[Bioc-devel] Rmd vignette failures

2020-09-23 Thread Leonardo Collado Torres 
As I was about to hit send, I checked Slack and I found about
https://github.com/Bioconductor/BiocStyle/issues/78. If you are in the
same situation as me, that info will be useful =) + the info on Slack



Original email:



Hi bioc-devel,

Today I got a bunch of emails because most of my packages failed with
errors such as:

Quitting from lines 31-39 (derfinderHelper.Rmd)
Error: processing vignette 'derfinderHelper.Rmd' failed with diagnostics:
argument is of length zero

The error basically points to the first R chunk in the Rmd files like
at 
https://github.com/leekgroup/derfinderHelper/blob/master/vignettes/derfinderHelper.Rmd#L30-L39
for each vignette. I've noticed a similar error in the GitHub Actions
logs for a package I'm actively working on (macOS and Windows using R
from r-lib; Linux using bioc-devel docker still worked details at
https://github.com/LieberInstitute/megadepth/runs/1152833313).

Are you aware of any change to pandoc or markdown that might be
related to this issue? I don't see anything at rstudio/rmarkdown
https://github.com/rstudio/rmarkdown/issues?q=argument+is+of+length+zero.

Best,
Leo

Leonardo Collado Torres, Ph. D.
Investigator

LIEBER INSTITUTE for BRAIN DEVELOPMENT
855 N. Wolfe St., Suite 300
Baltimore, MD 21205
lcolladotor.github.io
lcollado...@gmail.com

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Re: [Bioc-devel] BiocCheckGitClone error

2020-09-23 Thread Shepherd, Lori 
Yes.  Go ahead and submit the package to the tracker.  We can investigate this 
further with your assigned reviewer.  Sorry for the inconvenience.

Cheers,


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


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

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

[https://secure-web.cisco.com/1HQT4avzpKVe6j7PuRRxrsuWMDf9cWUZuvWvcmpy-Hm9ylUZcF1ZK9nij0XmQseltPyNpiVmy97v-prEItcNCrEAqe9fIjUDyu0csq6FZafOd080slA_qK4RzvNTFpksPzhjCbqJXkoQCSo1LZBF77jZxj3MjR8FCoZMJJ4U34udEfaunOUDkSlbg8LQPaGHtHgwcnYoVrpHPwzErSn4gBD2ViioFX0Ih7UCTGBvlWD1s5570xDsW6bkezIp2St53vPw6zUrY7552Hb1Flo43oOYZU90q15k8vJV2UjMlfP9FzDiX9wEkI4CumAgAmcQw/https%3A%2F%2Fipmcdn.avast.com%2Fimages%2Ficons%2Ficon-envelope-tick-round-orange-animated-no-repeat-v1.gif]
Garanti sans virus. 
www.avast.com

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

[https://secure-web.cisco.com/1HQT4avzpKVe6j7PuRRxrsuWMDf9cWUZuvWvcmpy-Hm9ylUZcF1ZK9nij0XmQseltPyNpiVmy97v-prEItcNCrEAqe9fIjUDyu0csq6FZafOd080slA_qK4RzvNTFpksPzhjCbqJXkoQCSo1LZBF77jZxj3MjR8FCoZMJJ4U34udEfaunOUDkSlbg8LQPaGHtHgwcnYoVrpHPwzErSn4gBD2ViioFX0Ih7UCTGBvlWD1s5570xDsW6bkezIp2St53vPw6zUrY7552Hb1Flo43oOYZU90q15k8vJV2UjMlfP9FzDiX9wEkI4CumAgAmcQw/https%3A%2F%2Fipmcdn.avast.com%2Fimages%2Ficons%2Ficon-envelope-tick-round-orange-animated-no-repeat-v1.gif]
Garanti sans virus. 
www.avast.com

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


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


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

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

Re: [Bioc-devel] BiocCheckGitClone error

2020-09-23 Thread Emilie Secherre 
I still couldn't fix the issue, therefore is that allowed to just don't
push the .Rproj file in github ?
Thanks in advance for your answer
Emilie


Garanti
sans virus. www.avast.com

<#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

Le mar. 22 sept. 2020 à 15:36, Emilie Secherre  a
écrit :

> I pushed famat.Rproj after .gitignore was created and pushed with
> "famat.Rproj" in it. That's why i don't understand why famat.Rproj is still
> in the clone folder.
>
>
> 
>  Garanti
> sans virus. www.avast.com
> 
> <#m_5808152295650690142_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
>
> Le mar. 22 sept. 2020 à 15:32, Shepherd, Lori <
> lori.sheph...@roswellpark.org> a écrit :
>
>> So I think the file probably got pushed up before you added it to
>> .gitignore.  So you would probably want to git rm the files,  commit, and
>> push.  Then you could add them back in after and if they were still listed
>> in the .gitignore then they would be ignored.
>>
>> Lori Shepherd
>>
>> Bioconductor Core Team
>>
>> Roswell Park Comprehensive Cancer Center
>>
>> Department of Biostatistics & Bioinformatics
>>
>> Elm & Carlton Streets
>>
>> Buffalo, New York 14263
>> --
>> *From:* Emilie Secherre 
>> *Sent:* Tuesday, September 22, 2020 9:04 AM
>> *To:* Shepherd, Lori 
>> *Cc:* bioc-devel@r-project.org 
>> *Subject:* Re: [Bioc-devel] BiocCheckGitClone error
>>
>> This time I used Git clone folder. Though, when I push famat package in
>> github, .gitignore file isn't uploaded, so I created a .gitignore file in
>> the github repository with "famat.Rproj" in it before pushing the whole
>> package. Unfortunately, the "famat.Rproj" file is still in the git clone
>> folder...
>>
>>
>> 
>>  Garanti
>> sans virus. www.avast.com
>> 
>> <#m_5808152295650690142_m_-1353067446180599254_x_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
>>
>> Le mar. 22 sept. 2020 à 14:12, Shepherd, Lori <
>> lori.sheph...@roswellpark.org> a écrit :
>>
>> We run BiocCheckGitClone on a raw clone of the github directory.   If you
>> are running it locally and had .gitignored those files before pushing to
>> github then you should be okay.   A way to test this would be to do a git
>> clone  of your github repository, in a different, temporary location to
>> see if those files are still present when you do a git clone and running
>> BiocCheckGitClone on that temporary cloned copy.
>>
>> Cheers
>>
>> Lori Shepherd
>>
>> Bioconductor Core Team
>>
>> Roswell Park Comprehensive Cancer Center
>>
>> Department of Biostatistics & Bioinformatics
>>
>> Elm & Carlton Streets
>>
>> Buffalo, New York 14263
>> --
>> *From:* Bioc-devel  on behalf of
>> Emilie Secherre 
>> *Sent:* Tuesday, September 22, 2020 4:57 AM
>> *To:* bioc-devel@r-project.org 
>> *Subject:* [Bioc-devel] BiocCheckGitClone error
>>
>> Hello,
>>
>> When i run R CMD and BiocCheck, i get no error or warnings. But, when
>> running BiocCheckGitClone, i'm getting this error :
>> System files found that should not be tracked : famat.Rproj, .Rhistory
>> The issue is that both files are in .gitignore, but this error isn't
>> removed... I'm using BiocCheckGitClone on the same file as BiocCheck.
>>
>> Thank you in advance for your answer,
>>
>> Emilie Secherre
>>
>> <
>>