track down.  Regardless the 
git link points to the same repository on git.bioconductor.org so users would 
download the correct version.  And yes I checked the repository locations and 
the only active one is in the Software  manifest so when users are doing 
BiocManager::install it would grab from the software repository.

Cheers,


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Julien 
Wollbrett 
Sent: Wednesday, May 13, 2020 5:10 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] BgeeCall package present twice

Hello,

For Bioconductor 3.11 I asked if it was possible to move BgeeCall from
workflow section to software section.
The package is now present in the software section. Thank you.
When I go to this page :
https://secure-web.cisco.com/1ifWHo9w6N8A_tWozVInX7SlCLk6o10Zy8eKyN4jISQTFiyxZw-Y9h4lXtl5NaB4oE44NT3efkyYu0lJPKEC0752nmSAxT5GNQWc18PwT5LOLHT-XloOsrmezREt-WImNjagRE5KsOUOGfmU2mvlIaOFsGtTHS4TNgy8LP12xxfkjSTFdDfjN_JYcDQYdMDzPVGTDITeY1HWFX0c08dPVqVruvdvpOH-n4pOEZ8lzE5PZYBBPWWAh0zpjWnx_7tbKvr4OAqGaYmq3KNUwteCIMmZpe4kLslEZI_8JXPkSfH_l-eUqOVNMsi_sgOlC2n3N4lKChf8FJ8PG4SlC0Smfr-AtetEnNwvQZVwPYRE8w38/https%3A%2F%2Fbioconductor.org%2Fhelp%2Fsearch%2Findex.html%3Fq%3Dbgeecall%2F
BgeeCall
appears twice (in workflow and software).

For both version the git URL is the same. Could you please confirm that
it is just an artefact? When updating the package do I update the one in
the Software section? When users install BgeeCall do they actually
install the package of the software section? Thank you.

Best Regards,

Julien Wollbrett


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Re: [Bioc-devel] Debugging not updated for coexnet package

[Shepherd, Lori]

If you followed the instructions for syncing the repository to 
git.bioconductor.org found here

http://bioconductor.org/developers/how-to/git/sync-existing-repositories/

you should follow the instructions for pushing to Bioconductor

http://bioconductor.org/developers/how-to/git/push-to-github-bioc/


check your remotes by doing a

git remote -v

if the bioconductor git server is upstream you would have to do

git push upstream master



Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Juan David 
Henao Sanchez 
Sent: Tuesday, May 12, 2020 4:37 PM
To: Bioc-devel 
Subject: [Bioc-devel] Debugging not updated for coexnet package

Dear all.

I received an error regarding my package coexnet when it is checking for
multiple platforms. I already fix the problem a couple of days ago and I
push the solution like:

git push origin master

However, I continue receiving the same error message and it is the same
previous version of my package.

There is something additional I have to do to update my package?

Thanks on advance,

I look forward to hearing from you soon.

Juan

--
Juan David Henao
Magister in Bioinformatics
Universidad Nacional de Colombia

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Re: [Bioc-devel] The new version of the package 'cbaf' is not downloadable for BioC 3.11

[Shepherd, Lori]

We have encountered some problems with the build report since last Friday as 
reported here
https://stat.ethz.ch/pipermail/bioc-devel/2020-May/016766.html

It is possibly related to that.  We are hopeful we have resolved the builder 
issues and once it returns to a normal state we are hopeful this will resolve 
on its own.

Cheers,


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Arman Shahrisa 

Sent: Thursday, May 7, 2020 11:57 AM
To: bioc-devel 
Subject: [Bioc-devel] The new version of the package 'cbaf' is not downloadable 
for BioC 3.11

Hi to all,

I�m maintainer of the package  �cbaf�. I have pushed changes to both devel and 
stable branches almost two days ago. The package check has only been carried 
out for the stable release so far. There has been only one error on macOS 
server as a result of the version of Java used on the server. Despite this, the 
older version is listed on the cbaf web page for BioC 3.11.

https://secure-web.cisco.com/1AcNMU_2RNz5_Rl5kl5xdhVk-0dJ3GrNdCoaa0t9UvVAwqP1jwApZvMJU39pBinP7RLEwOVIXgEJ0fksXR71QrWGvgNIRShgiAr8vEMy_-cFP5OT9HuE64Zo9VVb_yGj25LBrvlDkKsiKMGRGFjNg-xR5Enmjh2beUBIjAw5VRKDQOMkeJSFugsX35HqpQbP8JIBsQS6A0XAR4WjRNaJ98S222iajXeLA7oZ09CWR1YkSr3NHHzC-iWlgjUjjl9n9BIu2Yfj20eEXTvf-KqUsT8Fuypye82cyupnJYXv6FcFJDdzHurdvlA6xy0JV7RGmcqIqmXdsKoCl8T7sKorSiVvncBM80T2JrBe2gJFvsso/https%3A%2F%2Fbioconductor.org%2Fpackages%2Frelease%2Fbioc%2Fhtml%2Fcbaf.html

Am I missing something?

Best regards,
Arman


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Re: [Bioc-devel] annotationhub troubleshooting

[Shepherd, Lori]

This is a known reported issue.  See open issue:

https://github.com/Bioconductor/AnnotationHub/issues/10


It actually is not coming from AnnotationHub but from interactiveDisplayBase 
package.  I have reported the issue to those maintainers who have yet to make a 
fix.

In the meantime there is a user interface at 
https://annotationhub.bioconductor.org ; it is not quite as convenient as doing 
it directly in R and having the shiny app but a temporary solution until the 
underlying functionality is fixed.


Cheers,


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Pierre Germon 

Sent: Thursday, May 7, 2020 3:09 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] annotationhub troubleshooting

Dear Bioconductor Support Site,

I have loaded AnnotatioHub in R( ver 4.0) using Rstudio (1.2.5042) under macosx 
(10.15.3) and I am currently trying to retrive bos taurus annotations.
I run the following script :
> ah <- AnnotationHub(localHub=FALSE)
snapshotDate(): 2020-04-27
> display(ah)

And I get the following pop-up window:

DataTables warning: table id=DataTables_Table_0 - Requested unknown parameter 
'6' for row 0. For more information about this error, please see 
http://secure-web.cisco.com/1y7T8RYvRdXaKEroMp5RqE-W864wx8bA4RqkxtLVhjHdp2KhK4jzqnGIjdtPnnntfnGaEUiXB24miZ-yVdBx4cqj4fTKNow4ylp8VUlPvPUst3PRsACcgmlEHNkGpZyUUpu0jwqIxdQYY90Ph7OVnHBvS-lzLk_ENuooraLRDLcCQTxuKkGKBt5ZaNx1m3QdEbA8fJU2Kl9akLfsl0KHwOwWSXvnSYipRyVShT3IgCtmE89qMinNP4O05DidJ-zZS4ME7_4nobqStsCWnBjxZiHclEEn6aOmBtfFS2wDbjDBlTfbEjF_noFMZ1EnEXUCY0hHKBP18NxbJhxFp-ZCmlg/http%3A%2F%2Fdatatables.net%2Ftn%2F4


The same script used to work 6 month ago. Is there anything I can do to correct 
this issue ?

Thanks very much in advance,

Pierre

INRAE

Pierre GERMON
UMR 1282 ISP - Infectiologie et Sant� Publique
INRAE Centre Val de Loire - b�timent 311
Route de Crotelles
37380 Nouzilly

T�l. : +33 2 47 42 78 86
T�l. IP : 74 78 86
pierre.ger...@inrae.fr

val-de-loire.inrae.fr/infectiologie-santepublique




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Re: [Bioc-devel] Windows Development Build Error Message for COHCAP

[Shepherd, Lori]

We currently do not have a devel devel Mac builder so this is true for all 
packages.  We are working on a replacement.


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Charles Warden 
Sent: Monday, May 4, 2020 12:04 PM
To: Herv�� Pag��s ; Shepherd, Lori 
; 'bioc-devel@r-project.org' 

Subject: RE: [Bioc-devel] Windows Development Build Error Message for COHCAP

Hi Everybody,

It looks like the error is now fixed (from changing the Perl code) in the 
release and devel versions:

https://secure-web.cisco.com/1rwACYNhrzVovETfJlqiLYgx4VYKabnfwXimhOWWMwCxnQDtrwantaRsPH_X_f6kyTeNPzVs9BWzaYvKyE1J32IOvPpDPFBtvUPeakl35MuvJDbMyxHdEk3KEuM2ohLE6Dzy7zwNrgAW7tv6pN2SfzkzYIKIHyj6NsIAC85s82ys71aY6M3qoXkRe42IOaPrMOaDKbQHFvZRIXsve00bbpILuLb2aDsCwFu4nc-h0baKL3wAavkmzKuR3ylG9d-iy6Xd8Fa-YjHzKEfnb7zb0kXE0krD49l5_J3jamvI9BlD73WRb-jSN3j2p8o_9czY3dqRiZOLxO7slZfC0ADwAMA/https%3A%2F%2Fwww.bioconductor.org%2Fpackages%2Frelease%2Fbioc%2Fhtml%2FCOHCAP.html

https://secure-web.cisco.com/1U_Wn1Yz4M7uaaynffS2E0dB0mGlhnf4RGqc7NrlPm299KzGFANDAGbdG5kdorSM1zErIoFN9yDkKK4oPSMvA9mEuf86uDmFYyoMfBHHGXWI4CEMYCDQw8b4mMYRmwimYsFqtqXw4Xol5YXp0IfewFP5WQSmpDv9Zf1Bvw2eomILm9jGKZ-FIR2t8mQwbSz9-wxaYtWvwWBlYF0RspD81jqkxuM45ZRPJXJk4h5k7XChQiVzgg60EsG-sf4ehk8x7yrDfA-CBJT6V3PIn6y_pdeu98Yinj4uJ_xNKR6v3S-lhNQWzo_NZBDcKXVbVEYVVEh09hlp9H92O0U7TMYRNNQ/https%3A%2F%2Fwww.bioconductor.org%2Fpackages%2Fdevel%2Fbioc%2Fhtml%2FCOHCAP.html

I noticed there wasn't a Mac test for the devel version, but perhaps that is 
true for all packages?

Thank you very much for your help!

Sincerely,
Charles

-Original Message-
From: Herv�� Pag��s 
Sent: Tuesday, April 28, 2020 10:55 AM
To: Charles Warden ; Shepherd, Lori 
; 'bioc-devel@r-project.org' 

Subject: Re: [Bioc-devel] Windows Development Build Error Message for COHCAP

It is not clear what the purpose of these "if" statement is. Apparently to set 
the $os_name variable but then where is this variable used and for what?

So you might want to revisit the need for these tests. Maybe you don't need 
them after all.

Another problem is that the temporary files generated by your Perl scripts are 
generated in the current working directory. As discussed earlier, this is not 
good. Please make sure that all temporary files are generated in tempdir().

Thanks!
H.


On 4/28/20 10:43, Charles Warden wrote:
> Hi H,
>
> Thank you for pointing that out.
>
> I am currently not seeing errors on my Windows computer, but I see that I 
> need to add "msys" for Windows on your system (and add quotes as well as make 
> the error message more clear).  I have a 64-bit Windows computer and I didn't 
> get an error message, but I can see how this could cause problems.  I 
> apologize for not realizing that.
>
> It sounds like I should wait a little while to do that.  However, I think 
> this does sound correct, and I will make that change.
>
> Thank You,
> Charles
>
> -Original Message-
> From: Herv�� Pag��s 
> Sent: Tuesday, April 28, 2020 10:32 AM
> To: Charles Warden ; Shepherd, Lori
> ; 'bioc-devel@r-project.org'
> 
> Subject: Re: [Bioc-devel] Windows Development Build Error Message for
> COHCAP
>
> Hi Charles,
>
> The error you get on Windows is because your Perl script integrate_island.pl 
> fails on this platform. It contains the following code:
>
> if (($os eq "MacOS")||($os eq "darwin")||($os eq "linux"))
>   {
>   #Mac
>   $os_name = "MAC";
>   }#end if ($os eq "MacOS")
> elsif ($os eq "MSWin32")
>   {
>   #PC
>   $os_name = "PC";
>   }#end if ($os eq "MacOS")
> else
>   {
>   print "Need to specify folder structure for $os!\n";
>   exit;
>   }#end else
>
> The major problem with this code is that the script will exit
> **normally** without doing anything if the detected OS is not one of the 
> expected ones. So the 'temp_paired_367853.txt' file is not produced and your 
> R code later fails to open it (when you try to read the file with 
> read.table()).
>
> Note that before exiting, your Perl script displays:
>
> Need to specify folder structure for msys!
>
> which you can see in the report. This gives you a BIG clue of what the 
> problem is and how to fix it.
>
> If you develop your package on Windows (and it seems you do), the
> problem should be very reproducible for you, granted that you use R
> 4.0.0 for that of course.
>
> Thanks,
> H.
>
>
> On 4/28/20 09:02, Charles Warden

[Bioc-devel] Removal of Information in OrgDb generated from NCBI -- Feedback needed.

[Shepherd, Lori]

Hello Bioconductor maintainers

The core team was made aware of an issue with one of the make orgDb functions 
in AnnotationForge:


https://github.com/Bioconductor/AnnotationForge/issues/13


Investigating further, NCBI will no longer be updating the gene2unigene file. 
The url has moved to an ARCHIVE directory and there is an explanation and 
notice of retirement found here:


ftp://ftp.ncbi.nih.gov/repository/UniGene/README



We use this function in creating OrgDb's for the AnnotationHub as well as the 
recommended way for users to make custom OrgDb's from NCBI.

Temporarily we are working on updating the url to the new location but we are 
thinking of removing the gene2unigene data from the orgDbs. We would like to 
ask the community especially those that utilize the orgDb objects frequently if 
this data is still necessary and would the removal of UNIGENE cause a large
disruption to current packages/functions/utilization of objects?

Any feedback is greatly appreciated.

Thank you



Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


This email message may contain legally privileged and/or confidential 
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Re: [Bioc-devel] No build report

[Shepherd, Lori]

There are only automatic emails when a package fails.  You can get the daily 
build reports by going to

http://bioconductor.org/checkResults/

That has the devel (3.12) and release (3.11) build reports updated daily.



Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Cao, Quy 
Sent: Wednesday, April 29, 2020 11:48 AM
To: Herv� Pag�s ; Shepherd, Lori 
; Nitesh Turaga ; 
Bioc-devel 
Subject: RE: [Bioc-devel] No build report

Hi Herve,

I definitely didn't look into the right place. I was waiting for an email about 
my package build report. Thank you so much for pointing this out.

Regards,

Quy

-Original Message-
From: Herv� Pag�s 
Sent: Wednesday, April 29, 2020 11:44 AM
To: Cao, Quy ; Shepherd, Lori 
; Nitesh Turaga ; 
Bioc-devel 
Subject: Re: [Bioc-devel] No build report

Hi Quy,

Are you looking at the right place? Build report for BioC 3.11 is here

   
https://secure-web.cisco.com/1gMA68k6fiM2uje0S7wCCvZoW8u_6EGGaV8Nc0tYuHFhQZZe2IJJAyERr0wx2-P9f-fbCA5I_rJN2lKuHy59xxp0BVEmADd2Ui7AwZcU-MyyAUJWJi1rjNgIyTV7rW0QdemQ3jKJZdyp1qeT7xDqBzsRsqIJOWBrKZ_dWHw8DgqQUJ8ObOc7XPdi6_FqCicm6Tf6sZ3bQ1A8bORqlfuuLH6T47y6ns4SZJvgkoopG8m6QXE0mvNfLXkN0dyns9DreZ_7engePoAannsWaBO0jNg3_pW4QzRAMZ8TfXw9fWp2_iPCjClDg3L5j7xdJW4q8ReWTXdEnvT2JzAfJSVCs-MR6KE50KkrHPpmWkcTQna8/https%3A%2F%2Fbioconductor.org%2FcheckResults%2F3.11%2Fbioc-LATEST%2F

and I see PERFect there, since at least Monday.

Best,
H.


On 4/29/20 08:01, Cao, Quy wrote:
> Dear Lori,
>
> I haven't seen a build report for the package yet. Should I be waiting for a 
> little bit more?
>
> Thanks,
>
> Quy
>
> From: Shepherd, Lori 
> Sent: Monday, April 27, 2020 11:00 AM
> To: Cao, Quy ; Nitesh Turaga
> ; Bioc-devel 
> Subject: Re: No build report
>
> It looks like you had merge conflicts with the version bump to 1.1.1  until 
> late Sat night:
>
> commit 199ad444e10c81c472deefe5dff5e32dff977b41
> Author: Quy Xuan Cao mailto:quy@umontana.edu>>
> Date:   Sat Apr 25 23:33:03 2020 -0400
>
>  Bump up to version 1.1.1 on github
>
>
> This would be too late to be picked up on Sunday's build report but should be 
> reflected in today's (normally posted sometime between 3-5PM EST).  If it 
> isn't reflected in today's report, We (the core team)  are doing the freeze 
> and bump and branch for the RELEASE_3_11 and it should resolve itself after 
> that.
>
> Cheers,
>
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Comprehensive Cancer Center
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
>
> 
> From: Bioc-devel
> mailto:bioc-devel-bounces@r-project.
> org>> on behalf of Cao, Quy
> mailto:quy@umconnect.umt.edu>>
> Sent: Monday, April 27, 2020 10:15 AM
> To: Nitesh Turaga
> mailto:nturaga.b...@gmail.com>>; Bioc-devel
> mailto:bioc-devel@r-project.org>>
> Subject: [Bioc-devel] No build report
>
> Dear all,
>
> I have pushed my updated package PERFect to Bioconductor last weekend but I 
> haven't seen any build report yet. Is there something I can do in this 
> situation?
>
> Thanks,
>
> Quy
>
> -Original Message-
> From: Bioc-devel
> mailto:bioc-devel-bounces@r-project.
> org>> On Behalf Of Nitesh Turaga
> Sent: Monday, April 27, 2020 9:00 AM
> To: Leonardo Collado Torres
> mailto:lcollado...@gmail.com>>; Bioc-devel
> mailto:bioc-devel@r-project.org>>
> Cc: Carmina Barberena Jonas
> mailto:car.bar...@gmail.com>>
> Subject: Re: [Bioc-devel] regutools: request to add more git push
> access
>
> Hi Leo,
>
> I've added you and Alejandro to the regutools package.
>
> Carmina and Emiliano, please confirm the email addresses you'll be using. I 
> can add you both as well, and create BiocCredentials accounts for you.
>
>
> Nitesh
>
> On 4/26/2020 11:42 PM, Leonardo Collado Torres wrote:
>> Hi Nitesh,
>>
>> Could you add me (l.collado-torres) and Alejandro Reyes (what's your
>> svn username Alejandro?) to regutools' list of contributors that have
>> git push access? I think this is what we are supposed to do from
>> re-reading 
>> https://secure-web.cisco.com/1MIwt-sjl5gY10-P6VV_cJ144ZwWaRi038-Ms6c7tQ8ggiPlfLpEj9_KwCCKuo6-vp8PMPnHjFhdIuPNEpaA8JGBFlqq_fnKDuR1DcQ-etYA86uUEigbL6v7bHqhBzAvMWs-r-E3s2hqZBd9keG4_2zOnJPdx6EOZ6U53OGjwdZdOqLsfVsMUvR5zrOY9dLYn3VgLFwBAz1h-XyzBsa0YFZo3zEUv4ZzazLV2qIrT4yMqzyZpDbD5LkxkXwG4FrmFTCyH9R14JUuZqMr4MP0WPTP_VZMhylNzpnk7-VxPRSoQtZRPlilZHzQXPGY7ijsI/https%3A%2F%2Furldefense.proofpoint.com

Re: [Bioc-devel] Bioconductor 3.11 is Released!

[Shepherd, Lori]

Thank you for letting us know.  I'll look into your NEWS file and see why it 
wasn't included.  If there was an issue with formatting I will contact you off 
the bioc mailing list.

Cheers,


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: David Jimenez-Morales 
Sent: Wednesday, April 29, 2020 1:06 AM
To: Shepherd, Lori 
Cc: Bioc-devel@r-project.org 
Subject: Re: [Bioc-devel] Bioconductor 3.11 is Released!

Congratulations to the entire Bioconductor team for another successful release!

I have one question. I cannot find the package 
artMS<https://secure-web.cisco.com/1Csi0-aBRbgCUKmcxoFTBJzcjzewplIP_LLb2Xoafte2sE3uxSOcalLURdC6wQUOJsYZrIuwQ7Sxaog7GZUp6PvRc3NPG_biSNkOhJc4tTN1RpWUpSzqp4M5dl-MeBjkXNjLve3KEeAM-ntAOX78NynzabECgrUd_wCupHOlcqxGJzpV3__fjG_nl3wUIXHu7_eXjfPc28zb4nq1VFc9clokXq1NH7vv4kdMqfYaJwR_KZSYORsBp5nXTR_x2Gg6QUt9aQQ2jmIf7qjKsU-sR4xpdwIs0qK8sqGyaK_SkTJybwsCzVBDPN30jSfCj5_hveEuNlGXFSFRS3FL17gvAqHpcJbnfGcKOcxEH0HFmStM/https%3A%2F%2Fbioconductor.org%2Fpackages%2Frelease%2Fbioc%2Fhtml%2FartMS.html>
 in the 
News<https://secure-web.cisco.com/1qCZzQCWWidp54Uyr8tfWu3b44g_65s666Fzjmzn8JyTJoF3E2kZDUY8tAyxRCvKKuiGDFNzBortTw9cI3W2ozGbDQQQkGxjMP2Ga4Fz47A_2qUiBS7GUzP-B--DQ9K4MNuMjuYpAQzetowGbiYP2BMgJMgk2Fqt7aGqhZ0tgeQlmx6ZBilRqU9K9zP5ro5Q97rvJx-uaY0OQYsGiQCbE2Lpdyw25HNi4xyLsqJe6Dov5pHfugPqIDgHvfvjl6tvVtSnt2mZifz1erwEU5nZ-LxIIXR_FohiWm8cZxGvFQs_xN3T__9A5m2Nnjbm6Z5JElJcIigwMUb76B9zvqg7oWRjBiB-dSPGFbHBPlG2A0V4/https%3A%2F%2Fbioconductor.org%2Fnews%2Fbioc_3_11_release%2F>.
 Is
  there anything wrong with the artMS news 
format<https://secure-web.cisco.com/1yh6HXESg_01EZ20is0aqubqGFFtN3VRSB3aotHErh_lThlnum7qUaKcOY4wyF_tX2gltq5fnC_VXkp1ROppu6s4-8ynRFG_p7oLTwgYFyQovAMGb8-Am3hb8ym9Zc1d_BRZTUePnLpZ-r_zSdGP4EQZ8NH2HUlXtuh12hb5eDZKFCF8zSWOULjldSZsPlLbN-GtbIXRfoWZIsuX7ggRcEBQbFclp1aZQTgx_Tpi42B_ABaKaRgN4m16cVhBPMd31gYvE6RK-vs8kffJtuExoi2ZPuEcOiGKL8KWyvawW0QzbHkjeLxQfd_ZIwdBQ6qCaj8nPgMk-sR77BopOc4xxZ0RfX2IK2sGC89u3d4bpopw/https%3A%2F%2Fbioconductor.org%2Fpackages%2Frelease%2Fbioc%2Fnews%2FartMS%2FNEWS>?
 If so, please, let me know to make sure I write the it in the right format.

Again, thank you very much for everything that you do!
David

On Tue, Apr 28, 2020 at 3:46 PM Shepherd, Lori 
mailto:lori.sheph...@roswellpark.org>> wrote:
Thanks to all developers and community members for contributing to the project!

Please see the full release announcement:


https://bioconductor.org/news/bioc_3_11_release/<https://secure-web.cisco.com/1qCZzQCWWidp54Uyr8tfWu3b44g_65s666Fzjmzn8JyTJoF3E2kZDUY8tAyxRCvKKuiGDFNzBortTw9cI3W2ozGbDQQQkGxjMP2Ga4Fz47A_2qUiBS7GUzP-B--DQ9K4MNuMjuYpAQzetowGbiYP2BMgJMgk2Fqt7aGqhZ0tgeQlmx6ZBilRqU9K9zP5ro5Q97rvJx-uaY0OQYsGiQCbE2Lpdyw25HNi4xyLsqJe6Dov5pHfugPqIDgHvfvjl6tvVtSnt2mZifz1erwEU5nZ-LxIIXR_FohiWm8cZxGvFQs_xN3T__9A5m2Nnjbm6Z5JElJcIigwMUb76B9zvqg7oWRjBiB-dSPGFbHBPlG2A0V4/https%3A%2F%2Fbioconductor.org%2Fnews%2Fbioc_3_11_release%2F>


The Bioconductor Core Team



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recipient(s), you are hereby notified that any disclosure, copying, 
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[Bioc-devel] Bioconductor 3.11 is Released!

[Shepherd, Lori]

Thanks to all developers and community members for contributing to the project!

Please see the full release announcement:


https://bioconductor.org/news/bioc_3_11_release/


The Bioconductor Core Team



This email message may contain legally privileged and/or confidential 
information.  If you are not the intended recipient(s), or the employee or 
agent responsible for the delivery of this message to the intended 
recipient(s), you are hereby notified that any disclosure, copying, 
distribution, or use of this email message is prohibited.  If you have received 
this message in error, please notify the sender immediately by e-mail and 
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Re: [Bioc-devel] Checking that last commit made the cut

[Shepherd, Lori]

That is the correct location to check.  Notice the date at the top of the page 
is still yesterday.  Today's report has not posted yet.   When today's report 
is posted check to see if it is updated.


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Sunny Jones 

Sent: Tuesday, April 28, 2020 1:27 PM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] Checking that last commit made the cut

Hi,

I'm the developer for the package MOMA that was just accepted this past
cycle. I was re-reading through the vignette on Sunday and realized I
needed to add an additional link to a resource and committed the changes
around 10 that evening (commit code:
c305b841659c3de07ddaef83634cbd7338427462)

Those were the only changes I'd made since my personal repo was
added/synced and I realize it was last minute but is there anyway to
confirm that it made it into the final build? According the the
http://secure-web.cisco.com/1vdVYeMnomibwMYi8yXF8cMrtxVbcrNL316RjqZDO2BF3OUdaLqKY_kTpr1k7_QnUbJsrUlQW5AOJYks6oHxhNVRJVwoaPwQcVZDXbE8iZ8PPO_8nmqJsLGS9p9fPDFI15Dggesankf8aeg7JyOAA1TshguAgkgVLO4NxTX0Fxx09omQLlm2823QaZ8RNwkStBIKEt9Kwh6Z_we1yUb8wVCE6LnlKOc9Op6BCGKOVXSH4ZJB-oDXpujUDNDpIzfPfjQU66Vm9PHrb48a29Ee4TKoczs7gpqjsUbExKMRSHIhstrHcquIFwCfE-2o2ZD_By55H6CZn6fHB7KUuSulcanMMWicUfyGGb7HWiOqm1ec/http%3A%2F%2Fbioconductor.org%2FcheckResults%2Fdevel%2Fbioc-LATEST%2F%23M
 it's not listed
as the last commit but I wasn't sure if there was another way to check.

Thanks,
Sunny

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Re: [Bioc-devel] Windows Development Build Error Message for COHCAP

[Shepherd, Lori]

I can investigate more on the windows machine after we are done with the 
release (later this week -- possibly early next)

 I would highly recommend not reverting the change to using a temporary 
directory.  We don't normally allow anyone to write to anywhere but a temporary 
directory except in extreme circumstances.  New packages that are reviewed 
would not get accepted in Bioconductor if they did this.


We appreciate your effort on trying to debug this and will help you shortly.


Cheers,


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Charles Warden 
Sent: Monday, April 27, 2020 12:27 PM
To: Herv�� Pag��s ; Shepherd, Lori 
; 'bioc-devel@r-project.org' 

Subject: RE: [Bioc-devel] Windows Development Build Error Message for COHCAP

Hi,

I am not sure if I am going to have to wait to submit extra revisions.  
However, I am unfortunately having the same issue (even though I tested using 
the temporary directory instead of the current working directory, in COHCAP 
(v.1.33.4).

I also tested changing the file path to the temporary in v.1.33.6, but that 
also didn't fix the problem (and I might change that back).

I am also still not able to reproduce this error message on my end.

For example, this is what the output of the build command looks like:

C:\Users\Charles\Documents>"C:\Program Files\R\R-4.0.0\bin\R.exe" CMD build 
COHCAP
* checking for file 'COHCAP/DESCRIPTION' ... OK
* preparing 'COHCAP':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... OK
* cleaning src
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building 'COHCAP_1.33.6.tar.gz'

And, I can also install COHCAP successfully using devtools (in R-4.0.0), 
although it does have some warnings:

> library("devtools")
Loading required package: usethis
> devtools::install_github("cwarden45/COHCAP")
Skipping install of 'COHCAP' from a github remote, the SHA1 (09b017ba) has not 
changed since last install.
  Use `force = TRUE` to force installation
> devtools::install_github("cwarden45/COHCAP", force=TRUE)
Downloading GitHub repo cwarden45/COHCAP@master



   checking for file 
'C:\Users\Charles\AppData\Local\Temp\RtmpOIc4WV\remotes370c11a9aa0\cwarden45-COHCAP-09b017b/DESCRIPTION'
 ...

   checking for file 
'C:\Users\Charles\AppData\Local\Temp\RtmpOIc4WV\remotes370c11a9aa0\cwarden45-COHCAP-09b017b/DESCRIPTION'
 ...

��  checking for file 
'C:\Users\Charles\AppData\Local\Temp\RtmpOIc4WV\remotes370c11a9aa0\cwarden45-COHCAP-09b017b/DESCRIPTION'
 (339ms)




-  preparing 'COHCAP':
   checking DESCRIPTION meta-information ...

   checking DESCRIPTION meta-information ...

��  checking DESCRIPTION meta-information
-  cleaning src




-  checking for LF line-endings in source and make files and shell scripts




-  checking for empty or unneeded directories




-  building 'COHCAP_1.33.6.tar.gz'




Installing package into ��C:/Users/Charles/Documents/R/win-library/4.0��
(as ��lib�� is unspecified)
* installing *source* package 'COHCAP' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/PROGRA~1/R/R-40~1.0/include" 
-DNDEBUG  -I'C:/Users/Charles/Documents/R/win-library/4.0/Rcpp/include' 
-I'C:/Users/Charles/Documents/R/win-library/4.0/BH/include'-O2 -Wall  
-mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/PROGRA~1/R/R-40~1.0/include" 
-DNDEBUG  -I'C:/Users/Charles/Documents/R/win-library/4.0/Rcpp/include' 
-I'C:/Users/Charles/Documents/R/win-library/4.0/BH/include'-O2 -Wall  
-mfpmath=sse -msse2 -mstackrealign -c Rcpp_BH_ANOVA.cpp -o Rcpp_BH_ANOVA.o
In file included from 
C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/aux_/na_assert.hpp:23,
 from 
C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/arg.hpp:25,
 from 
C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/placeholders.hpp:24,
 from 
C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/apply.hpp:24,
 from 
C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/aux_/iter_apply.hpp:17,
 from 
C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/aux_/find_if_pred.hpp:14,
 from 
C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/find_if.hpp:17,
 from 
C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/find.hpp:17,
 from 
C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/aux_/contains_impl.hpp:20,

Re: [Bioc-devel] No build report

[Shepherd, Lori]

It looks like you had merge conflicts with the version bump to 1.1.1  until 
late Sat night:

commit 199ad444e10c81c472deefe5dff5e32dff977b41
Author: Quy Xuan Cao 
Date:   Sat Apr 25 23:33:03 2020 -0400

Bump up to version 1.1.1 on github


This would be too late to be picked up on Sunday's build report but should be 
reflected in today's (normally posted sometime between 3-5PM EST).  If it isn't 
reflected in today's report, We (the core team)  are doing the freeze and bump 
and branch for the RELEASE_3_11 and it should resolve itself after that.

Cheers,



Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Cao, Quy 

Sent: Monday, April 27, 2020 10:15 AM
To: Nitesh Turaga ; Bioc-devel 

Subject: [Bioc-devel] No build report

Dear all,

I have pushed my updated package PERFect to Bioconductor last weekend but I 
haven't seen any build report yet. Is there something I can do in this 
situation?

Thanks,

Quy

-Original Message-
From: Bioc-devel  On Behalf Of Nitesh Turaga
Sent: Monday, April 27, 2020 9:00 AM
To: Leonardo Collado Torres ; Bioc-devel 

Cc: Carmina Barberena Jonas 
Subject: Re: [Bioc-devel] regutools: request to add more git push access

Hi Leo,

I've added you and Alejandro to the regutools package.

Carmina and Emiliano, please confirm the email addresses you'll be using. I can 
add you both as well, and create BiocCredentials accounts for you.


Nitesh

On 4/26/2020 11:42 PM, Leonardo Collado Torres wrote:
> Hi Nitesh,
>
> Could you add me (l.collado-torres) and Alejandro Reyes (what's your
> svn username Alejandro?) to regutools' list of contributors that have
> git push access? I think this is what we are supposed to do from
> re-reading 
> https://secure-web.cisco.com/1ss3pRMDsJo76mWIsyzXe9lDXoItH2sFabu1CE0znVtuQca1EmsAJSreHomRLs6G6xn_gOm6dFEx0dX7CnDzGwE4_uklxxTxCsGVOB_KCeo13s4UraPVR7afmm8_rnmkVrEWTGiTb3jvNrN_QDpXBQaMnWw2ymPtot2vNWY5mQp3d5vGiB0NhIRQnxoz7znJB70m6qEvbzJu1oIbjW5EkXrqiXt8ED0uwY1-b_L9vGSG6xw1MD3dFa2e6DuqHVr1fhCs4SFAGup5Ih2Ns9dFNEsoptDSjsEznRqTC8DIP4FHujFuZGPlFEcQXq37L_uE3_FlIEFSaT4zaqdX3r_cPnQ/https%3A%2F%2Fgithub.com%2FBioconductor%2FContributions%2Fissues%2F1393%23issuecomment-597202057.
>
> Carmina & Emiliano might want git push access too, but they do not
> have BioC git accounts as far as I know.
>
> Anyway, for now, I just wanted to add two commits already on GitHub
> and push them to BioC's git repo following
> http://secure-web.cisco.com/1cFasDB_kkp19Ri6C4NTgSGk39cBX_QF8Xn6DTqLzEL0ijtRrKn9gGLKXPGMHF0rrpS7AHZXUEHFchYfU-i08pRgke3QTkgyYR60jav1vUCef7Y_hfWdJr6A5EoeSXiE3GAXDGelk7GufWzF-PMrSGMVZIR19bEGVB2jmYRSCDg_Y3Bx2mhfjHjvOTuf8LldH6lSBbyW8MTvNOy9n9Ilybk5z-jUdXNyixRmRmuioLC0jmip-_8jinrjB1qPyFmIVPsy_vCLy_yPiZMsrsgK7TqeETN4FLwh0W0ey1uMCUDDrqdSgpLcdyxmKWXuvt6ZPa7PjgeUFJfPT-u8RRYzHgEcJ4K0T5K2GXZqmlChCMOo/http%3A%2F%2Fbioconductor.org%2Fdevelopers%2Fhow-to%2Fgit%2Fsync-existing-repositori
> es/
> before BioC 3.11's freeze.
>
> Thanks,
> Leo
>
> ___
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recipient(s), you are hereby notified that any disclosure, copying, 
distribution, or 

Re: [Bioc-devel] Windows Development Build Error Message for COHCAP

[Shepherd, Lori]

In your vignette you also use   `getwd()`  to define your output directory.  
Please change this to use a temporary directory  `tempdir()`


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Shepherd, Lori 

Sent: Thursday, April 23, 2020 8:00 AM
To: Charles Warden ; 'bioc-devel@r-project.org' 

Subject: Re: [Bioc-devel] Windows Development Build Error Message for COHCAP

Thank you for your inquiry

R 4.0.0 can be downloaed from the following page. This patched page exists a 
few weeks out from the official R release for the patched version of R windows:


https://secure-web.cisco.com/1rVmbsYV5l6Byh8Yxia7uE_vjkELNEv9x-phlPOD4JZps4zzXWvkm5y5iT6tN_xdLE5OKhw5aFcayOxFdH1TZaOdeZSnP4jNV20TSyigyof9gxL32zvj2VKmeAycLaq__vn63nmNQcrcNfrV307jWUNM0QeREQq8TO7cM1fYdIpG1-OKb47JpH7YMFZqJyWENSteiqzz76lEINnJxX5SIY6_YknZtLWp8xRWkVjlTNKiT72Y6eAPRrCvC9FN1_Gqz4logMBLltKQBvUBbE7JY99_EtVCHLQqhmnbGg4dVxKOD75bWlau_K7grnxO6NCbAOjFnVUHVM-IEkSQruW_KPA/https%3A%2F%2Fcran.r-project.org%2Fbin%2Fwindows%2Fbase%2Frpatched.html


2.  Landing pages can have different versions of the file for different 
platforms when a package will build cleanly for one platform but not another.  
We only propagate and make available successfully built packages.


3.  You can wait a day or two if you like but realize the 3.11 release is fast 
approaching.  If this stay ERROR and it is not fixed by monday you will have to 
push fixes to both a release 3.11 and the new devel branch (master branch 
prepping for 3.12 in fall).


4.  I'll try and log on our windows builder later today to see if I can track 
down any additional information for you to help debug.  If I find anything I 
will contact you about it.


Cheers,


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Charles Warden 

Sent: Wednesday, April 22, 2020 12:00 PM
To: 'bioc-devel@r-project.org' 
Subject: [Bioc-devel] Windows Development Build Error Message for COHCAP

Hi,

I noticed that I received a few error messages in the Windows build for COHCAP:

http://secure-web.cisco.com/14soK-lir-qt5k3KJCJKxxSPwdESxh91c_rkfAkfpDOqOUvXzM0n9MzRO_j5W5YsMzlMpHKj8hD4qgXS8qgJycZANUXuMoVlTuxKCDTotDQku3EGNvVwLIWjyC4ZeIDnSRnFJE4KnTbacOABfRotIDmjhuZqWJmXADjmoBsUTEpAhwIEMAHLe-De7YiQGt-OJNvo_Op4ArktJnzOfxhWMOUG0kZvelbmwKwV_MmvFVJpgOljB5EAcUHLuOLpvN1dlH5gsWhslkm1FvMX9gmvNJ2y0T3onSd5pHZ2FbwM8-8sgSPEbuxXjtT1WQUYyFdqUIBNQY7Xv8iEdEBt1q7qVTw/http%3A%2F%2Fbioconductor.org%2FcheckResults%2Fdevel%2Fbioc-LATEST%2FCOHCAP%2Ftokay2-buildsrc.html

I changed the default settings to avoid an earlier error message (again, just 
on Windows), but I am currently getting an error message that I am having some 
trouble reproducing.

Can you help me with either of the following questions?


  1.  I apologize for the simple question, but where can I download the Windows 
executable for R-4.0.0?  I was able to reproduce and fix an earlier issue with 
R-devel (on Linux), but I was not certain how to get the error message for 
Windows.  I have tried to reproduce the error using the devtools installation 
from the GitHub code 
(https://secure-web.cisco.com/1CMIdB2_FCZaFouyijL6DJBleIv1z6kjb0vJp48UqtfezzRyresTr07xJ9yP83U_HqxDPiTYbIIG_3bYDlfcvr9QH832g8VnWkkNG5dK1P2qxQbm9OWI_b3EERjUTwhY2H8cb6Lsko1ITsutzNvWoL_Dp_fvzUxN0nDwb6eghpCrMMy6ndFekSqrQdkZO0IhVKxvMXODM3MkIZRsiEaomyhKOn6lUKila6pgUgDSfQ9PypaW7BcQcWhGb9U-f8TL9fvtbUqBaB83MoDiXfJKsO_UoJLrlyh8sR6wJ5tNHkt3e-7uUwzz6H360PSI3rxp1a5gXTxLcMp9ymSQR6UF1CQ/https%3A%2F%2Fgithub.com%2Fcwarden45%2FCOHCAP),
 but that can be installed successfully (with Windows R-3.6.3).
  2.  The .zip file for the Windows version on the devel page is different 
(http://secure-web.cisco.com/1L5TyDrJci1NAZMGxCrXIKm2wn3kgWC_9LSEIs73dOegI5BFj7AhvLaYz0i17qdT2pElt5CByZhFvxEMQ2Uunp62vwJ4s_-0G-gi1gOdMQ9Z_rf-1WN7sEym8bdEQgX4sO0SE8JaTNDZUG-zwsHvCZJP6ZYlq4valW3HrFbWU8PbZ5_9r-zCQUNwVxenocEirsb8kzp5kABBj0hI9c9EvH1C2o0oAQ0O9sIKULrkHAmQqjUg3cS8axxnfC_GUNGY2Be1EHLD0Na98zDHgOce95-bK82bGVtTnR5g2ynyW9qcQqeG0SD0_LuQo3YEkSPh3gptJfBs-_myNtkqDePCZCg/http%3A%2F%2Fbioconductor.org%2Fpackages%2F3.11%2Fbioc%2Fhtml%2FCOHCAP.html),
 where I see cohcap_1.33.1.zip for Windows.  I think I saw the first error 
message in 1.33.1, and I made an intermediate change before changing the 
defaults to avoid the error message.  However, the strange thing was that I 
thought I saw an "OK" status while I was waiting for the 1.33.3 version to 
appear in the build reports (which I thought was for COHCAP 1.33.2).  Do all of 
the packages get re-built, regardless of whether an update is uploaded?
 *   I am wondering if there is a chance that I might be able to wait a day 
o

Re: [Bioc-devel] Windows Development Build Error Message for COHCAP

[Shepherd, Lori]

Thank you for your inquiry

R 4.0.0 can be downloaed from the following page. This patched page exists a 
few weeks out from the official R release for the patched version of R windows:


https://cran.r-project.org/bin/windows/base/rpatched.html


2.  Landing pages can have different versions of the file for different 
platforms when a package will build cleanly for one platform but not another.  
We only propagate and make available successfully built packages.


3.  You can wait a day or two if you like but realize the 3.11 release is fast 
approaching.  If this stay ERROR and it is not fixed by monday you will have to 
push fixes to both a release 3.11 and the new devel branch (master branch 
prepping for 3.12 in fall).


4.  I'll try and log on our windows builder later today to see if I can track 
down any additional information for you to help debug.  If I find anything I 
will contact you about it.


Cheers,


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Charles Warden 

Sent: Wednesday, April 22, 2020 12:00 PM
To: 'bioc-devel@r-project.org' 
Subject: [Bioc-devel] Windows Development Build Error Message for COHCAP

Hi,

I noticed that I received a few error messages in the Windows build for COHCAP:

http://secure-web.cisco.com/14soK-lir-qt5k3KJCJKxxSPwdESxh91c_rkfAkfpDOqOUvXzM0n9MzRO_j5W5YsMzlMpHKj8hD4qgXS8qgJycZANUXuMoVlTuxKCDTotDQku3EGNvVwLIWjyC4ZeIDnSRnFJE4KnTbacOABfRotIDmjhuZqWJmXADjmoBsUTEpAhwIEMAHLe-De7YiQGt-OJNvo_Op4ArktJnzOfxhWMOUG0kZvelbmwKwV_MmvFVJpgOljB5EAcUHLuOLpvN1dlH5gsWhslkm1FvMX9gmvNJ2y0T3onSd5pHZ2FbwM8-8sgSPEbuxXjtT1WQUYyFdqUIBNQY7Xv8iEdEBt1q7qVTw/http%3A%2F%2Fbioconductor.org%2FcheckResults%2Fdevel%2Fbioc-LATEST%2FCOHCAP%2Ftokay2-buildsrc.html

I changed the default settings to avoid an earlier error message (again, just 
on Windows), but I am currently getting an error message that I am having some 
trouble reproducing.

Can you help me with either of the following questions?


  1.  I apologize for the simple question, but where can I download the Windows 
executable for R-4.0.0?  I was able to reproduce and fix an earlier issue with 
R-devel (on Linux), but I was not certain how to get the error message for 
Windows.  I have tried to reproduce the error using the devtools installation 
from the GitHub code 
(https://secure-web.cisco.com/1CMIdB2_FCZaFouyijL6DJBleIv1z6kjb0vJp48UqtfezzRyresTr07xJ9yP83U_HqxDPiTYbIIG_3bYDlfcvr9QH832g8VnWkkNG5dK1P2qxQbm9OWI_b3EERjUTwhY2H8cb6Lsko1ITsutzNvWoL_Dp_fvzUxN0nDwb6eghpCrMMy6ndFekSqrQdkZO0IhVKxvMXODM3MkIZRsiEaomyhKOn6lUKila6pgUgDSfQ9PypaW7BcQcWhGb9U-f8TL9fvtbUqBaB83MoDiXfJKsO_UoJLrlyh8sR6wJ5tNHkt3e-7uUwzz6H360PSI3rxp1a5gXTxLcMp9ymSQR6UF1CQ/https%3A%2F%2Fgithub.com%2Fcwarden45%2FCOHCAP),
 but that can be installed successfully (with Windows R-3.6.3).
  2.  The .zip file for the Windows version on the devel page is different 
(http://secure-web.cisco.com/1L5TyDrJci1NAZMGxCrXIKm2wn3kgWC_9LSEIs73dOegI5BFj7AhvLaYz0i17qdT2pElt5CByZhFvxEMQ2Uunp62vwJ4s_-0G-gi1gOdMQ9Z_rf-1WN7sEym8bdEQgX4sO0SE8JaTNDZUG-zwsHvCZJP6ZYlq4valW3HrFbWU8PbZ5_9r-zCQUNwVxenocEirsb8kzp5kABBj0hI9c9EvH1C2o0oAQ0O9sIKULrkHAmQqjUg3cS8axxnfC_GUNGY2Be1EHLD0Na98zDHgOce95-bK82bGVtTnR5g2ynyW9qcQqeG0SD0_LuQo3YEkSPh3gptJfBs-_myNtkqDePCZCg/http%3A%2F%2Fbioconductor.org%2Fpackages%2F3.11%2Fbioc%2Fhtml%2FCOHCAP.html),
 where I see cohcap_1.33.1.zip for Windows.  I think I saw the first error 
message in 1.33.1, and I made an intermediate change before changing the 
defaults to avoid the error message.  However, the strange thing was that I 
thought I saw an "OK" status while I was waiting for the 1.33.3 version to 
appear in the build reports (which I thought was for COHCAP 1.33.2).  Do all of 
the packages get re-built, regardless of whether an update is uploaded?
 *   I am wondering if there is a chance that I might be able to wait a day 
or two and see if I can get a status of "OK" for all steps on all of the test 
servers.  However, if that is true, then I am a little worried about what 
happens if there is a temporary error in the release version.


Thank you very much!

Sincerely,
Charles
Charles Warden, Bioinformatics Specialist
Integrative Genomics Core
City of Hope National Medical Center
Shamrock Monrovia Building (655 Huntington Dr, Monrovia, CA, 91016)
Room 1086
Internal Ext: 80375 | Direct: 626-218-0375

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Re: [Bioc-devel] Resubmitting additional packages as separate issues

[Shepherd, Lori]

I will assist you with this tomorrow and contact you in a private email when 
you can resubmit.

Get Outlook for Android


From: Bioc-devel  on behalf of Chris Eeles 

Sent: Wednesday, April 22, 2020 7:23:17 PM
To: Bioc-devel@r-project.org 
Subject: [Bioc-devel] Resubmitting additional packages as separate issues

Hello Bioc-devel,

I recently submitted three packages to Bioconductor Contributions (CoreGx, 
RadioGx and ToxicoGx). After consulting my reviewer I now wish to resubmit the 
two dependent packages (RadioGx and ToxicoGx) on separate issues. I deleted the 
comments from #1445 where I submitted the �additional packages� on that issue, 
but I am now unable to resubmit the packages.

Could someone assist with this?

Best,
---
Christopher Eeles
Software Developer
BHK 
Laboratory
Princess Margaret Cancer 
Centre
University Health 
Network

From: bioc-issue-bot 
Sent: April 22, 2020 6:59 PM
To: Bioconductor/Contributions 
Cc: Christopher Eeles ; Mention 

Subject: Re: [Bioconductor/Contributions] (inactive) ToxicoGx resubmission 
(#1485)


Dear 
@ChristopherEeles
 ,

You (or someone) has already posted that repository to our tracker.

See 
#1445

You cannot post the same repository more than once.

If you would like this repository to be linked to issue number: 1485,
Please contact a Bioconductor Core Member.
I am closing this issue.

�
You are receiving this because you were mentioned.
Reply to this email directly, view it on 
GitHub,
 or 
unsubscribe.

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Re: [Bioc-devel] Package CNVPanelizer needs my attention

[Shepherd, Lori]

I'm sorry I don't see any question or response to this?  Was there something 
you had a question about?

The package CNVPanelizer is failing on the builders across all platforms and 
needs attention.


http://bioconductor.org/checkResults/devel/bioc-LATEST/CNVPanelizer/


The ERROR has to do with changes in base R (4.0) and is a combination of matrix 
is now of class array and implementing length > 1 logic check.  Please see the 
troubleshooting documentation for advice on how to reproduce and fix these 
ERRORs.


 
http://bioconductor.org/developers/how-to/troubleshoot-build-report/




Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Thomas Wolf 

Sent: Wednesday, April 22, 2020 5:18 PM
To: bioc-devel@r-project.org ; christiano oliveira 

Subject: Re: [Bioc-devel] Package CNVPanelizer needs my attention


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Re: [Bioc-devel] Author name displayed incorrectly in package landing page

[Shepherd, Lori]

You might have better luck updating the Author and Maintainer fields in the 
DESCRIPTION to Authors@R syntax.
It should also be noted there should only be one maintainer for the package.




Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Selles Vidal, 
Lara 
Sent: Wednesday, April 22, 2020 4:00 PM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] Author name displayed incorrectly in package landing page

Dear Bioconductor team,

I have recently realized the first author name in my rfaRm package is not 
displayed as intended in its landing page 
(https://secure-web.cisco.com/193JLq6IONh193nJKdBg7jMaHfoif8o0_WybBViZbQ0UP8aawQ14kwkCj_noco8kT0YPE3BXsytvhz50ObX6wK1Fe4l7-IDK0iuJoSGJNgkvmbjLvhzez_pidtmTAo5yRDK4kIXyrtr4XOfz64zfhM5hq75JJyTPeo8hOVt82rBZSsGEnglY-YtRN_f_XuGS0Ym64ZRjSqVy0Vqc6bqRgN5si-CXc2FIgMB1CKvYy504gmAGJWnwvxG9AAu7xfts8Fdzkq41r8Wo0ls7RzjqMd2lcl6rbr7_YVMXW4J-Rh9mulm1rNBt6cxB0RuxP6V55tG47KoMCP74tp38ozju5-CrZi3W2679q7ywr_niUN0M/https%3A%2F%2Fbioconductor.org%2Fpackages%2FrfaRm).

In short, I put my name as �Lara Selles Vidal� in the Author: field of the 
DESCRIPTION file. My first name is just �Lara�, and �Selles Vidal� are my 
surnames. However, it has been interpreted as Vidal, LS. The intended behaviour 
would have been Selles Vidal, L

Is there any workaround for this?

Thanks a lot in advance!

Best wishes,

Lara

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[Bioc-devel] Bioc 3.11 Feature Freeze

[Shepherd, Lori]

Developers,

The release of Bioconductor 3.11 is one week out. Today marks the 'feature 
freeze' of 3.11 where we ask that all commits are limited to bug fixes and 
documentation (no more API changes).

Thanks you for your cooperation.



Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


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Re: [Bioc-devel] version inconsistence in the development version page and the build page of a bioconductor package, cogena

[Shepherd, Lori]

We don't update the pages with broken versions of packages.  3.21.1 as you 
showed has an  ERROR so it will not propagate and the landing page will keep 
the last working version in this case 3.21.0.
Please see the follow page that not only explains this but also has advice on 
the length 1 vector error

https://bioconductor.org/developers/how-to/troubleshoot-build-report/

You will need R 4.0.0 the latest versions of packages in bioc 3.11 and certain 
extra environment variables set.

Hope this helps.

Get Outlook for Android


From: Bioc-devel  on behalf of Zhilong Jia 

Sent: Monday, April 20, 2020 8:31:15 PM
To: bioc-devel 
Subject: [Bioc-devel] version inconsistence in the development version page and 
the build page of a bioconductor package, cogena

Hi, Bioconductor community,

I found it is inconsistent in the versions of the development package,
cogena. I am maintaining this package.

For example, the build page of my package cogena is 3.21.1 (
https://secure-web.cisco.com/1niMGhyNTfF8jiS5lT3i2Rb3xXWhDkoi1JCl6-XZhhtc6_q449aZfO9FUdvp1a2c7GCevNe1_DPydUg6-u3uHkXh5x77uXa04a7mh3tnD-zBRH-tfFCcReiQF5B5Bxl83osIerP6lYuO9Io7M6Bi0OtD2cbC2p31KXBttzZiQZa2x7tcP1rDR6AltBZcBh4IBPx0-SRE5eC8vT6Bmgg0hqQvuKmJyKQdzDQIwu8ocj25e4ol-zRV9iwJClHFPjFSH56xcLdChTAhJ6MfzT5ki1pfehEriqRK_00mlrFchYjxCLuHa7g-FEnBL-aaO_566lOJAvYZbFwT3PfZWxymtEw/https%3A%2F%2Fmaster.bioconductor.org%2FcheckResults%2F3.11%2Fbioc-LATEST%2Fcogena%2Fmalbec2-buildsrc.html),
while for the development package page (
https://secure-web.cisco.com/1KpxQxYvyy55wIJ5hN86YJuSNvX5N7NMotupZMpxXv0lrPSg9rGMiK991I6Lbz4ywU6KjoiVPMcA_VfI47h2g06WSnGFaY1BkizciL2pvhjdR84HKt7RrYbSTVQRGtQjeNxt5mm-JRo4JCk-9rr7qmFTxpOa4OVKX6ml7WrrqpwG9xVZ3MLE3bnnqpNG2WBeWdy_KteX-dvLlQGnGb5afa_Q0omTtf97GymH33obzHhmMmVn4-u164K85pZHtjW1lEopDwDT0phA7amxtJpP-2ANp7jwWPrBqBC98WppUqE3vHhhyOuiTYaSi4WoTtgkuCy8MC_iwJ1fBKYHSE2iH-g/https%3A%2F%2Fbioconductor.org%2Fpackages%2F3.11%2Fbioc%2Fhtml%2Fcogena.html),
 the code is
3.21.0. So where can I check the code of the build version of this package?
Bioconductor supply git service, so can we browser code at git.bioconductor
as well. just like GitHub?

Recently, there is a check error report ("EXPR must be a length 1 vector" (
https://secure-web.cisco.com/1niMGhyNTfF8jiS5lT3i2Rb3xXWhDkoi1JCl6-XZhhtc6_q449aZfO9FUdvp1a2c7GCevNe1_DPydUg6-u3uHkXh5x77uXa04a7mh3tnD-zBRH-tfFCcReiQF5B5Bxl83osIerP6lYuO9Io7M6Bi0OtD2cbC2p31KXBttzZiQZa2x7tcP1rDR6AltBZcBh4IBPx0-SRE5eC8vT6Bmgg0hqQvuKmJyKQdzDQIwu8ocj25e4ol-zRV9iwJClHFPjFSH56xcLdChTAhJ6MfzT5ki1pfehEriqRK_00mlrFchYjxCLuHa7g-FEnBL-aaO_566lOJAvYZbFwT3PfZWxymtEw/https%3A%2F%2Fmaster.bioconductor.org%2FcheckResults%2F3.11%2Fbioc-LATEST%2Fcogena%2Fmalbec2-buildsrc.html
)
 ) about cogena. I am not sure what's the problem. Probably related to
rmarkdown or R4.0. So far I cannot install R4.0 smoothly, though the
Bioconductor 3.11 needs this version to build.

Thank you.

Zhilong

--
Zhilong JIA
zhilong...@gmail.com

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Re: [Bioc-devel] Unable to reproduce vignette build error

[Shepherd, Lori]

I am able to reproduce this locally.
Make sure you are using R 4.0.0 and have updated versions of all Bioconductor 
packages
BiocManager::valid()
BiocManager::install()

I did an "R CMD Stangle Installing_and_Using_BrainSABER.Rmd" to produce an R 
file of code for the vignette and also tried to run the vignette manually with
source("Installing_and_Using_BrainSABER.R", echo=TRUE)

The code that produces the ERROR is:

> # Or using the auto-trimmed toySet
> auto_euc_sim <- getSimScores(data = toySet, similarity_method = "euclidean")

> auto_cos_sim <- getSimScores(data = toySet, similarity_method = "cosine")

> ## getAS, results = 
> 'hide'--
> # Using manually filtered data scores
> euc_mats <- getSimMatrix(  [TRUNCATED]
Error in `[<-`(`*tmp*`, a, s, value = sim_score[i]) :
  subscript out of bounds


 Or more precisely:

> euc_mats <- getSimMatrix(sim_score = euc_sim, relevantGenes = 
> trimmed_AIBSARNA)
Error in `[<-`(`*tmp*`, a, s, value = sim_score[i]) :
  subscript out of bounds
> traceback()
2: getSimMatrix(sim_score = sim_score[, x], relevantGenes = relevantGenes)
1: getSimMatrix(sim_score = euc_sim, relevantGenes = trimmed_AIBSARNA)

Hopefully this will help you pinpoint and debug more.


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of USD Biomedical 
Engineering 
Sent: Monday, April 20, 2020 3:16 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] Unable to reproduce vignette build error

Dear Bioconductor Team,

In the past week the vignette for our package BrainSABER has been failing
to build on the automated builder with a 'subscript out of bounds' error. I
am unable to reproduce this error on my local system (Windows x86_64
running devel versions of R and Bioconductor 3.11), therefore I can't get
to the bottom of the issue. I also do not have Docker available to test in
an independent environment.

BrainSABER passed the autobuilder back in March, and I made sure all recent
changes were unrelated to the failure. I'm not sure if this is a builder
issue or an issue with both the package and my local testing environment.
Do you have any insight or suggestions?

Best,
Evgeni

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[Bioc-devel] Important Upcoming Release 3.11 Deadlines This Week!!

[Shepherd, Lori]

Some Important Release Deadlines are fast approaching. See also the release 
schedule online

The last day for any NEW package to be accepted and released under Bioc 3.11 is 
this Wed. April 22th. Packages accepted after this day will remain in 
Bioconductor devel and included in the Bioc 3.12 release in fall.

This Friday April 24th is the last recommended day to commit changes 
(documentation , bug fixes, etc) to the devel branch. This is to allow all 
changes to propagate and build on the build system prior to branching. The 
branch will be frozen and branched on Monday April 27th making Sunday April 
26th the absolute last day to push changes. All packages should be passing 
building and check without ERROR and WARNINGS by Friday April 24th. If a 
package is failing across all three platforms the package will be considered 
for deprecation depending on the length and severity of the ERRORS.

Please remember to update your NEWS files (In proper format!) by Friday April 
24th for it to be included in the release announcement.  Here is an example 
from last release 3.10:
http://bioconductor.org/news/bioc_3_10_release/
If NEWS files are not updated or in the proper format they will not be included.


If anyone has any questions of concerns please feel free to ask.

Thank you

Link to release schedule online:
https://bioconductor.org/developers/release-schedule/




Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


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Re: [Bioc-devel] Nominations for Bioconductor Awards!

[Shepherd, Lori]

Yikes!  Sorry everyone.  That did not format like I thought it would!

Let's recap:


Bioconductor is excited to announce an opportunity to recognize those making 
significant outstanding contributions to the Bioconductor community. The 
Bioconductor project proudly launches the first call for Bioconductor Awards, 
honoring various forms of contributions to the project. Four awardees will be 
selected, each having contributed to the project in an outstanding way based on 
one or more of specific criteria.  The deadline for nominations is June 15!
Please see the support site announcement for the links with more information as 
well as the nomination form


https://support.bioconductor.org/p/130094/



Cheers,


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Shepherd, Lori 

Sent: Friday, April 17, 2020 1:37 PM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] Nominations for Bioconductor Awards!

Bioconductor is excited to announce an opportunity to recognize those making 
significant outstanding contributions to the Bioconductor community. The 
Bioconductor project proudly launches the first call for Bioconductor Awards, 
honoring various forms of contributions to the project. Four awardees will be 
selected, each having contributed to the project in an outstanding way based on 
one or more of the criteria found at:  
https://secure-web.cisco.com/16tUFz5Y9fiV3wv_pZMAWX8bU4HXzuPOui85-nQ6NxdiPfAd9AGquEUvWb6C-LqP7Yon62aBX8ULdJ8idAqvXqfsS_80ScouEVrCiYdbsjwPmqVEbnGoAIln4gcIdTSltcXdtZqN-SrpDdJ6V6xiB1LzQMUtGkSIQQOK0X37ra7bPWibIkPd2WsBLOzOazj46TnTNdgTH2udZ-EV99vyCBNSU-6hxSFMVD1JaO0xxTHknOWiTg8zKGBRgQfMmGNrGMj9W2UN-O9HYRD-hYd7fveCzPkaRvBnIl3inUB37KohceYdqJ8OfRdo9efhwHjq7MJPEWCxzuPDs4fppgD4R_w/https%3A%2F%2Fdocs.google.com%2Fdocument%2Fd%2F1ccXPFc_bGZoW3DgfgXf13_4i5TXySvXQCdRR8UJr__I%2Fedit.

Please fill out the nomination form by June 15 : 
https://secure-web.cisco.com/1xiPaCt8pwJs16iKlj7jvaYfJRuP-w9MsvNcZNvld32dl1SpBeEFARwBSlrUJXVOXsfzBL4GIhwPelo-KTR-VUpxPNz9UDtDERtyuf6l1El6gEPTLcOq8K1SF_3MogKWaY6dWWiMfhD43WIzp_VYutvmEhB1vW3JbN9QJkXBkfOC9KUqOPsypOz6Ppj4zSuGJsJt6g2iiPit6j_nrEPTKKHxXHa9zfcfYga9asnMOvYvKeqW4szgu3T-sfVaCWjw2Jl-YIN9jFdGmAmLDc3ki0_x-CCZEyJMLAVFYBpXivjgUUOar5_hewa3T0s6Ift_kLY_qQL5sO2Lia8vQDZ-guw/https%3A%2F%2Fdocs.google.com%2Fforms%2Fd%2Fe%2F1FAIpQLSdaI6KHsezSQLWcCAzRCLlOz_fJai59PcyIz03ifutbwmXaVw%2Fviewform



Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


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[Bioc-devel] Nominations for Bioconductor Awards!

[Shepherd, Lori]

Bioconductor is excited to announce an opportunity to recognize those making 
significant outstanding contributions to the Bioconductor community. The 
Bioconductor project proudly launches the first call for Bioconductor Awards, 
honoring various forms of contributions to the project. Four awardees will be 
selected, each having contributed to the project in an outstanding way based on 
one or more of the criteria found at:  
https://docs.google.com/document/d/1ccXPFc_bGZoW3DgfgXf13_4i5TXySvXQCdRR8UJr__I/edit.

Please fill out the nomination form by June 15 : 
https://docs.google.com/forms/d/e/1FAIpQLSdaI6KHsezSQLWcCAzRCLlOz_fJai59PcyIz03ifutbwmXaVw/viewform



Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


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Re: [Bioc-devel] regarding imports github R packages, in new R package's description file

[Shepherd, Lori]

This mailing list is for Bioconductor package development and Bioconductor 
submissions not CRAN.

Bioconductor only allows dependencies from CRAN or Bioconductor and does not 
allow github only repositories.

If you indeed meant to submit to CRAN you should check with CRAN's submission 
policies on what they allow:
https://cran.r-project.org/web/packages/policies.html




Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Krishan Gupta 

Sent: Friday, April 17, 2020 12:45 PM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] regarding imports github R packages, in new R package's 
description file

I want to build a new package to submit on CRAN, but my package has
two dependencies harmony and iCTC which are available only on github.
So now I can import these dependencies in description files.
Imports:
BiocManager,
caret,
klaR,
randomForest,
gbm,
devtools,
harmony,
iCTC
I did as shown above but I got an error,
checking package dependencies ... ERROR
Packages required but not available: 'harmony', 'iCTC'
How can I resolve the error?
*Thanks and Regards*

*Krishan Gupta*

*PhD16008PhD Scholar*

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Re: [Bioc-devel] Question for building error

[Shepherd, Lori]

 The current ERROR
"polygon edge not found"
is  a Bioconductor builder issue having to do with fonts not being found.

We are working on a solution but for now you can ignore.


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Yang,Peng 

Sent: Friday, April 17, 2020 12:26 PM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] Question for building error

Dear Bioconductor team,

I met a building errors for our package, DeMixT 1.3.6, under Mac OS planform on 
Apr 16th. And it shows failed to create vignettes.

Since R 4.0.0 no longer support OpenMP, I disabled OpenMP under Mac version and 
it passed the building process after I committed the change on Apr 12th.

However, I did not see the specific reason why failed to create vignettes this 
time, may I ask how can I fix this issue?

Thank you so much,
Peng

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Re: [Bioc-devel] HiCBricks Bioc 3.11 Mac build is failing

[Shepherd, Lori]

Firstly,  macv2 is R devel so to accurately test  you should be using R 4.0.0  
with Bioc 3.11 packages.

However, this ERROR is  a Bioconductor builder issue having to do with fonts 
not being found.  We are working on a solution but for now you can ignore.


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Koustav Pal 

Sent: Friday, April 17, 2020 8:18 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] HiCBricks Bioc 3.11 Mac build is failing

Hi,

My package, HiCBricks is showing failed builds on the Mac builder macv2.

I have checked the packaged on my Mac running Catalina 10.15 and R 3.6.1. The 
build is ok.

Also, GitHub travis-ci build reports are fine.

The error message is �polygon edge not found�

Any help is much appreciated.

Koustav Pal, PhD
Post-Doctoral Fellow in Genome Architecture,
Computational Genomics Group,
IFOM - The FIRC Institute of Molecular Oncology,
Via Adamello 16,
20139 Milano, Italy.
Phone: +393441130157
E-mail: koustav@ifom.eu




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Re: [Bioc-devel] Cairo error in Windows server

[Shepherd, Lori]

I just reinstalled Cairo again to both architectures.  Cairo is known to be a 
particular challenging package for our builders.  It looks like a new version 
appeared on CRAN this past weekend.




Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Yue Zhao (Jason) 
Sent: Monday, April 13, 2020 5:14 PM
To: Shepherd, Lori 
Cc: bioc-devel 
Subject: Re: [Bioc-devel] Cairo error in Windows server

Hi Lori,

Thanks for the previous update, but the same error shows up again today, would 
you please check the Cairo in the Windows server? Thank you!

PS. the error message: 
http://bioconductor.org/checkResults/release/bioc-LATEST/animalcules/tokay1-checksrc.html

Best,
Jason


--

Yue (Jason) Zhao

PhD Candidate, Bioinformatics Program

Boston University

yu...@bu.edu<mailto:yu...@bu.edu>


On Mon, Mar 16, 2020 at 12:37 PM Shepherd, Lori 
mailto:lori.sheph...@roswellpark.org>> wrote:
I have just reinstalled Cairo on our builders and tested the install on both 
the 64-bit and 32-bit mode.  Hopefully this should clear up in tomorrows build 
report.  Please let us know if this continues to be an issue.


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel 
mailto:bioc-devel-boun...@r-project.org>> on 
behalf of Yue Zhao (Jason) mailto:yu...@bu.edu>>
Sent: Monday, March 16, 2020 10:38 AM
To: bioc-devel mailto:bioc-devel@r-project.org>>
Subject: [Bioc-devel] Cairo error in Windows server

Hello Bioc Community,

The CHECK in the windows server throws an error message that is not seen in
other platforms and local windows computer:

Error: .onLoad failed in loadNamespace() for 'Cairo', details:
  call: library.dynam("Cairo", pkgname, libname)
  error: DLL 'Cairo' not found: maybe not installed for this architecture?


The link to the report:
http://bioconductor.org/checkResults/release/bioc-LATEST/animalcules/tokay1-checksrc.html

We have tired to find solutions, but it seems like a problem with the
windows server at Bioc? Please let me know if you have some advice, I
really appreciate it.

Thanks!

Best,
Jason


*--*

*Yue (Jason) Zhao*

PhD Candidate, Bioinformatics Program

Boston University

yu...@bu.edu<mailto:yu...@bu.edu>

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Re: [Bioc-devel] Warning in tokay2

[Shepherd, Lori]

Please see this post:

https://stat.ethz.ch/pipermail/bioc-devel/2019-April/014999.html


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of VALLEJOS 
MENESES Catalina 
Sent: Tuesday, April 14, 2020 9:51 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] Warning in tokay2

Dear all,

The build report for BASiCS currently includes a warning in tokay2 (but malbec2 
and machv2 are ok). This seems to be an issue associated to the documentation 
of brewer.pal in RColorBrewer:


file link 'brewer.pal' in package 'RColorBrewer' does not exist and so has been 
treated as a topic

I can see that other packages have similar warnings in tokay2. Has anyone found 
a solution for it?

Many thanks in advance,

Best wishes,

Cata

The University of Edinburgh is a charitable body, registered in Scotland, with 
registration number SC005336.

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Re: [Bioc-devel] Unit tests pass locally but fail on Bioconductor machines

[Shepherd, Lori]

There are many changes to base R hence the switch from 3.6 to 4.0.   I would 
highly suggest using R 4.0.  There is a R-alpha version now available for all 
platforms with the R - 4.0 release schedule for later this month.  Please use 
the R-alpha version .

on CRAN.r-project.org you should see a section
Sources of R alpha and beta releases (daily snapshots, created only in time 
periods before a planned release) with links to R-alpha for linux.  There is a 
link here to R-alpha for mac  http://mac.r-project.org/   and one here for 
windows:  https://cran.rstudio.com/bin/windows/base/rpatched.html

This should allow you to download the most stable R-4.0 alpha before the 
release at the end of the month.
Hope this helps.




Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Christian 
Holland 
Sent: Tuesday, April 7, 2020 7:22 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] Unit tests pass locally but fail on Bioconductor machines

Hi there,

the unit tests (implemented with testthat) of my package 
(https://github.com/saezlab/dorothea ) run 
smoothly on local machines (tested for Linux, Windows and macOS). However, on 
the Bioconductor machines (both Linux and Window) a particular test fails. The 
feature that distinguish this particular test from all other (that passed 
without any problems) is the use of the ExpressionSet class from the Biobase 
package. Locally I am using the Biobase version 2.46.0.

You can see the build output from Bioconductor here: 
http://bioconductor.org/spb_reports/dorothea_buildreport_20200407063358.html 


Is it possible that this error is somehow related to the used R Version? 
Locally I am still using 3.6.2 but if I understand correctly the package is 
build and checked on Bioconductor machines with R version 4.0. So far I 
refrained from installing the development version of R4.0 as it crashed RStudio 
for a colleague of mine.

Many thanks for your support.

Christian



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Re: [Bioc-devel] Request to undeprecate MANOR

[Shepherd, Lori]

Yes we will undeprecated the MANOR package.


Are you working on the ERROR's in the devel report?  These cannot be ignored.






Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Pierre Neuvial 

Sent: Monday, April 6, 2020 4:58 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] Request to undeprecate MANOR

Hi,

I have updated the Maintainer email address for the MANOR package, so
the package is not "Unresponsive/not-maintained" anymore.

Also, I believe (*) I have fixed the build error that occurs for OS X
on http://bioconductor.org/checkResults/release/bioc-LATEST/MANOR/
(a file encoding issue in the vignette).

(*) I have just pushed the changes so I the build reports have not
been updated yet.

There are also build errors on the devel branch
http://bioconductor.org/checkResults/devel/bioc-LATEST/MANOR/
but I understand these are due to the deprecation of the package.

Can the MANOR package be undeprecated?

All the best,

Pierre

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Re: [Bioc-devel] R Dependency Warning

[Shepherd, Lori]

If you have compressed data it can be ignored.
4.0.0  is what the package would be released under so I recommend that.


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Sunny Jones 

Sent: Friday, April 3, 2020 2:13 PM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] R Dependency Warning

Hello,

I'm in the process of submitting two packages to Bioconductor, MOMA and its
associated data package moma.gbmexample. I keep getting this warning about
the R dependency:

* Checking R Version dependency...
* WARNING: Unless package includes compressed data, remove R
  version dependency

Both packages do have compressed data and I have tried both making the
dependency 4.0.0 and 3.6 but have gotten the error both times. Which is the
correct R version to list as the dependency on the upcoming release
version? Or is this a warning that should be ignored given that I do have
compressed data?

Thank you
Sunny Jones

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[Bioc-devel] Last Day to Submit New Packages for Bioconductor Release 3.11

[Shepherd, Lori]

The final day to submit new packages to the Bioconductor contributions tracker 
to have a shot at being included in the upcoming 3.11 release is TODAY   5 PM  
EST!

Please note: submission by this date does not guarantee it will be included - 
the package must undergo an official review and be accepted by Wednesday April 
22nd.

Submit new packages at  https://github.com/Bioconductor/Contributions

Submissions after Today and those that are not accepted by April 22nd will 
still be able to be in Bioconductor but will be included in the development 
branch until the 3.12 release in Fall. Please do not expect rush reviews or 
exceptions; reviews of packages submitted after today Friday April 3rd will be 
time-dependent of the reviewer based on other pre-release preparation.




Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


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Re: [Bioc-devel] CNORfeeder building error

[Shepherd, Lori]

When I look at the git.bioconductor.org checkout of your package,

There are no R functions and no man functions for those exports.

Your commit on Mar 30 only updated the NAMESPACE and vignette.



base) lori@lori-HP-ZBook-15-G2:~/b/Rpacks/CNORfeeder(master)$ grep -r 
"buildFeederObjectDynamic" *
NAMESPACE:"buildFeederObjectDynamic",
vignettes/CNORfeeder-vignette.Rnw:feederObject = buildFeederObjectDynamic(model 
= model, cnolist = cnolist,


Please check your commits.  You may have forgotten to git add the relevant 
files.




Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Enio Gjerga 

Sent: Thursday, April 2, 2020 3:54 PM
To: Herv� Pag�s 
Subject: [Bioc-devel] CNORfeeder building error

Hello,

I am the maintainer of the CNORfeeder package. When I updated the package I
added a few other functions. However, from the building I get the following
error:

package ornamespace load failed for �CNORfeeder� in
namespaceExport(ns, exports):
undefinedexports: *the names of the new functions I have added*

I have added these function names on the NAMESPACE as exports and also they
are in the /man function documentation (as .Rd files) and of course as R
functions in /R.

Please, what might be the reason for this? Should these new functions also
be declared somewhere else which I am missing?

I have run the 'R CMD INSTALL CNORfeeder' command in my terminal and the
package seem to be built just fine. I am using Mac OS X El Captain.

Best,
Enio
--
Enio GJERGA
PhD student
JRC-COMBINE RWTH Aachen
Tel : +4917685132057

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Re: [Bioc-devel] Development branch build error from celda

[Shepherd, Lori]

I think this is an intermittent connectivity issue and is safe to ignore. While 
today's build report has not yet officially posted, I check the report for you 
package and it seems to be all OK.
Thank you for your diligence on investigating package ERRORs.

Cheers,


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Wang, Zhe 

Sent: Thursday, April 2, 2020 1:46 AM
To: Bioc-devel@r-project.org 
Subject: [Bioc-devel] Development branch build error from celda

Hi,

I am the maintainer of Bioconductor package celda. Recently there is an build 
check error on the development branch specifically on Windows i386 platform. I 
cannot reproduce this error on my local x64 Windows machine. The error report 
is as follows:

* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... ERROR
Running examples in 'celda-Ex.R' failed
Warning in file(con, "r") :
  cannot open file '../celda-Ex_i386.Rout': Permission denied
Error in file(con, "r") : cannot open the connection
Execution halted

Does anyone have any idea about how I can fix this?

Thanks,
Zhe

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Re: [Bioc-devel] Help with tokay2 errors

[Shepherd, Lori]

On quick glance into the logs on tokay2 it looks like it may be an issue with 
MotifDb and not your package.
In merge_motif it doesn't get to evaluating the code as it is hung up on trying 
to load the MotifDb library.  Once this library is called,
There are numerous:

*** recursive gc invocation

and somewhere in the middle of all these repeated lines is

Error: package or namespace load failed for 'MotifDb':
 .onLoad failed in loadNamespace() for 'MotifDb', details:
  call: base::colSums(x, na.rm = na.rm, dims = dims, ...)
  error: bad binding access
Execution halted




Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Benjamin 
Jean-Marie Tremblay 
Sent: Saturday, March 28, 2020 4:22 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] Help with tokay2 errors

Hi,

Recently I've been having several examples fail on the tokay2 test machine,
specifically the i386 examples. Unfortunately I don't have access to a
windows machine to diagnose these failures right now, and the output that I
can see shows no errors; the examples just end abruptly. I don't see these
failures on my own computer (regular macOS, also docker bioc-devel image), so
I�m at a bit of a loss as to how to go about fixing these.

http://bioconductor.org/checkResults/devel/bioc-LATEST/universalmotif/tokay2-checksrc.html

Any help would be greatly appreciated.

Thanks,

Benjamin Tremblay
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Re: [Bioc-devel] Final List of Deprecated Packages for Bioc3.11

[Shepherd, Lori]

Software package: DChIPRep

and

Workflow package: maEndToEnd

User requested deprecation.




Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

____
From: Shepherd, Lori
Sent: Monday, March 30, 2020 11:36 AM
To: bioc-devel@r-project.org 
Subject: Final List of Deprecated Packages for Bioc3.11

The Bioconductor Team is continuing to identify packages that will be 
deprecated in the next release to allow for the Bioconductor community to 
respond accordingly. The list will be updated monthly. This is the current list 
of deprecated packages for Bioc 3.11 :

Maintainer requested deprecation:

Software:

QUALIFIER
motifRG
triform
CVE
proteoQC
affypdnn
splicegear
Genominator
IdMappingAnalysis
IdMappingRetrieval
manta
RefNet
AnalysisPageServer
scfind
kimod
plw
cn.mops
cobindR
LMGene
sRAP
gCMAP
gCMAPWeb
DESeq


Annotation:

org.At.tair.db
hom.At.inp.db
hom.Ce.inp.db
hom.Dm.inp.db
hom.Dr.inp.db
hom.Hs.inp.db
hom.Mm.inp.db
hom.Rn.inp.db
hom.Sc.inp.db
KEGG.db (use KEGGREST instead)


Unresponsive/not-maintained packages:

Software:

SELEX
CTDquerier
MTseeker
readat
anamiR
MEAL
BiSeq
CALIB
cellGrowth
chroGPS
DEDS
LVSmiRNA
MANOR
MCRestimate
nem
PAPi
pcaGoPromoter
pint
RIPSeeker
SANTA
waveTiling
BayesPeak
bgafun
lol
M3D
MergeMaid
IPPD
biosvd
birta
DupChecker
FEM
geecc
MaxContrastProjection
mitoODE
MoPS
PowerExplorer
Vega


ExpermentData:

MTseekerData
RIPSeekerData


The follow Annotation packages were deprecated in 3.10 and removed from 3.11 
but not previously announced.

MafDb.ESP6500SI.V2.SSA137.hs37d5
MafDb.EXP6500SI.V2.SSA137.GRCh38

It should be noted, we did try to reach out to these package maintainers 
multiple times and they were either unresponsive or had emails bounce. We 
encourage anyone that is familiar with a package maintainer on this list to 
reach out to them and notify them directly. Packages can be un-deprecated if a 
maintainer fixes the package to build/check cleanly before the next release and 
requests un-deprecation on the bioc-devel@r-project.org mailing list.

We will be sending emails out to packages that have been broken across all 
platforms for an extended period of time as those are packages that are up for 
immediate deprecation if not corrected in a timely fashion.

We will still be keeping track of failing packages and compiling a list to 
deprecate immediately after the release. This could have been because the 
package has reverse dependencies or was identified to late to deprecate in 
3.11. We encourage anyone that knows the maintainers of these packages to reach 
out to them to fix their package to avoid deprecation. The current list for 
immediate deprecation in 3.12 is:

DESeq
MotIV
NOISeq
omicade4
PGSEA
Starr
VanillaICE


Thank you


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


This email message may contain legally privileged and/or confidential 
information.  If you are not the intended recipient(s), or the employee or 
agent responsible for the delivery of this message to the intended 
recipient(s), you are hereby notified that any disclosure, copying, 
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[Bioc-devel] Devel Builder Updates

[Shepherd, Lori]

We will be updating the devel builders to the lastest R 4.0.0 later today.  
This should not affect the daily builder but may interrupt the Single Package 
Builder for new submission.  Build report status for a platform on the single 
package builder may be missing during the update period.  The downtown should 
be brief.   Thank you for your understanding.

Cheers,


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


This email message may contain legally privileged and/or confidential 
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[Bioc-devel] connectivity to hubs

[Shepherd, Lori]

There has been an issue reported that there is some connectivity / timeout 
issues happening to experimenthub and annotationhub.  It seems to be 
intermittent but we are aware and investigating the issue.

Thank you


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


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Re: [Bioc-devel] Final List of Deprecated Packages for Bioc3.11

[Shepherd, Lori]

BiSeq has fixed their package and reached out for undeprecation. The package 
will remain in Bioconductor.


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Shepherd, Lori 

Sent: Monday, March 30, 2020 11:36 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] Final List of Deprecated Packages for Bioc3.11

The Bioconductor Team is continuing to identify packages that will be 
deprecated in the next release to allow for the Bioconductor community to 
respond accordingly. The list will be updated monthly. This is the current list 
of deprecated packages for Bioc 3.11 :

Maintainer requested deprecation:

Software:

QUALIFIER
motifRG
triform
CVE
proteoQC
affypdnn
splicegear
Genominator
IdMappingAnalysis
IdMappingRetrieval
manta
RefNet
AnalysisPageServer
scfind
kimod
plw
cn.mops
cobindR
LMGene
sRAP
gCMAP
gCMAPWeb
DESeq


Annotation:

org.At.tair.db
hom.At.inp.db
hom.Ce.inp.db
hom.Dm.inp.db
hom.Dr.inp.db
hom.Hs.inp.db
hom.Mm.inp.db
hom.Rn.inp.db
hom.Sc.inp.db
KEGG.db (use KEGGREST instead)


Unresponsive/not-maintained packages:

Software:

SELEX
CTDquerier
MTseeker
readat
anamiR
MEAL
BiSeq
CALIB
cellGrowth
chroGPS
DEDS
LVSmiRNA
MANOR
MCRestimate
nem
PAPi
pcaGoPromoter
pint
RIPSeeker
SANTA
waveTiling
BayesPeak
bgafun
lol
M3D
MergeMaid
IPPD
biosvd
birta
DupChecker
FEM
geecc
MaxContrastProjection
mitoODE
MoPS
PowerExplorer
Vega


ExpermentData:

MTseekerData
RIPSeekerData


The follow Annotation packages were deprecated in 3.10 and removed from 3.11 
but not previously announced.

MafDb.ESP6500SI.V2.SSA137.hs37d5
MafDb.EXP6500SI.V2.SSA137.GRCh38

It should be noted, we did try to reach out to these package maintainers 
multiple times and they were either unresponsive or had emails bounce. We 
encourage anyone that is familiar with a package maintainer on this list to 
reach out to them and notify them directly. Packages can be un-deprecated if a 
maintainer fixes the package to build/check cleanly before the next release and 
requests un-deprecation on the bioc-devel@r-project.org mailing list.

We will be sending emails out to packages that have been broken across all 
platforms for an extended period of time as those are packages that are up for 
immediate deprecation if not corrected in a timely fashion.

We will still be keeping track of failing packages and compiling a list to 
deprecate immediately after the release. This could have been because the 
package has reverse dependencies or was identified to late to deprecate in 
3.11. We encourage anyone that knows the maintainers of these packages to reach 
out to them to fix their package to avoid deprecation. The current list for 
immediate deprecation in 3.12 is:

DESeq
MotIV
NOISeq
omicade4
PGSEA
Starr
VanillaICE


Thank you


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


This email message may contain legally privileged and/or confidential 
information.  If you are not the intended recipient(s), or the employee or 
agent responsible for the delivery of this message to the intended 
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distribution, or use of this email message is prohibited.  If you have received 
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[Bioc-devel] Bioc2020 - Call for BOF/HAK/FAQ Sections

[Shepherd, Lori]

Bioc2020 is proceeding with planning for the conference to be held July 29-31, 
with contingency planning for an online-only conference if necessary. 
https://bioc2020.bioconductor.org/


As part of the program we want to encourage community involvement and 
interactive projects. This may take the form of birds-of-a-feather
discussion topics (like an open forum discussion) but could extend to ideas 
like short hack-a-thon projects (e.g., create a Pull Request for feature x in 
package y)  or the compilation of short FAQ/how-to topics (e.g., how do I 
liftover hg19 coordinates to hg38 with Bioconductor resources).  We encourage 
submissions from novice R/Bioconductor users and minority groups.


We want to have some of these sessions planned and will also encourage 
spontaneous sessions to form on the day of the conference (pending an in-person 
meeting). In an effort to schedule topics that are of most interest to the 
Bioconductor community at large, we encourage submission of session ideas on 
the bioc2020 github as an open issue. 
(https://github.com/Bioconductor/BioC2020/issues)


Please include in the issue title if it's a birds-of-a-feather (BOF), 
hack-a-thon (HAK), or how-to/FAQ (FAQ), and include a short description of the 
goals of the session.


For example:

(BOF) Annotation harmonization
(HAK) Add metadata column  to package 
(FAQ) How to do a lift over from hg19 to hg38


Please announce your session suggestion in the Bioconductor slack channel 
#bioc2020. This will encourage the Bioconductor community to contribute to the 
session. Sign up for the Bioconductor community slack can be found 
https://bioc-community.herokuapp.com/



Thank you

Lori Shepherd on behalf of the Bioc2020 planning committee



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Re: [Bioc-devel] The errror from build report of ASpediaFI

[Shepherd, Lori]

For What Its Worth ---

I can reproduce this on my linux machine.  I would suggest making sure you are 
using R-4.0.0 and all the latest package versions as there have been recent 
updates to S4Vectors and possibly others that you depend/import.

# if the following suggests updating packages please do so.

BiocManager::valid( )
BiocManager::install( )




Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Bioinformatics 
NCC 
Sent: Tuesday, March 31, 2020 12:55 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] The errror from build report of ASpediaFI

Hello,

I am a maintainer of the ASpediaFI package.

Recently, I made few changes to the package and found the error in the
build report only for the Windows platform.

R CMD build and check ran without errors on my machine (Windows) and Linux
server as well, so I wonder what caused the error.


The error from the report is:

Quitting from lines 293-299 (ASpediaFI.rnw) Error: processing vignette
'ASpediaFI.rnw' failed with diagnostics: cannot coerce type 'S4' to vector
of type 'double' --- failed re-building 'ASpediaFI.rnw' SUMMARY: processing
the following file failed: 'ASpediaFI.rnw' Error: Vignette re-building
failed. Execution halted

Thanks,

DY

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