Re: [Bioc-devel] Vignette examples

2020-09-10 Thread Sean Davis 
Hi, Emilie.

A useful tidbit to include when asking questions such as yours is to
include a link to the repository with code that folks can quickly go
through. Is your code available?

Sean


On Thu, Sep 10, 2020 at 10:38 AM Emilie Secherre 
wrote:

> Hello,
>
>
>
> I'm currently making a bioconductor package. When i'm running R CMD check,
> all the examples i used in function vignettes have one issue : could not
> find function "mypckgfunction". Is there a way to fix this issue ? The
> examples work perfectly when i'm using them in a R script, and are used in
> unit tests without any warning, it's just about examples in vignettes...
>
>
>
> Thank you in advance for your answer,
>
> Emilie Secherre
>
> [[alternative HTML version deleted]]
>
> ___
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> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>


-- 
Sean Davis, MD, PhD
Center for Cancer Research
National Cancer Institute
National Institutes of Health
Bethesda, MD 20892
https://seandavi.github.io/
https://twitter.com/seandavis12

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Re: [Bioc-devel] FW: Java version issue on Bioconductor test platform

2020-09-10 Thread Pages, Herve 
Hi Arman,

Sure, if xlsx is broken and won't be fixed, use something else. Maybe 
try openxlsx? Similar to xlsx but doesn't require Java:

   https://CRAN.R-project.org/package=openxlsx

But why would you use something else on Mac only? It's easier from a 
maintenance point of view if you use the same code on all platforms, 
whenever possible.

Best,
H.


On 9/9/20 11:06, Arman Shahrisa wrote:
> Hi to all,
> 
> I have sent several emails to the maintainer of “xlsx” package but 
> unfortunately, he is unresponsive.
> 
> Am I allowed to use an alternative package for exporting data only for 
> mac users?
> 
> Best regards,
> 
> Arman
> 
> *From: *Arman Shahrisa 
> *Sent: *Thursday, September 3, 2020 10:59
> *To: *Pages, Herve ; bioc-devel 
> 
> *Subject: *RE: [Bioc-devel] Java version issue on Bioconductor test platform
> 
> Hi Herve,
> 
> The last response in the previous topic suggested that the maintainer 
> has already fixed the problem on GitHub but not CRAN.
> 
> https://stat.ethz.ch/pipermail/bioc-devel/2020-May/016791.html 
> 
> 
> This is from May and the problem still persists. I’ll try contacting the 
> maintainer of xlsx.
> 
> Best regards,
> 
> Arman
> 
> *From: *Pages, Herve 
> *Sent: *Thursday, September 3, 2020 01:06
> *To: *Arman Shahrisa ; bioc-devel 
> 
> *Subject: *Re: [Bioc-devel] Java version issue on Bioconductor test platform
> 
> Hi Arman,
> 
> You already asked about this in May:
> https://stat.ethz.ch/pipermail/bioc-devel/2020-May/016788.html 
> 
> 
> Have you followed up with the xlsx maintainers as suggested by Lluís?
> 
> Cheers,
> H.
> 
> On 8/29/20 11:12, Arman Shahrisa wrote:
>  > Hi to all,
>  >
>  > I�m maintainer of the package �cbaf�. I have been monitoring reports 
> for my package for months. I know there were some issues with mac 
> server. However, it seems that error shown from mac server regarding my 
> package is caused by some incompatible java application installed on 
> Bioconductor server. I would be grateful if you would kindly check this 
> issue for me.
>  >
>  > Best wishes,
>  > Arman
>  >
>  >
>  >    [[alternative HTML version deleted]]
>  >
>  >
>  > ___
>  > Bioc-devel@r-project.org mailing list
>  > 
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>  >
> 
> -- 
> Hervé Pagès
> 
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
> 
> E-mail: hpa...@fredhutch.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
> 

-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpa...@fredhutch.org
Phone:  (206) 667-5791
Fax:(206) 667-1319
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Re: [Bioc-devel] Vignette examples

2020-09-10 Thread Shepherd, Lori 
Did you export the function in the package?



Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


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

Hello,



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



Thank you in advance for your answer,

Emilie Secherre

[[alternative HTML version deleted]]

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Re: [Bioc-devel] Vignette examples

2020-09-10 Thread Manders-2, F.M. 
Hi Emilie,

There are two possible problems I could think of.
Did you remember to load your package in the vignette?
Are your functions exported in the NAMESPACE of your package?

With kind regards,
Freek Manders

On 10/09/2020, 16:38, "Bioc-devel on behalf of Emilie Secherre" 
 wrote:

Hello,



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



Thank you in advance for your answer,

Emilie Secherre

[[alternative HTML version deleted]]

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[Bioc-devel] Vignette examples

2020-09-10 Thread Emilie Secherre 
Hello,



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



Thank you in advance for your answer,

Emilie Secherre

[[alternative HTML version deleted]]

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Re: [Bioc-devel] fetch upstream of an existing package

2020-09-10 Thread Turaga, Nitesh 
Please follow 
http://bioconductor.org/developers/how-to/git/bug-fix-in-release-and-devel/ .

Notice that the branch name is RELEASE_3_11 (case sensitive).

Nitesh


From: Irene Zeng 
Date: Thursday, September 10, 2020 at 5:33 AM
To: "Turaga, Nitesh" , "Shepherd, Lori" 

Cc: bioc-devel 
Subject: Re: [Bioc-devel] fetch upstream of an existing package


Here are some further codes:

"
OEM@OEM-PC MINGW64 ~/Documents/GitHub/sparsenetgls (release_3_11)
$ git fetch --all
Fetching origin
Fetching upstream
Enter passphrase for key '/c/Users/OEM/.ssh/id_rsa':

OEM@OEM-PC MINGW64 ~/Documents/GitHub/sparsenetgls (release_3_11)
$ git checkout release_3_11
Already on 'release_3_11'

OEM@OEM-PC MINGW64 ~/Documents/GitHub/sparsenetgls (release_3_11)
$ git push upstream release_3_11
Enter passphrase for key '/c/Users/OEM/.ssh/id_rsa':
fatal: release_3_11 cannot be resolved to branch
fatal: the remote end hung up unexpectedly
"
I have successfully push the changes yesterday, perhaps the change was not 
shown in the report on 9th Sep?
Irene



From: Irene Zeng
Sent: Thursday, 10 September 2020 9:26 p.m.
To: Turaga, Nitesh; Shepherd, Lori
Cc: bioc-devel
Subject: Re: [Bioc-devel] fetch upstream of an existing package


Hi, Nitsh , Lori.

Thank you for your helps, the development version has changed and clear in the 
building report, but not the release version.

I have merged and pushed changes from the release branch, but it does not show 
to

connect to the upstream release.

"
OEM@OEM-PC MINGW64 ~/Documents/GitHub/sparsenetgls (master)
$ git checkout release_3_11
Switched to branch 'release_3_11'

OEM@OEM-PC MINGW64 ~/Documents/GitHub/sparsenetgls (release_3_11)
$ git merge upstream/release_3_11
Already up to date.

OEM@OEM-PC MINGW64 ~/Documents/GitHub/sparsenetgls (release_3_11)
$ git push upstream release_3_11
"
Not sure why?
Irene


From: Turaga, Nitesh 
Sent: Wednesday, 9 September 2020 3:15 a.m.
To: Shepherd, Lori
Cc: Irene Zeng; bioc-devel
Subject: Re: [Bioc-devel] fetch upstream of an existing package

The RSS error should be fixed.


On Sep 8, 2020, at 7:58 AM, Shepherd, Lori 
mailto:lori.sheph...@roswellpark.org>> wrote:

I RSS feed ERROR did not prevent the changes from being pushed to 
git.bioconductor.org
 .  The changes should be reflected in either today's or tomorrow's build 
report.

Please note:  The package was failing in release and devel so don't forget to 
also push changes to RELEASE_3_11 branch (with appropriate release version 
number)

Cheers,

Lori Shepherd
Bioconductor Core Team
Roswell Park Comprehensive Cancer Center
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263

From: Irene Zeng mailto:i.z...@auckland.ac.nz>>
Sent: Sunday, September 6, 2020 5:08 AM
To: Shepherd, Lori 
mailto:lori.sheph...@roswellpark.org>>; Turaga, 
Nitesh mailto:nitesh.tur...@roswellpark.org>>
Cc: bioc-devel mailto:bioc-devel@r-project.org>>
Subject: Re: [Bioc-devel] fetch upstream of an existing package

Hello Lori,
I have redone the merge and push, Now, it has pushed the changes, but I have 
the following messages:

"
$ git merge upstream/master
Already up to date.

OEM@OEM-PC MINGW64 ~/Documents/GitHub/sparsenetgls (master)
$ git push origin master
Everything up-to-date

OEM@OEM-PC MINGW64 ~/Documents/GitHub/sparsenetgls (master)
$ git push upstream master
Enter passphrase for key '/c/Users/OEM/.ssh/id_rsa':
  Enumerating objects: 91, done.
Counting objects: 100% (69/69), done.
Delta compression using up to 8 threads
Compressing objects: 100% (43/43), done.
Writing objects: 100% (43/43), 6.42 KiB | 939.00 KiB/s, done.
Total 43 (delta 32), reused 0 (delta 0), pack-reused 0
remote: fatal: this operation must be run in a work tree
remote: ERROR:root:Exception: Command '['git', 'rev-parse', '--show-toplevel']' 
returned non-zero exit status 128
remote: ERROR:root:local variable 'package_name' referenced before assignment
remote: Note: failed to update RSS feed;git repository updated successfully.
To