[Bioc-devel] issue to open a file from UCSC

[Martin, Tiphaine via Bioc-devel]

Hi,

I have an error in the package compilation because of issues accessing a file 
from UCSC.
Are you aware of such type of issue? What do I need to do?

Quitting from lines 337-345 [cometwebPlot] (coMET.Rnw)
Error: processing vignette 'coMET.Rnw' failed with diagnostics:
error in evaluating the argument 'object' in selecting a method for function 
'getTable': cannot open URL 
'https://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/chromInfo.txt.gz'

Thanks,
Tiphaine

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Re: [Bioc-devel] Failed to obtain 'hguid' cookie

[Martin, Tiphaine via Bioc-devel]

thank Herve for answering and pointing the discussion!
Thanks,
Tiphaine


Tiphaine Martin
Assistant Professor
Department of Oncological Sciences
The Tisch Cancer Institute at Mount Sinai
Icahn School of Medicine at Mount Sinai
Hess Center for Science and Medicine
1470 Madison Ave, 6th Floor
New York, NY 10029
tel: 1- 212-824-9253
Email: tiphaine.mar...@mssm.edu<mailto:tiphaine.mar...@mssm.edu>



From: Herv� Pag�s 
Sent: Friday, October 20, 2023 12:18 PM
To: Martin, Tiphaine ; bioc-devel@r-project.org 

Subject: Re: [Bioc-devel] Failed to obtain 'hguid' cookie

USE CAUTION: External Message.

Hi Tiphaine,

This is a known issue with the rtracklayer package. The issue itself is caused 
by a change that was made earlier this week on the UCSC servers.

The rtracklayer issue is being discussed here 
https://github.com/lawremi/rtracklayer/issues/95<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_lawremi_rtracklayer_issues_95&d=DwMDaQ&c=shNJtf5dKgNcPZ6Yh64b-ALLUrcfR-4CCQkZVKC8w3o&r=BH3UNPUNhOc-niJT9d00EAx3ah5AHfQlhQQ_SHtjigA&m=aiyZQTZv_ZSxY6VQIMOSvmmWhZ4A8I2UKZC1g5fxN2cpG2omYMbNLyTLMTYz6QGJ&s=Aqffrd9B_1NEWhK7QVNGtm151IjfzMRJ2lkJsbBgy6g&e=>.
 I'm waiting for my PR to be merged, hopefully soon.

Best,

H.

On 10/20/23 09:11, Martin, Tiphaine via Bioc-devel wrote:

Hi,

I have my package that failed to build its vignette because of failing to 
obtain 'hguid' cookie.

Could you please tell me how I can solve this?

thanks,
Tiphaine


Tiphaine Martin
Assistant Professor
Department of Oncological Sciences
The Tisch Cancer Institute at Mount Sinai
Icahn School of Medicine at Mount Sinai
Hess Center for Science and Medicine
1470 Madison Ave, 6th Floor
New York, NY 10029
tel: 1- 212-824-9253
Email: 
tiphaine.mar...@mssm.edu<mailto:tiphaine.mar...@mssm.edu><mailto:tiphaine.mar...@mssm.edu><mailto:tiphaine.mar...@mssm.edu>


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--
Herv� Pag�s

Bioconductor Core Team
hpages.on.git...@gmail.com<mailto:hpages.on.git...@gmail.com>


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[Bioc-devel] Failed to obtain 'hguid' cookie

[Martin, Tiphaine via Bioc-devel]

Hi,

I have my package that failed to build its vignette because of failing to 
obtain 'hguid' cookie.

Could you please tell me how I can solve this?

thanks,
Tiphaine


Tiphaine Martin
Assistant Professor
Department of Oncological Sciences
The Tisch Cancer Institute at Mount Sinai
Icahn School of Medicine at Mount Sinai
Hess Center for Science and Medicine
1470 Madison Ave, 6th Floor
New York, NY 10029
tel: 1- 212-824-9253
Email: tiphaine.mar...@mssm.edu


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[Bioc-devel] FW: coMET problems reported in the Multiple platform build/check report for BioC 3.13

[Martin, Tiphaine]

Hi,

I have a question. 
I receive an error message for my COMET package, but when I click on the link. 
I do not find the error.
Could you advise me what I need to do ?

Thanks
Tiphaine

-Original Message-
From: bbs-nore...@bioconductor.org  
Sent: Friday, June 25, 2021 3:15 PM
To: Martin, Tiphaine 
Subject: coMET problems reported in the Multiple platform build/check report 
for BioC 3.13

USE CAUTION: External Message.

[This is an automatically generated email. Please don't reply.]

Hi coMET maintainer,

According to the Multiple platform build/check report for BioC 3.13, the coMET 
package has the following problem(s):

  o ERROR for 'R CMD check' on nebbiolo1. See the details here:
  
https://urldefense.proofpoint.com/v2/url?u=https-3A__master.bioconductor.org_checkResults_3.13_bioc-2DLATEST_coMET_nebbiolo1-2Dchecksrc.html&d=DwIBAg&c=shNJtf5dKgNcPZ6Yh64b-A&r=BH3UNPUNhOc-niJT9d00EAx3ah5AHfQlhQQ_SHtjigA&m=rgMv9ROw_ncM46tcx-07OdVTBBbIlhZpGwpgxq9xgpg&s=1AzAzYYy6l2890lWG2Ng5hGmKLuDYJfsd-FO8QufqBU&e=

Please take the time to address this by committing and pushing changes to your 
package at 
https://urldefense.proofpoint.com/v2/url?u=http-3A__git.bioconductor.org&d=DwIBAg&c=shNJtf5dKgNcPZ6Yh64b-A&r=BH3UNPUNhOc-niJT9d00EAx3ah5AHfQlhQQ_SHtjigA&m=rgMv9ROw_ncM46tcx-07OdVTBBbIlhZpGwpgxq9xgpg&s=89Ispas4yShTDHeE6MM3NfRybC3vrMLsvZq261gpHw4&e=

Notes:

  * This was the status of your package at the time this email was sent to you.
Given that the online report is updated daily (in normal conditions) you
could see something different when you visit the URL(s) above, especially if
you do so several days after you received this email.

  * It is possible that the problems reported in this report are false 
positives,
either because another package (from CRAN or Bioconductor) breaks your
package (if yours depends on it) or because of a Build System problem.
If this is the case, then you can ignore this email.

  * Please check the report again 24h after you've committed your changes to the
package and make sure that all the problems have gone.

  * If you have questions about this report or need help with the
maintenance of your package, please use the Bioc-devel mailing list:

  
https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_help_mailing-2Dlist_&d=DwIBAg&c=shNJtf5dKgNcPZ6Yh64b-A&r=BH3UNPUNhOc-niJT9d00EAx3ah5AHfQlhQQ_SHtjigA&m=rgMv9ROw_ncM46tcx-07OdVTBBbIlhZpGwpgxq9xgpg&s=0y_6VHYweZgGmbzIqIrSbGiFD2UeXm7EYIk2LI90cyE&e=

(all package maintainers are requested to subscribe to this list)

For immediate notification of package build status, please subscribe to your 
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Thanks for contributing to the Bioconductor project!

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Re: [Bioc-devel] Last day to make commit before the RELEASE_3_13

[Martin, Tiphaine]

Thanks a lot for this link and explanation
Tiphaine



Tiphaine Martin
Postdoc Fellow
Parsons lab
Department of Oncological Sciences
The Tisch Cancer Institute at Mount Sinai
Icahn School of Medicine at Mount Sinai
Hess Center for Science and Medicine
1470 Madison Ave, 6th Floor
New York, NY 10029
tel: 1- 212-824-9253
Email: tiphaine.mar...@mssm.edu<mailto:tiphaine.mar...@mssm.edu>



From: Kern, Lori 
Sent: Tuesday, May 18, 2021 10:44 AM
To: Martin, Tiphaine ; bioc-devel@r-project.org 

Subject: Re: Last day to make commit before the RELEASE_3_13

It looks like you just pushed the changes up Sunday May 16th.  It can take up 
to 48 hours to get through the build report and landing page depending on the 
time of the push to our system because the builders only pull, build, check 
once per day.  You missed the cut off to be on yesterday's report.  I expect to 
see the updated version on today's report.

See the top of this page for timing
http://bioconductor.org/developers/how-to/troubleshoot-build-report/<https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_developers_how-2Dto_troubleshoot-2Dbuild-2Dreport_&d=DwMFAg&c=shNJtf5dKgNcPZ6Yh64b-A&r=BH3UNPUNhOc-niJT9d00EAx3ah5AHfQlhQQ_SHtjigA&m=YRruJf2R7wFYfv_y1AMqK7Xb2Dp8QBIfClByi9rv2oo&s=JWEpYDhaacBe5MhNLVwGlwfr-1mtbG0NBx84Yl8dyGU&e=>
Bioconductor - Troubleshooting Build 
Report<https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_developers_how-2Dto_troubleshoot-2Dbuild-2Dreport_&d=DwMFAg&c=shNJtf5dKgNcPZ6Yh64b-A&r=BH3UNPUNhOc-niJT9d00EAx3ah5AHfQlhQQ_SHtjigA&m=YRruJf2R7wFYfv_y1AMqK7Xb2Dp8QBIfClByi9rv2oo&s=JWEpYDhaacBe5MhNLVwGlwfr-1mtbG0NBx84Yl8dyGU&e=>
Troubleshooting Build Report How and When does the builder pull? When will my 
changes propagate? Please remember the daily builder pulls, installs, builds, 
and checks ...
bioconductor.org<https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org&d=DwQFAg&c=shNJtf5dKgNcPZ6Yh64b-A&r=BH3UNPUNhOc-niJT9d00EAx3ah5AHfQlhQQ_SHtjigA&m=YRruJf2R7wFYfv_y1AMqK7Xb2Dp8QBIfClByi9rv2oo&s=T69zZoxDD5dlVR-PhYSTN2ssRN_ryN0PDugTqO6fxZY&e=>



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, 
Tiphaine 
Sent: Tuesday, May 18, 2021 10:32 AM
To: bioc-devel@r-project.org 
Subject: Re: [Bioc-devel] Last day to make commit before the RELEASE_3_13

Hi,
I submitted my update of my package to master Sunday (1.23.1). I did not see a 
new update in build/check report 
(http://secure-web.cisco.com/17AMCgK31b8cwSa9x6pbGruTkLWwGrTeu42AoLtib4FhptXpFa-f9vMSDnapiS4gIxwbiXLhPx-WZVbl8PXapb3fIqJQpLfbQYfUSo6Oxlk-1BNn5KQwfXLXmoaD6Bvl7YH2V_hEWV1JIGzEub1okwQIz6SagNlk31mQyKF3F6nb1ij0rex7VHbYacEGSbxthiLAGdagfkOOUcMfV_Z4uYBTxRUZ7mG3TVXbymEWOGya2n8P-8x2_5AeIDpDvOjFM1HnttZRilcN_dVr1MU2SznjnqUZjULBhXk4NcNGXO7xBoQqqr4qoEyuWMFxWH8Vzt2rqFEotbVlohOIN3Vh_JQ/http%3A%2F%2Fbioconductor.org%2FcheckResults%2Fdevel%2Fbioc-LATEST%2FcoMET%2F<https://urldefense.proofpoint.com/v2/url?u=http-3A__secure-2Dweb.cisco.com_17AMCgK31b8cwSa9x6pbGruTkLWwGrTeu42AoLtib4FhptXpFa-2Df9vMSDnapiS4gIxwbiXLhPx-2DWZVbl8PXapb3fIqJQpLfbQYfUSo6Oxlk-2D1BNn5KQwfXLXmoaD6Bvl7YH2V-5FhEWV1JIGzEub1okwQIz6SagNlk31mQyKF3F6nb1ij0rex7VHbYacEGSbxthiLAGdagfkOOUcMfV-5FZ4uYBTxRUZ7mG3TVXbymEWOGya2n8P-2D8x2-5F5AeIDpDvOjFM1HnttZRilcN-5FdVr1MU2SznjnqUZjULBhXk4NcNGXO7xBoQqqr4qoEyuWMFxWH8Vzt2rqFEotbVlohOIN3Vh-5FJ
 
Q_http-253A-252F-252Fbioconductor.org-252FcheckResults-252Fdevel-252Fbioc-2DLATEST-252FcoMET-252F&d=DwMFAg&c=shNJtf5dKgNcPZ6Yh64b-A&r=BH3UNPUNhOc-niJT9d00EAx3ah5AHfQlhQQ_SHtjigA&m=YRruJf2R7wFYfv_y1AMqK7Xb2Dp8QBIfClByi9rv2oo&s=DwiaGGpLLe8DdAPI_xNdmhKo-pXFVldQPpiFD3OG_ik&e=>)

Did I miss something when I submit it?
Thanks,
Tiphaine

-Original Message-
From: Bioc-devel  On Behalf Of Kern, Lori
Sent: Tuesday, May 18, 2021 7:13 AM
To: bioc-devel@r-project.org
Subject: [Bioc-devel] Last day to make commit before the RELEASE_3_13

USE CAUTION: External Message.

Hello Bioconductor developers,

We are still on track for Bioconductor Release 3.13 for this Thursday May 20th. 
 This means that tonight is the last day to commit changes to the devel branch 
before creating of the RELEASE_3_13 versions of your packages.  And any changes 
you make to your packages at this point will not be reflected in a build report 
before we branch.

There will be a temporary code freeze tomorrow morning (EST)  while the 
branching for RELEASE_3_13 occurs automatically by the core team.  You will 
receive emails when the freeze occurs and when commits to the branches can 
resume.

As clarification,  you will still be able to commit to the release 3.13 bra

Re: [Bioc-devel] Last day to make commit before the RELEASE_3_13

[Martin, Tiphaine]

Hi,
I submitted my update of my package to master Sunday (1.23.1). I did not see a 
new update in build/check report 
(http://bioconductor.org/checkResults/devel/bioc-LATEST/coMET/)

Did I miss something when I submit it?
Thanks,
Tiphaine 

-Original Message-
From: Bioc-devel  On Behalf Of Kern, Lori
Sent: Tuesday, May 18, 2021 7:13 AM
To: bioc-devel@r-project.org
Subject: [Bioc-devel] Last day to make commit before the RELEASE_3_13

USE CAUTION: External Message.

Hello Bioconductor developers,

We are still on track for Bioconductor Release 3.13 for this Thursday May 20th. 
 This means that tonight is the last day to commit changes to the devel branch 
before creating of the RELEASE_3_13 versions of your packages.  And any changes 
you make to your packages at this point will not be reflected in a build report 
before we branch.

There will be a temporary code freeze tomorrow morning (EST)  while the 
branching for RELEASE_3_13 occurs automatically by the core team.  You will 
receive emails when the freeze occurs and when commits to the branches can 
resume.

As clarification,  you will still be able to commit to the release 3.13 branch 
and the devel branch throughout the next release cycle. But any packages that 
have not been fixed for failures or bugs in devel would then have to be 
fixed/uploaded to both the RELEASE_3_13 branch and the devel master branch.


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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Re: [Bioc-devel] issue with ssh public key

[Martin, Tiphaine]

Hi,
This was my previous email.
Please could you put my new email 
tiphaine.mar...@mssm.edu<mailto:tiphaine.mar...@mssm.edu>
Could you remind me how I can change later if need it.
Thanks,
Tiphaine

From: Nitesh Turaga 
Sent: Monday, May 3, 2021 9:07 AM
To: Martin, Tiphaine ; bioc-devel@r-project.org
Subject: Re: issue with ssh public key

USE CAUTION: External Message.
The email registered is 
tiphaine.mar...@kcl.ac.uk<mailto:tiphaine.mar...@kcl.ac.uk> .

If this is not correct, I will have to change it on my end.

Best,

Nitesh

From: Bioc-devel 
mailto:bioc-devel-boun...@r-project.org>> on 
behalf of Martin, Tiphaine 
mailto:tiphaine.mar...@mssm.edu>>
Date: Saturday, May 1, 2021 at 11:47 PM
To: bioc-devel@r-project.org<mailto:bioc-devel@r-project.org> 
mailto:bioc-devel@r-project.org>>
Subject: [Bioc-devel] issue with ssh public key
Hi,

I try to submit update of my package comet
I do not remember about my ssh public key
I have this error message and I request it
tiphaine.mar...@mssm.edu<mailto:tiphaine.mar...@mssm.edu> is not associated 
with a maintainer of a Bioconductor package.


Could you help me please?

Thanks,
Tiphaine


Tiphaine Martin
Postdoc Fellow
Parsons lab
Department of Oncological Sciences
The Tisch Cancer Institute at Mount Sinai
Icahn School of Medicine at Mount Sinai
Hess Center for Science and Medicine
1470 Madison Ave, 6th Floor
New York, NY 10029
tel: 1- 212-824-9253
Email: 
tiphaine.mar...@mssm.edu<mailto:tiphaine.mar...@mssm.edu%3E<mailto:tiphaine.mar...@mssm.edu%3cmailto:tiphaine.mar...@mssm.edu%3E>


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[Bioc-devel] issue with ssh public key

[Martin, Tiphaine]

Hi,

I try to submit update of my package comet
I do not remember about my ssh public key
I have this error message and I request it
tiphaine.mar...@mssm.edu is not associated with a maintainer of a Bioconductor 
package.


Could you help me please?

Thanks,
Tiphaine


Tiphaine Martin
Postdoc Fellow
Parsons lab
Department of Oncological Sciences
The Tisch Cancer Institute at Mount Sinai
Icahn School of Medicine at Mount Sinai
Hess Center for Science and Medicine
1470 Madison Ave, 6th Floor
New York, NY 10029
tel: 1- 212-824-9253
Email: tiphaine.mar...@mssm.edu


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Re: [Bioc-devel] failling to build vignette

[Martin, Tiphaine]

Thanks! I am working to fix that!

Tiphaine


Tiphaine Martin
Postdoc Fellow
Parsons lab
Department of Oncological Sciences
The Tisch Cancer Institute at Mount Sinai
Icahn School of Medicine at Mount Sinai
Hess Center for Science and Medicine
1470 Madison Ave, 6th Floor
New York, NY 10029
tel: 1- 212-824-8403
Email: tiphaine.mar...@mssm.edu


From: Shepherd, Lori 
Sent: Monday, December 17, 2018 2:41:59 PM
To: Martin, Tiphaine; bioc-devel@r-project.org
Subject: Re: failling to build vignette


Maybe others will have better suggestions for how to debug exactly...

I am able to reproduce the error and just with a trial and error of deleting 
and adding chunks of the vignette ... it first seems to appear with the attempt 
to add the figure


\begin{figure}
<>=
extdata <- system.file("extdata", package="coMET",mustWork=TRUE)
myinfofile <- file.path(extdata, "cyp1b1_infofile_Grch38.txt")
myexpressfile <- file.path(extdata, 
"cyp1b1_infofile_exprGene_region_Grch38.txt")
mycorrelation <- file.path(extdata, "cyp1b1_res37_rawMatrix.txt")
configfile <- file.path(extdata, "config_cyp1b1_zoom_4webserver_Grch38.txt")
comet.web(config.file=configfile, mydata.file=myinfofile,
  cormatrix.file=mycorrelation ,mydata.large.file=myexpressfile,
  print.image=FALSE,verbose=FALSE)
@
%\incfig{fig:cometweb_simple}{\textwidth}{Plot with comet.web function.}
\caption{Plot with \Rfunction{comet.web} function.\label{fig:cometweb_simple}}
\end{figure}


Everything before this seems to R CMD build without this error appearing...



Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Martin, 
Tiphaine 
Sent: Monday, December 17, 2018 11:31:49 AM
To: bioc-devel@r-project.org
Subject: [Bioc-devel] failling to build vignette

Hi,

I need to advise to build my vignette. It seems that my vignette could not 
build under Bioconductor 3.9. I try to find where it fails, but I  don't find 
the bug.
I updated my vignette last February to work with new version of BiocStyle and 
it did well for Bioconductor 3.8, but it seems that my vignette fails again 
(http://bioconductor.org/checkResults/devel/bioc-LATEST/coMET/<https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_devel_bioc-2DLATEST_coMET_&d=DwMFAg&c=shNJtf5dKgNcPZ6Yh64b-A&r=BH3UNPUNhOc-niJT9d00EAx3ah5AHfQlhQQ_SHtjigA&m=dBNAJlpvc6U1QE6A0BaRRT_a3bMHRDe0DhDvCD_u4TM&s=tN1M5zjUQsGXBvBp3kfL-FiPmfWXaSXZaRIr0mieqy0&e=>)
 .
Could you tell me if there is a major update in BiocStyle or how I can find my 
bug?

Thanks,
Tiphaine
---
Tiphaine Martin, PhD
Postdoc Fellow
Parsons lab
Department of Oncological Sciences
The Tisch Cancer Institute at Mount Sinai
Icahn School of Medicine at Mount Sinai
Hess Center for Science and Medicine
1470 Madison Ave, 6th Floor
New York, NY 10029
tel: 1- 212-824-8403
Email: tiphaine.mar...@mssm.edu<mailto:tiphaine.mar...@mssm.edu%3E


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[Bioc-devel] failling to build vignette

[Martin, Tiphaine]

Hi,

I need to advise to build my vignette. It seems that my vignette could not 
build under Bioconductor 3.9. I try to find where it fails, but I  don't find 
the bug.
I updated my vignette last February to work with new version of BiocStyle and 
it did well for Bioconductor 3.8, but it seems that my vignette fails again 
(http://bioconductor.org/checkResults/devel/bioc-LATEST/coMET/) .
Could you tell me if there is a major update in BiocStyle or how I can find my 
bug?

Thanks,
Tiphaine
---
Tiphaine Martin, PhD
Postdoc Fellow
Parsons lab
Department of Oncological Sciences
The Tisch Cancer Institute at Mount Sinai
Icahn School of Medicine at Mount Sinai
Hess Center for Science and Medicine
1470 Madison Ave, 6th Floor
New York, NY 10029
tel: 1- 212-824-8403
Email: tiphaine.mar...@mssm.edu


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Re: [Bioc-devel] incompatibility between logo for build et the version and success of compilation

[Martin, Tiphaine]

Great, thanks Lori.



From: Shepherd, Lori 
Sent: 18 April 2018 17:46:24
To: Martin, Tiphaine; bioc-devel@r-project.org
Subject: Re: incompatibility between logo for build et the version and success 
of compilation


This page

http://bioconductor.org/packages/3.7/bioc/html/coMET.html<https://emea01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fbioconductor.org%2Fpackages%2F3.7%2Fbioc%2Fhtml%2FcoMET.html&data=01%7C01%7Ctiphaine.martin%40kcl.ac.uk%7C9fe05e23fbf447e4da5b08d5a54beeeb%7C8370cf1416f34c16b83c724071654356%7C0&sdata=iAhqrnkMugGlE%2BjtdxndP16ZzQp%2FkWkajxc33hR6DgA%3D&reserved=0>
gets updated when there is a successful build and once the package propagates 
on our system as determined by the latest build report.  It can be a little 
delayed behind the successful post here:

http://bioconductor.org/checkResults/devel/bioc-LATEST/coMET/<https://emea01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fbioconductor.org%2FcheckResults%2Fdevel%2Fbioc-LATEST%2FcoMET%2F&data=01%7C01%7Ctiphaine.martin%40kcl.ac.uk%7C9fe05e23fbf447e4da5b08d5a54beeeb%7C8370cf1416f34c16b83c724071654356%7C0&sdata=AF%2BJi3SJQAgDo96Zy19uwsqoyJ267JMdTrEt1lbKmok%3D&reserved=0>
but should update within the next 24 hours.

This is the most accurate.
http://bioconductor.org/checkResults/devel/bioc-LATEST/coMET/




Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________
From: Bioc-devel  on behalf of Martin, 
Tiphaine 
Sent: Wednesday, April 18, 2018 12:37:43 PM
To: bioc-devel@r-project.org
Subject: [Bioc-devel] incompatibility between logo for build et the version and 
success of compilation

Hi,


I updated the dev version of my package, 
http://bioconductor.org/packages/3.7/bioc/html/coMET.html<https://emea01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fbioconductor.org%2Fpackages%2F3.7%2Fbioc%2Fhtml%2FcoMET.html&data=01%7C01%7Ctiphaine.martin%40kcl.ac.uk%7C9fe05e23fbf447e4da5b08d5a54beeeb%7C8370cf1416f34c16b83c724071654356%7C0&sdata=iAhqrnkMugGlE%2BjtdxndP16ZzQp%2FkWkajxc33hR6DgA%3D&reserved=0>

if I am looking the webpage, it seems that my build fails and I can install 
only the version 11.3. however, if i am looking at the different compilations, 
everything is ok for the version 11.5

http://bioconductor.org/checkResults/devel/bioc-LATEST/coMET/<https://emea01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fbioconductor.org%2FcheckResults%2Fdevel%2Fbioc-LATEST%2FcoMET%2F&data=01%7C01%7Ctiphaine.martin%40kcl.ac.uk%7C9fe05e23fbf447e4da5b08d5a54beeeb%7C8370cf1416f34c16b83c724071654356%7C0&sdata=AF%2BJi3SJQAgDo96Zy19uwsqoyJ267JMdTrEt1lbKmok%3D&reserved=0>


Could you tell me which I need to trust ?


Best,

Tiphaine


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[Bioc-devel] incompatibility between logo for build et the version and success of compilation

[Martin, Tiphaine]

Hi,


I updated the dev version of my package, 
http://bioconductor.org/packages/3.7/bioc/html/coMET.html

if I am looking the webpage, it seems that my build fails and I can install 
only the version 11.3. however, if i am looking at the different compilations, 
everything is ok for the version 11.5

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


Could you tell me which I need to trust ?


Best,

Tiphaine


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Re: [Bioc-devel] Questions about tokay2 and import 'grDevices::windows' versus 'IRanges::windows'

[Martin, Tiphaine]

thanks, I am going to do that.

Best,

Tiphaine


From: Martin Morgan 
Sent: 01 March 2018 20:56:10
To: Martin, Tiphaine; bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Questions about tokay2 and import 
'grDevices::windows' versus 'IRanges::windows'



On 03/01/2018 09:32 AM, Martin, Tiphaine wrote:
> hi,
>
>
> I have a warning under windows (tokay2) for my devel version of my package 
> (coMET). I am not sure how to answer it:
>
>
> * checking whether package 'coMET' can be installed ... WARNING
> Found the following significant warnings:
>Warning: replacing previous import 'grDevices::windows' by 
> 'IRanges::windows' when loading 'coMET'
> > I am not sure that IRanges::windows is equal to
>
> 'grDevices::windows'. I don't have this error message under linux or MacOS.

use

   import(grDevices, except = 'windows')

in the NAMESPACE file, or similar approaches to restrict the symbols
imported to those you  want. See


https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcran.r-project.org%2Fdoc%2Fmanuals%2Fr-devel%2FR-exts.html%23Specifying-imports-and-exports&data=01%7C01%7Ctiphaine.martin%40kcl.ac.uk%7C64a7531422854f01d6ba08d57fb6e710%7C8370cf1416f34c16b83c724071654356%7C0&sdata=EVDDGRdSFnlepjgy4SVzjrmKjH0yeTysAoMUQRi3MiA%3D&reserved=0

Martin

>
>
> I will be happy to have some advices about that.
>
> Best,
>
> tiphaine
>
>[[alternative HTML version deleted]]
>
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[Bioc-devel] Questions about tokay2 and import 'grDevices::windows' versus 'IRanges::windows'

[Martin, Tiphaine]

hi,


I have a warning under windows (tokay2) for my devel version of my package 
(coMET). I am not sure how to answer it:


* checking whether package 'coMET' can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import 'grDevices::windows' by 'IRanges::windows' 
when loading 'coMET'

I am not sure that IRanges::windows is equal to

'grDevices::windows'. I don't have this error message under linux or MacOS.


I will be happy to have some advices about that.

Best,

tiphaine

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[Bioc-devel] Update in BioMart/ENSEMBL alters coMET

[Martin, Tiphaine]

Hi,


Could you inform me which modification you did in biomaRt ? or in ENSEMBL ?

Indeed, I have my R package (coMET) use biomaRt to access to data. From the 
last update in BiomaRt (12/14/2017), I have a new error message.


Do you change the name of database associated with ENSEMBL ?


This is my error message

Unexpected format to the list of available marts.
Please check the following URL manually, and try ?listMarts for advice.
http://grch37.ensembl.org:80/biomart/martservice?type=registry&requestid=biomaRt

 When I look at the list of dataset, I have




however, previously, the database name was hsapiens_gene_ensembl.

Does it mean that you are going to change the name of database for each new 
release ?

How, I can have the name of databases from ENSEMBL stable between different 
releases of ENSEMBL


Regards,

Tiphaine



Tiphaine Martin
Research Associate | King's College
The Department of Twin Research & Genetic Epidemiology | Genetics & Molecular 
Medicine Division
St Thomas' Hospital
4th Floor, Block D, South Wing
SE1 7EH, London
United Kingdom

Bioinformatician | The University of Western Australia,
Endocrinology & Diabetes,
Sir Charles Gairdner Hospital.
School of Medicine & Pharmacology,
The University of Western Australia,
Nedlands, Western Australia 6009.

email : tiphaine.mar...@kcl.ac.uk
Fax: +44 (0) 207 188 6761

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Re: [Bioc-devel] Push to both Bioconductor and GitHub for coMET package

[Martin, Tiphaine]

Oh, sorry for that. 
It seems that I can push it.

Regards,
tiphaine

-Original Message-
From: Martin Morgan [mailto:martin.mor...@roswellpark.org] 
Sent: 30 October 2017 17:17
To: Martin, Tiphaine ; bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Push to both Bioconductor and GitHub for coMET package

Please try again now.

The form asked for your svn id, but you provided your github id.

Martin

On 10/30/2017 04:21 PM, Martin, Tiphaine wrote:
> 
> Hi,
> 
> 
> I tried to push my update to GitHub and Bioconductor.
> 
> I succeed to  create my fork in my GitHub Id following this page (Pull 
> upstream changes). I then updated and pushed on GitHub my update, but I 
> cannot for bioconductor when I follow recommandation on this page (Sync an 
> existing GitHub repository with Bioconductor)
> 
>I have this error message when I run
> 
> "git push upstream master"
> 
> 
> FATAL: W any packages/coMET TiphaineCMartin DENIED by fallthru (or you 
> mis-spelled the reponame)
> fatal: Could not read from remote repository.
> 
> Please make sure you have the correct access rights and the repository exists.
> 
> Could you help me ?
> 
> 
> regards.
> 
> tiphaine
> 
> ___
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> 


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[Bioc-devel] Push to both Bioconductor and GitHub for coMET package

[Martin, Tiphaine]

Hi,


I tried to push my update to GitHub and Bioconductor.

I succeed to  create my fork in my GitHub Id following this page (Pull upstream 
changes). I then updated and pushed on GitHub my update, but I cannot for 
bioconductor when I follow recommandation on this page (Sync an existing GitHub 
repository with Bioconductor)

  I have this error message when I run

"git push upstream master"


FATAL: W any packages/coMET TiphaineCMartin DENIED by fallthru (or you 
mis-spelled the reponame)
fatal: Could not read from remote repository.

Please make sure you have the correct access rights and the repository exists.

Could you help me ?


regards.

tiphaine

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[Bioc-devel] FW: Push to both Bioconductor and GitHub for coMET package

[Martin, Tiphaine]

Hi,


I tried to push my update to GitHub and Bioconductor.

I succeed to  create my fork in my GitHub Id following this page (Pull upstream 
changes). I then updated and pushed on GitHub my update, but I cannot for 
bioconductor when I follow recommandation on this page (Sync an existing GitHub 
repository with Bioconductor)

  I have this error message when I run

"git push upstream master"


FATAL: W any packages/coMET TiphaineCMartin DENIED by fallthru (or you 
mis-spelled the reponame)
fatal: Could not read from remote repository.

Please make sure you have the correct access rights and the repository exists.

Could you help me ?


regards.

tiphaine



Tiphaine Martin
Research associate | King's College
The Department of Twin Research & Genetic Epidemiology | Genetics & Molecular 
Medicine Division St Thomas' Hospital 4th Floor, Block D, South Wing
SE1 7EH, London
United Kingdom

Bioinformatician | The University of Western Australia, Endocrinology & 
Diabetes, Sir Charles Gairdner Hospital.
School of Medicine & Pharmacology,
The University of Western Australia,
Nedlands, Western Australia 6009.

email : tiphaine.mar...@kcl.ac.uk
Fax: +44 (0) 207 188 6761

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[Bioc-devel] Push to both Bioconductor and GitHub for coMET package

[Martin, Tiphaine]

Hi,


I tried to push my update to GitHub and Bioconductor.

I succeed to  create my fork in my GitHub Id following this page 
(http://bioconductor.org/developers/how-to/git/pull-upstream-changes/). I then 
updated and pushed on GitHub my update, but I cannot for bioconductor when I 
follow recommandation on this page 
https://bioconductor.org/developers/how-to/git/sync-existing-repositories/

  I have this error message when I run

"git push upstream master"


FATAL: W any packages/coMET TiphaineCMartin DENIED by fallthru (or you 
mis-spelled the reponame)
fatal: Could not read from remote repository.

Please make sure you have the correct access rights and the repository exists.

Could you help me ?


regards.

tiphaine



Tiphaine Martin
Research associate | King's College
The Department of Twin Research & Genetic Epidemiology | Genetics & Molecular 
Medicine Division St Thomas' Hospital 4th Floor, Block D, South Wing
SE1 7EH, London
United Kingdom

Bioinformatician | The University of Western Australia, Endocrinology & 
Diabetes, Sir Charles Gairdner Hospital.
School of Medicine & Pharmacology,
The University of Western Australia,
Nedlands, Western Australia 6009.

email : tiphaine.mar...@kcl.ac.uk
Fax: +44 (0) 207 188 6761

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[Bioc-devel] Push to both Bioconductor and GitHub for coMET package

[Martin, Tiphaine]

Hi,


I tried to push my update to GitHub and Bioconductor.

I succeed to  create my fork in my GitHub Id following this page 
(http://bioconductor.org/developers/how-to/git/pull-upstream-changes/). I then 
updated and pushed on GitHub my update, but I cannot for bioconductor when I 
follow recommandation on this page 
http://bioconductor.org/developers/how-to/git/sync-existing-repositories/

  I have this error message when I run

"git push upstream master"


FATAL: W any packages/coMET TiphaineCMartin DENIED by fallthru
(or you mis-spelled the reponame)
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.

Could you help me ?


regards.

tiphaine



Tiphaine Martin
Research associate | King's College
The Department of Twin Research & Genetic Epidemiology | Genetics & Molecular 
Medicine Division
St Thomas' Hospital
4th Floor, Block D, South Wing
SE1 7EH, London
United Kingdom

Bioinformatician | The University of Western Australia,
Endocrinology & Diabetes,
Sir Charles Gairdner Hospital.
School of Medicine & Pharmacology,
The University of Western Australia,
Nedlands, Western Australia 6009.

email : tiphaine.mar...@kcl.ac.uk
Fax: +44 (0) 207 188 6761

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Re: [Bioc-devel] Cannot update the release in svn

[Martin, Tiphaine]

Hi,

I tried to run only "git push" on my branch release-3.3, but I have an error 
message
Username for 'https://github.com': TiphaineCMartin
Password for 'https://tiphainecmar...@github.com':
remote: Permission to Bioconductor-mirror/coMET.git denied to TiphaineCMartin.
fatal: unable to access 'https://github.com/Bioconductor-mirror/coMET.git/': 
The requested URL returned error: 403

So I don't know how to propagate my update done in the release-3.3 of 
bioconductor to my fork. If you have an idea, I will be happy to try.

Regards,
Tiphaine


From: Dan Tenenbaum 
Sent: 05 June 2016 04:42:54
To: Martin, Tiphaine
Cc: bioc-devel; Jim Hester
Subject: Re: [Bioc-devel] Cannot update the release in svn

- Original Message -
> From: "Tiphaine Martin" 
> To: "Dan Tenenbaum" 
> Cc: "bioc-devel" 
> Sent: Thursday, June 2, 2016 2:28:44 PM
> Subject: Re: [Bioc-devel] Cannot update the release in svn

> Sorry to answer only now, but I was busy to finish a paper in time.
>
> So I did it as you said and everything goes well.
> and the function "git svn dcommit --add-author-from"
> finished by
> "...
>   M   R/AnalyseFile.R
> r118127 = 3f9d47140ab77cf30381c5afa24007967ce3a615
> (refs/remotes/git-svn-release-3.3)
> No changes between 7019708a1dcfbe8759b8107fcb20823167d43c08 and
> refs/remotes/git-svn-release-3.3
> Resetting to the latest refs/remotes/git-svn-release-3.3
> "
> So I did then 2 last commands
> git checkout  version-1.4.3_release-3.3
> git merge  release-3.3
>
> But I didn't see modification on my fork of gitHub and when I go back to
> "release-3.3" (I run git checkout release-3.3), I have this message
> Switched to branch 'release-3.3'
> Your branch is ahead of 'bioc/release-3.3' by 7 commits.
>  (use "git push" to publish your local commits)
>
> Should I push them on the remote or something else ?

I think (and Jim (cc'd) can correct me if I am wrong)) that you can just say 
"git push" and the push will go to your own repository's 'release-3.3' branch.

git may tell you that there is no upstream branch and you can just paste the 
command that it suggests in order to fix this.

Dan



> Thanks
>
> Tiphaine
>
> 
> Tiphaine Martin
> PhD Research Student | King's College
> The Department of Twin Research & Genetic Epidemiology | Genetics & Molecular
> Medicine Division
> St Thomas' Hospital
> 4th Floor, Block D, South Wing
> SE1 7EH, London
> United Kingdom
>
> email : tiphaine.mar...@kcl.ac.uk
> Fax: +44 (0) 207 188 6761
>
> 
> From: Dan Tenenbaum 
> Sent: 30 May 2016 02:36
> To: Martin, Tiphaine
> Cc: bioc-devel
> Subject: Re: [Bioc-devel] Cannot update the release in svn
>
> - Original Message -
>> From: "Tiphaine Martin" 
>> To: "bioc-devel" 
>> Sent: Sunday, May 29, 2016 2:54:20 PM
>> Subject: [Bioc-devel] Cannot update the release in svn
>
>> Hi,
>>
>>
>> I cleaned my gitHub repository to have now the repository coMET in my gitHub 
>> as
>> the fork of coMET from bioconductor.
>>
>> I followed the directive from
>> http://bioconductor.org/developers/how-to/git-mirrors/
>>
>> as I need to correct bug in the current release
>>
>>
>> but when I try to run
>>
>>  1.  git svn rebase to get the latest SVN changes.
>>
>> I have an error message
>>
>>
>> git svn rebase
>>
>> Authentication realm: <https://hedgehog.fhcrc.org:443> The bioconductor
>> Subversion Repository
>>
>> Password for 'tiphaine':
>>
>> Can't create session: Unable to connect to a repository at URL
>> 'https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/coMET':
>> Unexpected server error 500 'Internal Server Error' on
>> '/bioconductor/branches/RELEASE_3_3/madman/Rpacks/coMET' at
>> /usr/share/perl5/Git/SVN.pm line 712.
>>
>>
>> So I cannot push my update in SVN.
>>
>>
>> Can you tell me if the bug is still on my side or on the side of svn of
>> bioconductor? and what I need to do to push my update.
>>
>
> "git svn" relies on svn's authentication mechanisms. So svn has to already 
> know
> about your credentials.
>
> Also, note that your svn username is 't.martin', not 'tiphaine' (which I guess
> is the username that you are logged into your computer as).
>

Re: [Bioc-devel] fail to load GenomicRanges

[Martin, Tiphaine]

Oups, sorry, yes in the release build report
 I missed this post.
Ok, I will see for the next build.

Regards,
Tiphaine


From: Martin Morgan 
Sent: 04 June 2016 16:38:01
To: Martin, Tiphaine; bioc-devel
Subject: Re: [Bioc-devel] fail to load GenomicRanges

Do you mean in the release build report?

http://bioconductor.org/checkResults/3.3/bioc-LATEST/

Did you see this?

https://stat.ethz.ch/pipermail/bioc-devel/2016-June/009338.html

? If you mean on your own installation, what happens when trying to
install zlibbioc in the normal way

   biocLite("zlibbioc")

? Please provide more detail in your posts, so it is easier to
understand what you are trying to tell us.

Martin


On 06/04/2016 11:30 AM, Martin, Tiphaine wrote:
> Hi,
>
> it seems that it missed a library in windows "zlibbioc" for GenomicRanges
>
> ** preparing package for lazy loading
> Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) :
>there is no package called 'zlibbioc'
> Error : package 'GenomicRanges' could not be loaded
> ERROR: lazy loading failed for package 'coMET'
>
> Regards,
>
>
> Tiphaine
>
>
> 
> Tiphaine Martin
> PhD Research Student | King's College
> The Department of Twin Research & Genetic Epidemiology | Genetics & Molecular 
> Medicine Division
> St Thomas' Hospital
> 4th Floor, Block D, South Wing
> SE1 7EH, London
> United Kingdom
>
> email : tiphaine.mar...@kcl.ac.uk
> Fax: +44 (0) 207 188 6761
>
>   [[alternative HTML version deleted]]
>
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> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>


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[Bioc-devel] fail to load GenomicRanges

[Martin, Tiphaine]

Hi,

it seems that it missed a library in windows "zlibbioc" for GenomicRanges

** preparing package for lazy loading
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) :
  there is no package called 'zlibbioc'
Error : package 'GenomicRanges' could not be loaded
ERROR: lazy loading failed for package 'coMET'

Regards,


Tiphaine



Tiphaine Martin
PhD Research Student | King's College
The Department of Twin Research & Genetic Epidemiology | Genetics & Molecular 
Medicine Division
St Thomas' Hospital
4th Floor, Block D, South Wing
SE1 7EH, London
United Kingdom

email : tiphaine.mar...@kcl.ac.uk
Fax: +44 (0) 207 188 6761

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Re: [Bioc-devel] Cannot update the release in svn

[Martin, Tiphaine]

Sorry to answer only now, but I was busy to finish a paper in time.

So I did it as you said and everything goes well. 
and the function "git svn dcommit --add-author-from"
finished by
"... 
M   R/AnalyseFile.R
r118127 = 3f9d47140ab77cf30381c5afa24007967ce3a615 
(refs/remotes/git-svn-release-3.3)
No changes between 7019708a1dcfbe8759b8107fcb20823167d43c08 and 
refs/remotes/git-svn-release-3.3
Resetting to the latest refs/remotes/git-svn-release-3.3
"
So I did then 2 last commands
git checkout  version-1.4.3_release-3.3
git merge  release-3.3

But I didn't see modification on my fork of gitHub and when I go back to 
"release-3.3" (I run git checkout release-3.3), I have this message
Switched to branch 'release-3.3'
Your branch is ahead of 'bioc/release-3.3' by 7 commits.
  (use "git push" to publish your local commits)

Should I push them on the remote or something else ?
Thanks

Tiphaine


Tiphaine Martin
PhD Research Student | King's College
The Department of Twin Research & Genetic Epidemiology | Genetics & Molecular 
Medicine Division
St Thomas' Hospital
4th Floor, Block D, South Wing
SE1 7EH, London
United Kingdom

email : tiphaine.mar...@kcl.ac.uk
Fax: +44 (0) 207 188 6761

________
From: Dan Tenenbaum 
Sent: 30 May 2016 02:36
To: Martin, Tiphaine
Cc: bioc-devel
Subject: Re: [Bioc-devel] Cannot update the release in svn

- Original Message -
> From: "Tiphaine Martin" 
> To: "bioc-devel" 
> Sent: Sunday, May 29, 2016 2:54:20 PM
> Subject: [Bioc-devel] Cannot update the release in svn

> Hi,
>
>
> I cleaned my gitHub repository to have now the repository coMET in my gitHub 
> as
> the fork of coMET from bioconductor.
>
> I followed the directive from
> http://bioconductor.org/developers/how-to/git-mirrors/
>
> as I need to correct bug in the current release
>
>
> but when I try to run
>
>  1.  git svn rebase to get the latest SVN changes.
>
> I have an error message
>
>
> git svn rebase
>
> Authentication realm: <https://hedgehog.fhcrc.org:443> The bioconductor
> Subversion Repository
>
> Password for 'tiphaine':
>
> Can't create session: Unable to connect to a repository at URL
> 'https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/coMET':
> Unexpected server error 500 'Internal Server Error' on
> '/bioconductor/branches/RELEASE_3_3/madman/Rpacks/coMET' at
> /usr/share/perl5/Git/SVN.pm line 712.
>
>
> So I cannot push my update in SVN.
>
>
> Can you tell me if the bug is still on my side or on the side of svn of
> bioconductor? and what I need to do to push my update.
>

"git svn" relies on svn's authentication mechanisms. So svn has to already know 
about your credentials.

Also, note that your svn username is 't.martin', not 'tiphaine' (which I guess 
is the username that you are logged into your computer as).

So you need to let svn know about your credentials, so do something like this:

svn log --limit 1 --username t.martin 
https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/coMET

This will prompt for your svn password and might also ask you if it is ok to 
store your credentials on your computer in cleartext. You should answer 'y' to 
the questions it asks you.

After doing this you should be able to successfully run the 'git svn rebase' 
command.

Dan


>
> Regards,
>
> Tiphaine
>
>
>
> 
> Tiphaine Martin
> PhD Research Student | King's College
> The Department of Twin Research & Genetic Epidemiology | Genetics & Molecular
> Medicine Division
> St Thomas' Hospital
> 4th Floor, Block D, South Wing
> SE1 7EH, London
> United Kingdom
>
> email : tiphaine.mar...@kcl.ac.uk
> Fax: +44 (0) 207 188 6761
>
>   [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

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[Bioc-devel] Cannot update the release in svn

[Martin, Tiphaine]

Hi,


I cleaned my gitHub repository to have now the repository coMET in my gitHub as 
the fork of coMET from bioconductor.

I followed the directive from 
http://bioconductor.org/developers/how-to/git-mirrors/

as I need to correct bug in the current release


but when I try to run

  1.  git svn rebase to get the latest SVN changes.

I have an error message


git svn rebase

Authentication realm:  The bioconductor 
Subversion Repository

Password for 'tiphaine':

Can't create session: Unable to connect to a repository at URL 
'https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/coMET':
 Unexpected server error 500 'Internal Server Error' on 
'/bioconductor/branches/RELEASE_3_3/madman/Rpacks/coMET' at 
/usr/share/perl5/Git/SVN.pm line 712.


So I cannot push my update in SVN.


Can you tell me if the bug is still on my side or on the side of svn of 
bioconductor? and what I need to do to push my update.


Regards,

Tiphaine




Tiphaine Martin
PhD Research Student | King's College
The Department of Twin Research & Genetic Epidemiology | Genetics & Molecular 
Medicine Division
St Thomas' Hospital
4th Floor, Block D, South Wing
SE1 7EH, London
United Kingdom

email : tiphaine.mar...@kcl.ac.uk
Fax: +44 (0) 207 188 6761

[[alternative HTML version deleted]]

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Re: [Bioc-devel] package build failing in Windows with "Failed to locate the 'texi2pdf' output file"

[Martin, Tiphaine]

Hi, 
I have the same issue build failing in Windows and Mac for the release version, 
but not for devel version that are similar as I didn't do some update from the 
last release.

I did some update on my GitHub recently and I tried to follow different advice 
to push my update to SVN of Bioconductor. I have the same error that I want to 
update any branch when I run "git svn dcommit --add-author-from".

 Unable to determine upstream SVN information from HEAD history.
 Perhaps the repository is empty. at /usr/lib/git-core/git-svn line 866.

Beforehand, I used git-svn bridge that could be the origin of issue, but I 
don't know how to handle because I tried to cherry-pick, it told me that I have 
empty pick.

  When I did Sunday, it creates a request for a pull on  
https://github.com/Bioconductor-mirror/coMET. This request is not more here and 
no of my branch are updated.

I don't know what to do. If one of you have any advice, I am happy to try it.

Regards,
Tiphaine


Tiphaine Martin
PhD Research Student | King's College
The Department of Twin Research & Genetic Epidemiology | Genetics & Molecular 
Medicine Division
St Thomas' Hospital
4th Floor, Block D, South Wing
SE1 7EH, London
United Kingdom

email : tiphaine.mar...@kcl.ac.uk
Fax: +44 (0) 207 188 6761


From: Bioc-devel  on behalf of Ramon 
Diaz-Uriarte 
Sent: 29 March 2016 09:34
To: bioc-devel@r-project.org
Cc: ramon.d...@iib.uam.es
Subject: [Bioc-devel] package build failing in Windows with "Failed to  locate 
the 'texi2pdf' output file"

Dear All,

I have a package, ADaCGH2, that I just noticed has failed to build in
Windows in the latest report
(https://www.bioconductor.org/checkResults/devel/bioc-LATEST/ADaCGH2/moscato2-buildsrc.html).
 The
error is the dreaded

Error in find_vignette_product(name, by = "texi2pdf", engine = engine) :
  Failed to locate the 'texi2pdf' output file (by engine 'utils::Sweave')
  for vignette


But I just run the build and check three times on a local windows machine
(with 3.3.0 alpha, r70387) and build and check are fine. Moreover, this
package has not changed at all in a long time, so I do not understand why
it should be failing now when it was not failing in previous reports
(though I am not sure when it first started failing) and there is, in fact,
a Windows binary for this version from the BioC page
(https://www.bioconductor.org/packages/3.3/bioc/html/ADaCGH2.html).

I am not sure how to proceed.

Best,

R.

--
Ramon Diaz-Uriarte
Department of Biochemistry, Lab B-25
Facultad de Medicina
Universidad Autónoma de Madrid
Arzobispo Morcillo, 4
28029 Madrid
Spain

Phone: +34-91-497-2412

Email: rdia...@gmail.com
   ramon.d...@iib.uam.es

http://ligarto.org/rdiaz

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Re: [Bioc-devel] BioC 3.1 branch created

[Martin, Tiphaine]

Hi Kevin,

Thanks,
I will try it later and check whether I have still this issue to connect it.

Tiphaine

From: Kevin Rue-Albrecht 
mailto:kevin@ucdconnect.ie>>
Date: Friday, 17 April 2015 11:30
To: Tiphaine Martin 
mailto:tiphaine.mar...@kcl.ac.uk>>
Cc: Dan Tenenbaum mailto:dtene...@fredhutch.org>>, 
bioc-devel mailto:bioc-devel@r-project.org>>
Subject: Re: [Bioc-devel] BioC 3.1 branch created

Hi Tiphaine,

I have followed both of your links,. and they both work for me. Probably just a 
glitch in the connection ?

Hi Dan,

I have a quick question of my own,
I would like to bridge the new release branch to my Github "release" 
repository, but:

  *   In the dropdown of the bridge creation, release 3.0 is still listed. I 
supposed I should wait that 3.1 is listed there, to create the good bridge?
  *   I had a GitHub repository bridged to the 3.0 release branch. Is it ok to 
use the same GitHub repository, and use "SVN wins" during the bridge creation? 
That should update GitHub with the new release code, right?

Many thanks,
Kevin

On 17 April 2015 at 11:43, Martin, Tiphaine 
mailto:tiphaine.mar...@kcl.ac.uk>> wrote:
Hi Dan,

When I try to access on my package, I have �Internal Server Error�. Maybe
I make a mistake somewhere.

https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/
coMET
https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/coMET

Regards,
Tiphaine

On 17/04/2015 05:44, "Dan Tenenbaum" 
mailto:dtene...@fredhutch.org>> wrote:

>
>
>- Original Message -
>> From: "Henrik Bengtsson" 
>> mailto:henrik.bengts...@ucsf.edu>>
>> To: "Dan Tenenbaum" mailto:dtene...@fredhutch.org>>
>> Cc: "bioc-devel" mailto:bioc-devel@r-project.org>>
>> Sent: Thursday, April 16, 2015 6:57:45 PM
>> Subject: Re: [Bioc-devel] BioC 3.1 branch created
>>
>> On Thu, Apr 16, 2015 at 1:23 PM, Dan Tenenbaum
>> mailto:dtene...@fredhutch.org>> wrote:
>> > The BioC 3.1 branch is now ready.
>> >
>> > Remember, you always have access to 2 versions of your package:
>> > the "release" and the "devel" versions.
>> >
>> > Right now the "release" version of your package (which is not
>> > officially released yet but will be tomorrow if
>> > everything goes well) is in the 3.1 branch and accessible at:
>> >
>> >
>>https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpack
>>s/
>> >
>> > Only bug fixes and documentation improvements should go here.
>> >
>> > As always the "devel" version of your package is at:
>> >
>> >  https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/
>> >
>> > Similarly for experiment packages, where your package is available
>> > in devel at
>> >
>> > https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/
>> >
>> > The release branch of it is in:
>> >
>> >
>>https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_3_1/experiment/pkgs
>>/
>> >
>> >
>> > Normal development of your package can now resume here.
>> >
>> > Please let us know if you have any questions.
>>
>> Was the wrong version bump done for the GitHub-SVN bridges, because
>> the 'bioc-sync' commits show release version numbers and not devel
>> ones?!
>>
>
>Not the wrong version bump, but it seems like the second one didn't come
>through.
>
>Should be sorted now. Sorry for the inconvenience.
>
>Dan
>
>
>
>> For instance, the aroma.light GitHub repository (master branch),
>> which
>> should reflect the Bioc devel version, 'bioc-sync' made a commit
>> bumping the version from 1.39.5 to 1.40.0.  Note that this version is
>> the version for the Bioc release - not Bioc devel.  I would expect it
>> to be a bump to 1.41.0. Details:
>>
>>
>>https://github.com/HenrikBengtsson/affxparser/commit/ef10d93df696d018de3e
>>426bc6c2c1b8256a9b06
>> (1.40.0)
>>
>>https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpack
>>s/affxparser/DESCRIPTION
>> (1.40.0)
>>
>>https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/affxparser/DE
>>SCRIPTION
>> (1.41.0)
>>
>> I've verified that the bridge is still to the Bioc devel SVN
>> (trunk/madman), because when I tweaked the Date in DESCRIPTION (with
>> the wrong Version field) and pushed to GitHub, that was reflected on
>> Bioc devel SVN  (trunk/madman).
>>
>> I see the same for aroma.light

Re: [Bioc-devel] BioC 3.1 branch created

[Martin, Tiphaine]

Hi Dan,

When I try to access on my package, I have ³Internal Server Error². Maybe
I make a mistake somewhere.

https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/
coMET
https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/coMET

Regards,
Tiphaine

On 17/04/2015 05:44, "Dan Tenenbaum"  wrote:

>
>
>- Original Message -
>> From: "Henrik Bengtsson" 
>> To: "Dan Tenenbaum" 
>> Cc: "bioc-devel" 
>> Sent: Thursday, April 16, 2015 6:57:45 PM
>> Subject: Re: [Bioc-devel] BioC 3.1 branch created
>> 
>> On Thu, Apr 16, 2015 at 1:23 PM, Dan Tenenbaum
>>  wrote:
>> > The BioC 3.1 branch is now ready.
>> >
>> > Remember, you always have access to 2 versions of your package:
>> > the "release" and the "devel" versions.
>> >
>> > Right now the "release" version of your package (which is not
>> > officially released yet but will be tomorrow if
>> > everything goes well) is in the 3.1 branch and accessible at:
>> >
>> > 
>>https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpack
>>s/
>> >
>> > Only bug fixes and documentation improvements should go here.
>> >
>> > As always the "devel" version of your package is at:
>> >
>> >  https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/
>> >
>> > Similarly for experiment packages, where your package is available
>> > in devel at
>> >
>> > https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/
>> >
>> > The release branch of it is in:
>> >
>> > 
>>https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_3_1/experiment/pkgs
>>/
>> >
>> >
>> > Normal development of your package can now resume here.
>> >
>> > Please let us know if you have any questions.
>> 
>> Was the wrong version bump done for the GitHub-SVN bridges, because
>> the 'bioc-sync' commits show release version numbers and not devel
>> ones?!
>> 
>
>Not the wrong version bump, but it seems like the second one didn't come
>through. 
>
>Should be sorted now. Sorry for the inconvenience.
>
>Dan
>
>
>
>> For instance, the aroma.light GitHub repository (master branch),
>> which
>> should reflect the Bioc devel version, 'bioc-sync' made a commit
>> bumping the version from 1.39.5 to 1.40.0.  Note that this version is
>> the version for the Bioc release - not Bioc devel.  I would expect it
>> to be a bump to 1.41.0. Details:
>> 
>> 
>>https://github.com/HenrikBengtsson/affxparser/commit/ef10d93df696d018de3e
>>426bc6c2c1b8256a9b06
>> (1.40.0)
>> 
>>https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpack
>>s/affxparser/DESCRIPTION
>> (1.40.0)
>> 
>>https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/affxparser/DE
>>SCRIPTION
>> (1.41.0)
>> 
>> I've verified that the bridge is still to the Bioc devel SVN
>> (trunk/madman), because when I tweaked the Date in DESCRIPTION (with
>> the wrong Version field) and pushed to GitHub, that was reflected on
>> Bioc devel SVN  (trunk/madman).
>> 
>> I see the same for aroma.light as well:
>> 
>> 
>>https://github.com/HenrikBengtsson/aroma.light/commit/64b2bbef5b81baebc5d
>>a548110a0bf1c25d208e2
>> (2.4.0)
>> 
>>https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpack
>>s/aroma.light/DESCRIPTION
>> (2.4.0)
>> 
>>https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/aroma.light/D
>>ESCRIPTION
>> (2.5.0)
>> 
>> Holding back with pushes via GitHub until I resolved. Let me know if
>> this is a FAQ.
>> 
>> Thanks,
>> 
>> Henrik
>> 
>> >
>> >
>> > Thanks!
>> >
>> > Dan
>> >
>> > ___
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>> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
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Re: [Bioc-devel] Warning message: multiple methods tables found for ‘score’

[Martin, Tiphaine]

I will commit my fix to coMET and cross fingers that the error doesn't appear 
in the build system

Tiphaine

From: Hervé Pagès 
Sent: 10 April 2015 20:30
To: Michael Lawrence; Martin, Tiphaine
Cc: bioc-devel
Subject: Re: [Bioc-devel] Warning message: multiple methods tables found for 
‘score’

On 04/10/2015 11:45 AM, Michael Lawrence wrote:
> The score generic was removed from IRanges in version 2.1.41. So your
> IRanges is up to date. My guess is that something is cached and you need
> to reinstall one or more of the other Bioc infrastructure packages...

That's a good point.

In any case, this should not prevent you from committing your fix to
coMET. The issue is specific to the state of your current installation
and it won't show up on the build system (where all dependencies are
re-installed every day at the beginning of the builds).

Also, for you, the issue will automatically go away when all package
versions get bumped the day of the release.

Cheers,
H.

>
> On Fri, Apr 10, 2015 at 11:35 AM, Martin, Tiphaine
> mailto:tiphaine.mar...@kcl.ac.uk>> wrote:
>
> Hi Herve,
>
> When I tried to update IRanges, I have only the version 2.1.43 and
> not 2.1.44.
> How to force BiocLite to have the lastest version of IRanges. did I
> miss something?
>
> source("http://bioconductor.org/biocLite.R";)
> Bioconductor version 3.1 (BiocInstaller 1.17.7), ?biocLite for help
> biocLite("IRanges")
> BioC_mirror: http://bioconductor.org
> Using Bioconductor version 3.1 (BiocInstaller 1.17.7), R version 3.2.0.
> Installing package(s) ‘IRanges’
> trying URL
> 
> 'http://bioconductor.org/packages/3.1/bioc/src/contrib/IRanges_2.1.43.tar.gz'
>
>
> Tiphaine
>
> ________
> From: Hervé Pagès mailto:hpa...@fredhutch.org>>
> Sent: 10 April 2015 19:20
> To: Martin, Tiphaine; bioc-devel
>     Subject: Re: [Bioc-devel] Warning message: multiple methods tables
> found for ‘score’
>
> Hi Martin,
>
> On 04/10/2015 11:12 AM, Martin, Tiphaine wrote:
>  > Dear Everybody,
>  >
>  >
>  > I updated my package because I have an error message. Before
> submitting my package on svn, I run
>  >
>  > R CMD check coMET
>  >
>  > I receive a new error message:
>  >
>  >
>  > Warning message:
>  > multiple methods tables found for �score�
>  >
>  >
>  > If I am looking at the reference manual of IRanges, I see that
> there is the function "score" and before updating, when I run
> ?score, the function "score" belonged to the package IRanges
>  >
>  > But now when I run ?score,  the function "score" belongs to the
> package:BiocGenerics.
>  >
>  >
>  > I am wondering if there is an conflict between two packages. How
> can I manage it?
>
> AFAIK there is no conflict. Your IRanges version is probably lagging
> behind. Remember to keep your installation up-to-date by running
> biocLite() (with no arguments) on a regular basis.
>
>  >
>  > How can I know which packages have the function "score"?
>
> Only the BiocGenerics package now defines the score() generic. There is
> no score() generic in the latest IRanges (2.1.44).
>
> Thanks for taking care of coMET.
>
> H.
>
>  >
>  >
>  > Thanks,
>  >
>  > Tiphaine
>  >
>  >
>  > 
>  > Tiphaine Martin
>  > PhD Research Student | King's College
>  > The Department of Twin Research & Genetic Epidemiology | Genetics
> & Molecular Medicine Division
>  > St Thomas' Hospital
>  > 4th Floor, Block D, South Wing
>  > SE1 7EH, London
>  > United Kingdom
>  >
>  > email : tiphaine.mar...@kcl.ac.uk <mailto:tiphaine.mar...@kcl.ac.uk>
>  > Fax: +44 (0) 207 188 6761 
>  >
>  >   [[alternative HTML version deleted]]
>  >
>  >
>  >
>  > ___
>  > Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org>
> mailing list
>  > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>  >
>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairvie

Re: [Bioc-devel] Warning message: multiple methods tables found for ‘score’

[Martin, Tiphaine]

Ok, thanks. I have just updated all package and run Martin's command line 
"BiocInstaller::biocValid() ". Everything was updated,


 I run a new session of R and load only Gviz package, Gviz finish with the same 
error messages and,  for example, impossible to create the plot GC content .


How to find the packages with the function "score", because when I do 
??"score", I found only in BiocGenerics package the function "score". So I 
don't know how to correct that.


If you have any advice, i'm all ears


Thanks,

Tiphaine


library("Gviz")

to <- 65980988

from <- 65921878

gcContent1 <- UcscTrack(genome = "mm9", chromosome = "chrX",
 track = "GC Percent", table = "gc5Base", from = from ,
 to = to, trackType = "DataTrack", start = "start",
 end = "end", data = "score", type = "hist", window = -1,
 windowSize = 1500, fill.histogram = "black",
 col.histogram = "black", ylim = c(30, 70), name = "GC Percent")


plotTracks(gcContent1,from= start, to=end)


sessionInfo()

R Under development (unstable) (2014-12-17 r67184)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_GB.UTF-8   LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_GB.UTF-8
 [5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_GB.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] grid  parallel  stats4stats graphics  grDevices utils
 [8] datasets  methods   base

other attached packages:
[1] Gviz_1.11.15  GenomicRanges_1.19.52 GenomeInfoDb_1.3.18
[4] IRanges_2.1.44S4Vectors_0.5.23  BiocGenerics_0.13.11

loaded via a namespace (and not attached):
 [1] acepack_1.3-3.3   AnnotationDbi_1.29.23
 [3] Biobase_2.27.3BiocParallel_1.1.27
 [5] biomaRt_2.23.5Biostrings_2.35.12
 [7] biovizBase_1.15.4 bitops_1.0-6
 [9] BSgenome_1.35.20  cluster_2.0.1
[11] colorspace_1.2-6  DBI_0.3.1
[13] dichromat_2.0-0   digest_0.6.8
[15] foreign_0.8-63Formula_1.2-1
[17] futile.logger_1.4 futile.options_1.0.0
[19] GenomicAlignments_1.3.34  GenomicFeatures_1.19.37
[21] ggplot2_1.0.1 gtable_0.1.2
[23] Hmisc_3.15-0  lambda.r_1.1.7
[25] lattice_0.20-31   latticeExtra_0.6-26
[27] MASS_7.3-40   matrixStats_0.14.0
[29] munsell_0.4.2 nnet_7.3-9
[31] plyr_1.8.1proto_0.3-10
[33] RColorBrewer_1.1-2Rcpp_0.11.5
[35] RCurl_1.95-4.5reshape2_1.4.1
[37] rpart_4.1-9   Rsamtools_1.19.52
[39] RSQLite_1.0.0 rtracklayer_1.27.12
[41] scales_0.2.4  splines_3.2.0
[43] stringr_0.6.2 survival_2.38-1
[45] tools_3.2.0       VariantAnnotation_1.13.48
[47] XML_3.98-1.1  XVector_0.7.4
[49] zlibbioc_1.13.3





From: Michael Lawrence 
Sent: 10 April 2015 19:45
To: Martin, Tiphaine
Cc: Herv� Pag�s; bioc-devel
Subject: Re: [Bioc-devel] Warning message: multiple methods tables found for 
�score�

The score generic was removed from IRanges in version 2.1.41. So your IRanges 
is up to date. My guess is that something is cached and you need to reinstall 
one or more of the other Bioc infrastructure packages...

On Fri, Apr 10, 2015 at 11:35 AM, Martin, Tiphaine 
mailto:tiphaine.mar...@kcl.ac.uk>> wrote:
Hi Herve,

When I tried to update IRanges, I have only the version 2.1.43 and not 2.1.44.
How to force BiocLite to have the lastest version of IRanges. did I miss 
something?

source("http://bioconductor.org/biocLite.R";)
Bioconductor version 3.1 (BiocInstaller 1.17.7), ?biocLite for help
biocLite("IRanges")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.1 (BiocInstaller 1.17.7), R version 3.2.0.
Installing package(s) �IRanges�
trying URL 
'http://bioconductor.org/packages/3.1/bioc/src/contrib/IRanges_2.1.43.tar.gz'


Tiphaine


From: Herv� Pag�s mailto:hpa...@fredhutch.org>>
Sent: 10 April 2015 19:20
To: Martin, Tiphaine; bioc-devel
Subject: Re: [Bioc-devel] Warning message: multiple methods tables found for 
�score�

Hi Martin,

On 04/10/2015 11:12 AM, Martin, Tiphaine wrote:
> Dear Everybody,
>
>
> I updated my package because I have an error message. Before submitting my 
> package on svn, I run
>
> R CMD check coMET
>
> I receive a new error message:
>
>
> Warning message:
> multiple methods tables found for ?score?
>
>
> If I am looking at the reference manual of IRanges, I see that there is the 
> function "score" and before updating, when I run ?score, the function "score" 
> belon

[Bioc-devel] New package: coMET

[Martin, Tiphaine]

Hi all,

I'm pleased to announce the availability of the coMET package 
(http://bioconductor.org/packages/devel/bioc/html/coMET.html , 
https://github.com/TiphaineCMartin/coMET), which visualises regional 
epigenome-wide association scan (EWAS) results and DNA co-methylation patterns. 
The R package is designed for human epigenetic data, but can also be applied to 
genomic and functional genomic datasets in any species such as gene expression.

coMET exists also in a Shiny-based web application 
(http://www.epigen.kcl.ac.uk/comet), which allows users to run a pre-formated 
version (currently only for human genome).
It is possible also to extract the correlations between omic features with 
their pvalues.

Please let me know of any issues you encounter.

Thanks,
Tiphaine Martin


Tiphaine Martin  I   PhD Student   I  TwinsUK

Department of Twin Research, Kings College London,

St Thomas' Hospital Campus, 3rd Floor South Wing Block D

Westminster Bridge Road, London SE1 7EH, UK



Email : tiphaine.mar...@kcl.ac.uk<mailto:tiphaine.mar...@kcl.ac.uk>

Direct: +44 (0) 207 188 1508

Fax: +44 (0) 207 188 6761


London Microbiome Meeting, 28th of May 2015: http://londonmicrobiome.org/

Mathematical and Quantitative Genomics conference, 29th of May: 
http://quantgen.soc.srcf.net/qg15/

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Re: [Bioc-devel] Bioconductor 3.1 release schedule now available

[Martin, Tiphaine]

Thank Kasper and Dan for your explanations.
Yes, it will be the first release of my package that has currently a
version number of 0.99.9

Regards,

Tiphaine

On 17/03/2015 02:34, "Dan Tenenbaum"  wrote:

>
>
>- Original Message -
>> From: "Kasper Daniel Hansen" 
>> To: "Tiphaine Martin" 
>> Cc: "Dan Tenenbaum" , "bioc-devel"
>>
>> Sent: Monday, March 16, 2015 6:43:40 PM
>> Subject: Re: [Bioc-devel] Bioconductor 3.1 release schedule now
>>available
>> 
>> 
>> If your package passes build and check without warnings it happens
>> automatically, including the version bump.
>> 
>
>Yes, the only time you need to let us know is if you DO NOT want your
>package in the release.
>
>> 
>> If this is the first release of your package, it should have a
>> version number of 0.99.Z (which seems to be the case). This is
>> checked / fixed when your package gets accepted.
>> 
>
>Actually it's done during the release process. So your package will
>remain at 0.99.z until the release but then in the new release branch it
>will be 1.0.0 and in the new devel (trunk) it will be 1.1.0. See
>http://bioconductor.org/developers/how-to/version-numbering/
>
>Dan
>
>
>> 
>> Best,
>> Kasper
>> 
>> 
>> On Mon, Mar 16, 2015 at 9:29 PM, Martin, Tiphaine <
>> tiphaine.mar...@kcl.ac.uk > wrote:
>> 
>> 
>> Dear Dan,
>> 
>> I have 2 naive questions.
>> I would like to know whether we (developers of a R package currently
>> only in the development version of Bioconductor) need to say that we
>> would like to have our packages accessible in the next version of
>> Bioconductor or it is automatic for any packages passing R CMD build
>> and check without warning.
>> If I have my new package that is going in the next release, should I
>> need to upgrade the version of my package ( from 0.99.Z to 1.0.0 )
>> and push it in svn or is it also done automatically ?
>> 
>> Regards,
>> 
>> Tiphaine
>> 
>> 
>> From: Bioc-devel < bioc-devel-boun...@r-project.org > on behalf of
>> Dan Tenenbaum < dtene...@fredhutch.org >
>> Sent: 27 February 2015 18:14
>> To: bioc-devel
>> Subject: Re: [Bioc-devel] Bioconductor 3.1 release schedule now
>> available
>> 
>> 
>> 
>> - Original Message -
>> > From: "Dan Tenenbaum" < dtene...@fredhutch.org >
>> > To: "bioc-devel" < bioc-devel@r-project.org >
>> > Sent: Friday, February 27, 2015 10:12:44 AM
>> > Subject: [Bioc-devel] Bioconductor 3.1 release schedule now
>> > available
>> > 
>> > Hi all,
>> > 
>> > The next version of Bioconductor will be 3.0 and its release
>> > schedule
>> > is now up on our website:
>> > 
>> 
>> 3.1 of course! Sorry for the typo.
>> Dan
>> 
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> 
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> 
>> 

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Re: [Bioc-devel] Bioconductor 3.1 release schedule now available

[Martin, Tiphaine]

Dear Dan,

I have 2 naive questions.
I would like to know whether we (developers of a R package currently only in 
the development version of Bioconductor) need to say that we would like to have 
our packages accessible in the next version of Bioconductor or it is automatic 
for any packages passing R CMD build and check without warning.
If I have my new package that is going in the next release, should I need to 
upgrade the version of my package ( from 0.99.Z to 1.0.0 ) and push it in svn 
or is it also done automatically ?

Regards,

Tiphaine


From: Bioc-devel  on behalf of Dan Tenenbaum 

Sent: 27 February 2015 18:14
To: bioc-devel
Subject: Re: [Bioc-devel] Bioconductor 3.1 release schedule now available

- Original Message -
> From: "Dan Tenenbaum" 
> To: "bioc-devel" 
> Sent: Friday, February 27, 2015 10:12:44 AM
> Subject: [Bioc-devel] Bioconductor 3.1 release schedule now available
>
> Hi all,
>
> The next version of Bioconductor will be 3.0 and its release schedule
> is now up on our website:
>

3.1 of course! Sorry for the typo.
Dan

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Re: [Bioc-devel] Change of schema of ENSEMBL biomart

[Martin, Tiphaine]

Hi Thomas,

Thanks a lot, I understand better my error in my build.
Regards,

Tiphaine

From: Thomas Maurel mailto:mau...@ebi.ac.uk>>
Date: Thursday, 18 December 2014 16:53
To: Tiphaine Martin 
mailto:tiphaine.mar...@kcl.ac.uk>>
Cc: "bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>" 
mailto:bioc-devel@r-project.org>>
Subject: Re: [Bioc-devel] Change of schema of ENSEMBL biomart

Dear Tiphaine,

Yes, we are trying to apply all the attribute re-naming on 
ensembl.org<http://ensembl.org> back to the GRCh37 archive.
We are planning to have a "news" page similar to what we have for 
ensembl.org<http://ensembl.org> for our next e!79 grch37 update planned for 
March 2015.

Please find below all the changes I've made to the GRCh37 Ensembl marts in the 
Ensembl Release 78:
  *   Ensembl Genes 78

  *   Added "Associated Gene Name" (internal name "external_gene_name") in the 
id list limit filter section
  *   Renamed "external_gene_id" attribute to "external_gene_name"
  *   Renamed "Reference ID" to "Variation Name" and "Source description" to 
"Variation source description" in the Variation attribute section for germline 
and somatic.
  *   Renamed internal name:
 *   For the "Variation name" attribute from "external_id" to 
"variation_name"
 *   For the "Variation Source" attribute from "source_name" to 
"germ_line_variation_source".
 *   For the "Variation name" somatic attribute from "somatic_reference_id" 
to "somatic_variation_name"
  *   Removed DN/DS attribute for species that don't have the data
  *   Added a "Transcript Type" filter and rename Gene biotype and transcript 
biotype attributes display name to "Gene type" and "transcript type"
  *   Re-ordered all the id list filters.

  *   Ensembl Variation 78

  *   Renamed the following attributes in snp, structvar, structvar som and 
snp_som:
 *   1000 genomes global MAF (all) to "1000 genomes global Minor Allele 
Frequency (all)"
 *   1000 genomes global MAC (all) to "1000 genomes global Minor Allele 
Count (all)"
 *   Position on chromosome (bp) to "Chromosome position start (bp)"
 *   Added "Chromosome position end (bp)"
 *   sequence region start to "Chromosome position start (bp)" and sequence 
region end to "Chromosome position end (bp)"
  *   Added Band filter for the structvar and structvar somatic templates
  *   Added Marker filter for the structvar and structvar somatic templates

  *   Vega 58

  *   Added "Associated Gene Name" (internal name "external_gene_name") in the 
id list limit filter section
  *   Renamed "external_gene_id" attribute to "external_gene_name"
  *   Add a "Transcript Type" filter and rename Gene biotype and transcript 
biotype attributes display name to "Gene type" and "transcript type"
  *   Renamed all the "External ID and DB" display name to "Associated Name" 
and "Associated Source"

Hope this helps,
Regards,
Thomas
On 18 Dec 2014, at 16:37, Martin, Tiphaine 
mailto:tiphaine.mar...@kcl.ac.uk>> wrote:

Hi Thomas,

I would like to know if you change also the schema of ENSEMBL mart of 
http://grch37.ensembl.org/biomart/martview, such as the "Associated Gene Name" 
attribute internal name from "external_gene_id" to �external_gene_name� like in 
the new release 77.  My request to ENSEMBL Mart worked well at least until 
25/11/2014. It seems that it does not work  again.

I would like to know if you can send a message sur bioc-devel, when you do any 
change in the schema of ENSEMBL mart ?

Thanks,

Tiphaine

From: Thomas Maurel mailto:mau...@ebi.ac.uk>>
Date: Friday, 17 October 2014 14:06
To: Tiphaine Martin 
mailto:tiphaine.mar...@kcl.ac.uk>>
Cc: "bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>" 
mailto:bioc-devel@r-project.org>>
Subject: Re: [Bioc-devel] Change of schema of ENSEMBL biomart

Dear Tiphaine,

The Ensembl marts on the biomart.org<http://biomart.org/> portal were recently 
updated from Ensembl release 75 to release 77. In release 76, we renamed the 
"Associated Gene Name" attribute internal name from "external_gene_id" to 
"external_gene_name". We have also added a new "Associated Gene Name" id list 
limit filter in release 77.
>From release 77 onward we have decided to declare all the attribute/filter 
>internal names changes on the Ensembl website declaration page:  
>http://www.ensembl.org/info/website/news.html#cat-other.
The data in the "hsapiens_gene_ensembl" dataset have also changed a lot since 
we moved fr

[Bioc-devel] Change of schema of ENSEMBL biomart

[Martin, Tiphaine]

Hi Everybody,


Yesterday, I observed that ENSEMBL changed a little their schema of  the 
dataset "hsapiens_gene_ensembl".

In my case, some of my functions were impacted by the change from 
"external_gene_id" to

"external_gene_name".


Maybe there are other change in this dataset or other datasets.


Regards,

Tiphaine

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Re: [Bioc-devel] runnable examples for internal function ?

[Martin, Tiphaine]

Yep you guess well about my colleagues :) sorry.

Thank you for your advices.
Tiphaine

From: Hervé Pagès 
Sent: 16 October 2014 19:43
To: Martin, Tiphaine; Michael Lawrence; Dan Tenenbaum
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] runnable examples for internal function ?

Hi Tiphaine,

On 10/15/2014 06:30 AM, Martin, Tiphaine wrote:
>
> Hi Herve,
>
> Thank you for your email. very useful.
> But I updated my NAMESPACE in order to list only functions that I want to 
> export.
> Even if I did that and if in addition, I keep different man files for 
> functions that I do not want to export, I have this error message.
> But if I removed them, I don't have error messages.
> I kept different man files for functions that I do not want to export to help 
> my colleagues. It seems that currently, it is not recommended in Bioconductor.

By "colleagues" I guess you mean "co-developers", not "users" of
your package right?

Yes it seems reasonable to expect 'R CMD BiocCheck' to only check
\value and \example for man pages that document exported things.
We should fix that.

Note that it's questionable whether it's a good idea or not to keep
around man pages for non exported things. IMO it's better to document
internal helpers using in-source comments. And since you already
have those in-source comments in place anyway (because you're
using roxygen2), all you need to do is find a way to block
roxygen2 from generating the man pages for these internal helpers.
Co-developers of your package will still be able to see useful
information and that information will be placed where developers
expect it to be: in the source code itself.

My 2 cents.

Cheers,
H.

>
> thank you for your help,
>
> Tiphaine
> ____
> From: Hervé Pagès 
> Sent: 14 October 2014 03:02
> To: Martin, Tiphaine; Michael Lawrence; Dan Tenenbaum
> Cc: bioc-devel@r-project.org
> Subject: Re: [Bioc-devel] runnable examples for internal function ?
>
> Hi Tiphaine,
>
> On 10/13/2014 04:31 PM, Martin, Tiphaine wrote:
>> Hi,
>>
>>
>> I wrote a list of functions used in my package called coMET. I decided with 
>> my colleagues to try to publish it in Bioconductor. Currently, it has not 
>> been yet submitted to bioconductor because I would like to be sure that it 
>> satisfies all your guidelines.
>> A list of functions is useful only internally. I saw that there are two 
>> methods to remove the function from the package index and to disable some of 
>> their automated tests: the first method is to put a dot as first letter, the 
>> second method is to put the "internal" keyword 
>> (http://cran.r-project.org/web/packages/roxygen2/vignettes/rdkeywords.html).
>
> That link is to the documentation of the roxygen2 package. Are you
> using roxygen2 to develop your package? You didn't say so.
> You say that "you saw that prefixing the function name with a dot
> or putting the 'internal' keyword in the man page will 'remove the
> function from the package index and disable some of its automated
> tests'". I guess that's something you saw in the roxygen2 documentation
> right? I don't use roxygene2 myself so I don't know what's the roxygen2
> way to control what's exposed or not to the user. However I know many
> BioC developers use it for their package so maybe they'll be able to
> provide some good advice here.
>
> Keep in mind that using a tool like roxygen2 adds an extra layer of
> convenience when developing your package but, unfortunately, it doesn't
> completely exempt you from learning and understanding some basic
> concepts like NAMESPACE, man pages aliases, keywords, etc...
> The ultimate reference for these things is still the "Writing R
> Extensions" manual:
>
> http://cran.r-project.org/doc/manuals/r-release/R-exts.html
>
> So, and FWIW, below I'll describe quickly how you need to proceed when
> you don't use a fancy tool like roxygen2 to automatically generate
> the NAMESPACE and man pages in your package:
>
> 1) The real true way to not expose a function to the user is to not
>  export it. What one exports from a package is controlled via
>  the NAMESPACE file. So first you need to learn about how to use
>  the NAMESPACE file to control exactly what you want to expose to
>  the user. See "Writing R Extensions" manual for the details.
>
> 2) Every symbol that is exported needs to be documented, that is, there
>  must be a man page with an alias for this symbol. And of course
>  opening the man page at the R prompt with ? shoul

[Bioc-devel] error about Display environment/ biomart for the build of my package

[Martin, Tiphaine]

Hi,


I have a type of warning message by bioconductor package tracker on Linux and 
Mac that I don't have when I did that  on my computers. So I don't know to 
correct or to check it on my computers. I think that it is related to the 
package trackViewer, which need to have tcl/tk package.


Error on Mac OS (check and BiocCheck steps)

** testing if installed package can be loaded
Warning in fun(libname, pkgname) :
  no display name and no $DISPLAY environment variable

Error on Linus (BiocCheck step)

* Installing package...
Warning in fun(libname, pkgname) :
  no DISPLAY variable so Tk is not available


I have an error message on window to connect to Biomart. In my package, I 
create Gviz's annotation tracks that connect to UCSC and ENSEMBL via Biomart 
connection.

This connection worked on Linux and Mac. So I would like to know if other 
people observed the biomart connection more difficulty under windows than under 
Mac and Linux or if it is just unlucky event.


Regards,

Tiphaine


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Re: [Bioc-devel] runnable examples for internal function ?

[Martin, Tiphaine]

Hi Herve,

Thank you for your email. very useful.
But I updated my NAMESPACE in order to list only functions that I want to 
export.
Even if I did that and if in addition, I keep different man files for functions 
that I do not want to export, I have this error message.
But if I removed them, I don't have error messages.
I kept different man files for functions that I do not want to export to help 
my colleagues. It seems that currently, it is not recommended in Bioconductor.

thank you for your help,

Tiphaine

From: Hervé Pagès 
Sent: 14 October 2014 03:02
To: Martin, Tiphaine; Michael Lawrence; Dan Tenenbaum
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] runnable examples for internal function ?

Hi Tiphaine,

On 10/13/2014 04:31 PM, Martin, Tiphaine wrote:
> Hi,
>
>
> I wrote a list of functions used in my package called coMET. I decided with 
> my colleagues to try to publish it in Bioconductor. Currently, it has not 
> been yet submitted to bioconductor because I would like to be sure that it 
> satisfies all your guidelines.
> A list of functions is useful only internally. I saw that there are two 
> methods to remove the function from the package index and to disable some of 
> their automated tests: the first method is to put a dot as first letter, the 
> second method is to put the "internal" keyword 
> (http://cran.r-project.org/web/packages/roxygen2/vignettes/rdkeywords.html).

That link is to the documentation of the roxygen2 package. Are you
using roxygen2 to develop your package? You didn't say so.
You say that "you saw that prefixing the function name with a dot
or putting the 'internal' keyword in the man page will 'remove the
function from the package index and disable some of its automated
tests'". I guess that's something you saw in the roxygen2 documentation
right? I don't use roxygene2 myself so I don't know what's the roxygen2
way to control what's exposed or not to the user. However I know many
BioC developers use it for their package so maybe they'll be able to
provide some good advice here.

Keep in mind that using a tool like roxygen2 adds an extra layer of
convenience when developing your package but, unfortunately, it doesn't
completely exempt you from learning and understanding some basic
concepts like NAMESPACE, man pages aliases, keywords, etc...
The ultimate reference for these things is still the "Writing R
Extensions" manual:

   http://cran.r-project.org/doc/manuals/r-release/R-exts.html

So, and FWIW, below I'll describe quickly how you need to proceed when
you don't use a fancy tool like roxygen2 to automatically generate
the NAMESPACE and man pages in your package:

1) The real true way to not expose a function to the user is to not
export it. What one exports from a package is controlled via
the NAMESPACE file. So first you need to learn about how to use
the NAMESPACE file to control exactly what you want to expose to
the user. See "Writing R Extensions" manual for the details.

2) Every symbol that is exported needs to be documented, that is, there
must be a man page with an alias for this symbol. And of course
opening the man page at the R prompt with ? should display
useful information about that symbol.
'R CMD check' is the tool that will check that every exported
symbol is documented. It will also perform many checks on the
man pages to make sure that they are formatted properly.

3) As Dan said previously, any function that is exported also needs
to have runnable examples and a \value section in its man page.
Note that this is a Bioconductor requirement, 'R CMD check'
doesn't check that. 'R CMD BiocCheck' is the tool that will
perform this check and any other Bioconductor specific check.

> I decided to use the second method to reduce to rewrite now all my package.

Note that, for "plain package development" (i.e. without using a
a fancy tool like roxygen2), using the "internal" keyword in a man
page has no effect on whether the function is exported or not.

>
>
> When I run the new version of BiocCheck Version 1.1.18 with empty \value and 
> \example sections for function with "internal" keyword , I have error message 
> asking to add no-empty runnable examples.
>
> When I run the new version of BiocCheck Version 1.1.18 without \value and 
> \example sections for function with "internal" keyword , I have error message 
> asking to add non-empty \value sections.
>
> with BiocCheck, version 1.0.2, I had a message for functions with "internal" 
> keyword such as "
> Checking exported objects have runnable examples...
> * CONSIDER: Adding runnable examples to the following

Re: [Bioc-devel] runnable examples for internal function ?

[Martin, Tiphaine]

Hi,


I wrote a list of functions used in my package called coMET. I decided with my 
colleagues to try to publish it in Bioconductor. Currently, it has not been yet 
submitted to bioconductor because I would like to be sure that it satisfies all 
your guidelines.
A list of functions is useful only internally. I saw that there are two methods 
to remove the function from the package index and to disable some of their 
automated tests: the first method is to put a dot as first letter, the second 
method is to put the "internal" keyword 
(http://cran.r-project.org/web/packages/roxygen2/vignettes/rdkeywords.html).
I decided to use the second method to reduce to rewrite now all my package.


When I run the new version of BiocCheck Version 1.1.18 with empty \value and 
\example sections for function with "internal" keyword , I have error message 
asking to add no-empty runnable examples.

When I run the new version of BiocCheck Version 1.1.18 without \value and 
\example sections for function with "internal" keyword , I have error message 
asking to add non-empty \value sections.

with BiocCheck, version 1.0.2, I had a message for functions with "internal" 
keyword such as "
Checking exported objects have runnable examples...
* CONSIDER: Adding runnable examples to the following man pages
which document exported objects:"

I would like to know if I made a mistake to use internal keyword for this type 
of functions. What do I need to do ?

Which sections are mandatory in manual file and for which function I need to do 
a manual file ?


Regards,
Tiphaine



From: Michael Lawrence 
Sent: 13 October 2014 21:52
To: Dan Tenenbaum
Cc: Martin, Tiphaine; bioc-devel@r-project.org
Subject: Re: [Bioc-devel] runnable examples for internal function ?

It would be nice to know the use case of the internal keyword here. I've use it 
to avoid listing functions in the index (RGtk2 has thousands of functions). But 
in general, it's not a good idea to be exporting things that are truly 
internal. Perhaps internal methods on exported generics, but even then, it's 
probably best to keep the aliases with the generic, or something.


On Mon, Oct 13, 2014 at 1:33 PM, Dan Tenenbaum 
mailto:dtene...@fhcrc.org>> wrote:


- Original Message -
> From: "Tiphaine Martin" 
> mailto:tiphaine.mar...@kcl.ac.uk>>
> To: bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>
> Sent: Monday, October 13, 2014 1:29:08 PM
> Subject: [Bioc-devel] runnable examples for internal function ?
>
> Hi,
>
>
> I would like to know if I need to add a runnable example for each
> function that has keyword either internal or not.
>

I don't know what you mean by this, but maybe I should.

>
> I ask that because with BiocCheck, version 1.0.2, I had a message for
> function with keyword "internal" such as "
>
> Checking exported objects have runnable examples...
> * CONSIDER: Adding runnable examples to the following man pages
>   which document exported objects:"
>

If the function is exported, it must have a runnable example.


> and now, I have an error message with BiocCheck, version 1.1.18
>
> * Checking exported objects have runnable examples...
> Error in if (line == "## No test: " || insideDontTest || line == "##
> End(No test)") { :
>   missing value where TRUE/FALSE needed
> Calls:  ... checkExportsAreDocumented ->
> doesManPageHaveRunnableExample -> removeDontTest
> Execution halted
>

Can you file an issue at https://github.com/Bioconductor/BiocCheck/issues and 
include the name of the package?
I will get to it as soon as I can.

Dan


>
> Regards,
>
> Tiphaine
>
>
>
> 
> Tiphaine Martin
> PhD Research Student | King's College
> The Department of Twin Research & Genetic Epidemiology | Genetics &
> Molecular Medicine Division
> St Thomas' Hospital
> 4th Floor, Block D, South Wing
> SE1 7EH, London
> United Kingdom
>
> email : tiphaine.mar...@kcl.ac.uk<mailto:tiphaine.mar...@kcl.ac.uk>
> Fax: +44 (0) 207 188 6761
>
>   [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org<mailto:Bioc-devel@r-project.org> mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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[Bioc-devel] runnable examples for internal function ?

[Martin, Tiphaine]

Hi,


I would like to know if I need to add a runnable example for each function that 
has keyword either internal or not.


I ask that because with BiocCheck, version 1.0.2, I had a message for function 
with keyword "internal" such as "

Checking exported objects have runnable examples...
* CONSIDER: Adding runnable examples to the following man pages
  which document exported objects:"

and now, I have an error message with BiocCheck, version 1.1.18

* Checking exported objects have runnable examples...
Error in if (line == "## No test: " || insideDontTest || line == "## End(No 
test)") { :
  missing value where TRUE/FALSE needed
Calls:  ... checkExportsAreDocumented -> 
doesManPageHaveRunnableExample -> removeDontTest
Execution halted


Regards,

Tiphaine




Tiphaine Martin
PhD Research Student | King's College
The Department of Twin Research & Genetic Epidemiology | Genetics & Molecular 
Medicine Division
St Thomas' Hospital
4th Floor, Block D, South Wing
SE1 7EH, London
United Kingdom

email : tiphaine.mar...@kcl.ac.uk
Fax: +44 (0) 207 188 6761

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Re: [Bioc-devel] Non-ASCII in datase from Biomart EMBL via Gviz package

[Martin, Tiphaine]

both methods work well. 
Thanks,
Tiphaine


From: Hahne, Florian 
Sent: 13 October 2014 08:46
To: Vincent Carey; Martin, Tiphaine
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Non-ASCII in datase from Biomart EMBL via Gviz package

Hi Tiphaine,
You can follow Vince¹s advice and transform all the data into proper ASCII
character. Or you can just get rid of the culprit (being the @biomart slot
of the object) before serialising. The easiest way to do that is:
foo@biomart <- NULL
The slot is only present to cache the BiomaRt connection, which is lost
anyways when serialising. The object is smart enough to realise that and
just reconnects the next time it is plotted. That is how I handled things
for the serialised BiomartGeneRegionTracks in Gviz.
Florian



On 12/10/14 20:35, "Vincent Carey"  wrote:

>I don't know exactly how you are triggering this warning.  If you have the
>ability to prefilter your content before serializing, that may be best.
>The following
>is from the gwascat package.  You have very little chance, I believe, of
>getting an
>institutional guarantee that only ascii will go into their emissions.
>
>fixNonASCII = function(df) {
> hasNonASCII = function(x) {
>   asc = iconv(x, "latin1", "ASCII")
>   any(asc != x | is.na(asc))
>   }
> havebad = sapply(df, function(x) hasNonASCII(x))
> if (!(any(havebad))) return(df)
> message("NOTE: input data had non-ASCII characters replaced by '*'.")
> badinds = which(havebad)
> for (i in 1:length(badinds))
>   df[,badinds[i]] = iconv(df[,badinds[i]], to="ASCII", sub="*")
> df
>}
>
>
>
>On Sun, Oct 12, 2014 at 2:14 PM, Martin, Tiphaine
>> wrote:
>
>> Hi,
>>
>>
>> I need to create dataset BiomartGeneRegionTrack via Gviz package to run
>> examples in my packages. But when I run
>>
>> "R CMD check coMET", i have warning message for the checking :
>>
>>
>>  checking data for non-ASCII characters ... WARNING
>>   Warning: found non-ASCII strings
>>   '[alpha cell,acidophil cell,acinar cell,adipoblast,adipocyte,amacrine
>> cell,beta cell,capsular cell,cementocyte,chief
>> cell,chondroblast,chondrocyte,chromaffin cell,chromophobic
>> cell,corticotroph,delta cell,dendritic cell,enterochromaffin
>>
>>cell,ependymocyte,epithelium,erythroblast,erythrocyte,fibroblast,fibrocyt
>>e,follicular
>> cell,germ cell,germinal epithelium,giant cell,glial
>>cell,glioblast,goblet
>> cell,gonadotroph,granulosa cell,haemocytoblast,hair
>> cell,hepatoblast,hepatocyte,hyalocyte,interstitial cell,juxtaglomerular
>> cell,keratinocyte,keratocyte,lemmal cell,leukocyte,luteal
>>cell,lymphocytic
>> stem cell,lymphoid cell,lymphoid stem cell,macroglial
>>cell,mammotroph,mast
>>
>>cell,medulloblast,megakaryoblast,megakaryocyte,melanoblast,melanocyte,mes
>>angial
>> cell,mesothelium,metamyelocyte,monoblast,monocyte,mucous neck
>>cell,muscle
>> cell,myelocyte,myeloid cell,myeloid stem cell,myoblast,myoepithelial
>>
>>cell,myofibrobast,neuroblast,neuroepithelium,neuron,odontoblast,osteoblas
>>t,osteoclast,osteocy!
>>  te,oxyntic cell,parafollicular cell,paraluteal cell,peptic
>> cell,pericyte,phaeochromocyte,phalangeal
>>cell,pinealocyte,pituicyte,plasma
>>
>>cell,platelet,podocyte,proerythroblast,promonocyte,promyeloblast,promyelo
>>cyte,pronormoblast,reticulocyte,retinal
>> pigment epithelium,retinoblast,somatotroph,stem cell,sustentacular
>> cell,teloglial cell,zymogenic cell,small cell,Th1,Cell
>>Type,Mller
>> cell,primary oocyte,Claudius' cell,Th2,follicular dendritic
>> cell,astrocyte,white,T-lymphoblast,basal cell,T-lymphocyte,helper
>>induced
>> T-lymphocyte:Th2,B-lymphocyte,neutrophil,oocyte,unclassifiable (Cell
>> Type),natural killer cell,helper induced T-lymphocyte,brown,CD4+,Hensen
>> cell,lymphocyte,cardiac muscle cell,lymphoblast,Paneth cell,alveolar
>> macrophage,macrophage,squamous cell,oligodendrocyte,smooth muscle
>> cell,gamete,spermatid,Schwann cell,CD34+,spermatocyte,helper induced
>>
>>T-lymphocyte:Th1,astroblast,eosinophil,oligodendroblast,basophil,peripher
>>al
>> blood mononuclear cell,histiocyte,Sertoli cel!
>>  l,endothelium,granulocyte,spermatozoon,Merkel cell,skeletal muscle cel
>> l,thymocyte,foam cell,ovum,secondary spermatocyte,Langerhans
>>cell,primary
>> spermatocyte,transitional,Purkinje cell,Kupffer cell,secondary
>> oocyte,B-lymphoblast]' in object 'biomTrack'
>>
>>
>> chrom <- "chr2"
>> start <- 38290160
>> end <

[Bioc-devel] Non-ASCII in datase from Biomart EMBL via Gviz package

[Martin, Tiphaine]

Hi,


I need to create dataset BiomartGeneRegionTrack via Gviz package to run 
examples in my packages. But when I run

"R CMD check coMET", i have warning message for the checking :


 checking data for non-ASCII characters ... WARNING
  Warning: found non-ASCII strings
  '[alpha cell,acidophil cell,acinar cell,adipoblast,adipocyte,amacrine 
cell,beta cell,capsular cell,cementocyte,chief 
cell,chondroblast,chondrocyte,chromaffin cell,chromophobic 
cell,corticotroph,delta cell,dendritic cell,enterochromaffin 
cell,ependymocyte,epithelium,erythroblast,erythrocyte,fibroblast,fibrocyte,follicular
 cell,germ cell,germinal epithelium,giant cell,glial cell,glioblast,goblet 
cell,gonadotroph,granulosa cell,haemocytoblast,hair 
cell,hepatoblast,hepatocyte,hyalocyte,interstitial cell,juxtaglomerular 
cell,keratinocyte,keratocyte,lemmal cell,leukocyte,luteal cell,lymphocytic stem 
cell,lymphoid cell,lymphoid stem cell,macroglial cell,mammotroph,mast 
cell,medulloblast,megakaryoblast,megakaryocyte,melanoblast,melanocyte,mesangial 
cell,mesothelium,metamyelocyte,monoblast,monocyte,mucous neck cell,muscle 
cell,myelocyte,myeloid cell,myeloid stem cell,myoblast,myoepithelial 
cell,myofibrobast,neuroblast,neuroepithelium,neuron,odontoblast,osteoblast,osteoclast,osteocy!
 te,oxyntic cell,parafollicular cell,paraluteal cell,peptic 
cell,pericyte,phaeochromocyte,phalangeal cell,pinealocyte,pituicyte,plasma 
cell,platelet,podocyte,proerythroblast,promonocyte,promyeloblast,promyelocyte,pronormoblast,reticulocyte,retinal
 pigment epithelium,retinoblast,somatotroph,stem cell,sustentacular 
cell,teloglial cell,zymogenic cell,small cell,Th1,Cell Type,Mller 
cell,primary oocyte,Claudius' cell,Th2,follicular dendritic 
cell,astrocyte,white,T-lymphoblast,basal cell,T-lymphocyte,helper induced 
T-lymphocyte:Th2,B-lymphocyte,neutrophil,oocyte,unclassifiable (Cell 
Type),natural killer cell,helper induced T-lymphocyte,brown,CD4+,Hensen 
cell,lymphocyte,cardiac muscle cell,lymphoblast,Paneth cell,alveolar 
macrophage,macrophage,squamous cell,oligodendrocyte,smooth muscle 
cell,gamete,spermatid,Schwann cell,CD34+,spermatocyte,helper induced 
T-lymphocyte:Th1,astroblast,eosinophil,oligodendroblast,basophil,peripheral 
blood mononuclear cell,histiocyte,Sertoli cel!
 l,endothelium,granulocyte,spermatozoon,Merkel cell,skeletal muscle cel
l,thymocyte,foam cell,ovum,secondary spermatocyte,Langerhans cell,primary 
spermatocyte,transitional,Purkinje cell,Kupffer cell,secondary 
oocyte,B-lymphoblast]' in object 'biomTrack'


chrom <- "chr2"
start <- 38290160
end <- 38303219
gen <- "hg19"

  biomTrack <- BiomartGeneRegionTrack(genome = gen,
  chromosome = chr, start = start,
  end = end,  name = "ENSEMBL",
  fontcolor="black", groupAnnotation = 
"group",
  just.group = "above",showId=showId )


Do you have an idea to correct this error? I think that we need to discuss with 
EMBL to correct that, do we ?


Tiphaine



Tiphaine Martin
PhD Research Student | King's College
The Department of Twin Research & Genetic Epidemiology | Genetics & Molecular 
Medicine Division
St Thomas' Hospital
4th Floor, Block D, South Wing
SE1 7EH, London
United Kingdom

email : tiphaine.mar...@kcl.ac.uk
Fax: +44 (0) 207 188 6761

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