Re: [Bioc-devel] Failure to create PDF vignette with BiocStyle 2.4.1

[Vincent Carey]

I ran into this -- BiocStyle was modified by Andrzej to solve it.  I am now
at BiocStyle 2.5.39 and biocValid() does
not complain.  So try updating BiocStyle.

On Tue, Oct 3, 2017 at 9:29 PM, Stefan Mutter 
wrote:

> Hi,
>
>
> I hope I am writing this to the right list.
>
>
> I am currently trying to author a vignette for a package, we will be
> submitting to Bioconductor. The PDF vignette creation fails inside a code
> block which I cannot explain. I have attached a small example that contains
> the same code block (the one labelled producesError) than my vignette and
> at least on my machine it reproduces the error.
>
>
> The process can create the .tex file, but fails in converting the .tex
> file to a pdf. The error message  in RStudio is:
>
>
> This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015) (preloaded
> format=pdflatex)
>
>  restricted \write18 enabled.
>
> entering extended mode
>
> Latexmk: Errors, so I did not complete making targets
>
> Collected error summary (may duplicate other messages):
>
>   pdflatex: Command for 'pdflatex' gave return code 256
>
> Latexmk: Use the -f option to force complete processing,
>
>  unless error was exceeding maximum runs of latex/pdflatex.
>
>
> The log file contains the following error:
>
>
> ! Undefined control sequence.
>
>  ...{"MALE"}\NormalTok {] }\OperatorTok
>
>   {==}\StringTok {
> }\DecValT...
>
> l.137 ...=}\StringTok{ }\DecValTok{1}\NormalTok{)}
>
>
> This points to a problem inside the code block with the which statement,
> but it is unclear to me how the which statement can be a problem?
>
>
> It would be really appreciated if you could help me.
>
>
> Cheers,
>
> Stefan
>
>
> My session info is:
>
> R version 3.4.1 (2017-06-30)
>
> Platform: x86_64-apple-darwin15.6.0 (64-bit)
>
> Running under: macOS Sierra 10.12.6
>
>
> Matrix products: default
>
> BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/
> A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
>
> LAPACK: /Library/Frameworks/R.framework/Versions/3.4/
> Resources/lib/libRlapack.dylib
>
>
> locale:
>
> [1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8
>
>
> attached base packages:
>
> [1] stats graphics  grDevices utils datasets  methods   base
>
>
> other attached packages:
>
> [1] Numero_0.99.0
>
>
> loaded via a namespace (and not attached):
>
>  [1] compiler_3.4.1  backports_1.1.1 BiocStyle_2.4.1 magrittr_1.5
> rprojroot_1.2
>
>  [6] htmltools_0.3.6 tools_3.4.1 yaml_2.1.14 Rcpp_0.12.13
> stringi_1.1.5
>
> [11] rmarkdown_1.6   knitr_1.17  stringr_1.2.0   digest_0.6.12
>  evaluate_0.10.1?
>
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[Bioc-devel] Failure to create PDF vignette with BiocStyle 2.4.1

[Stefan Mutter]

Hi,


I hope I am writing this to the right list.


I am currently trying to author a vignette for a package, we will be submitting 
to Bioconductor. The PDF vignette creation fails inside a code block which I 
cannot explain. I have attached a small example that contains the same code 
block (the one labelled producesError) than my vignette and at least on my 
machine it reproduces the error.


The process can create the .tex file, but fails in converting the .tex file to 
a pdf. The error message  in RStudio is:


This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015) (preloaded 
format=pdflatex)

 restricted \write18 enabled.

entering extended mode

Latexmk: Errors, so I did not complete making targets

Collected error summary (may duplicate other messages):

  pdflatex: Command for 'pdflatex' gave return code 256

Latexmk: Use the -f option to force complete processing,

 unless error was exceeding maximum runs of latex/pdflatex.


The log file contains the following error:


! Undefined control sequence.

 ...{"MALE"}\NormalTok {] }\OperatorTok

  {==}\StringTok { }\DecValT...

l.137 ...=}\StringTok{ }\DecValTok{1}\NormalTok{)}


This points to a problem inside the code block with the which statement, but it 
is unclear to me how the which statement can be a problem?


It would be really appreciated if you could help me.


Cheers,

Stefan


My session info is:

R version 3.4.1 (2017-06-30)

Platform: x86_64-apple-darwin15.6.0 (64-bit)

Running under: macOS Sierra 10.12.6


Matrix products: default

BLAS: 
/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib

LAPACK: 
/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib


locale:

[1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8


attached base packages:

[1] stats graphics  grDevices utils datasets  methods   base


other attached packages:

[1] Numero_0.99.0


loaded via a namespace (and not attached):

 [1] compiler_3.4.1  backports_1.1.1 BiocStyle_2.4.1 magrittr_1.5
rprojroot_1.2

 [6] htmltools_0.3.6 tools_3.4.1 yaml_2.1.14 Rcpp_0.12.13
stringi_1.1.5

[11] rmarkdown_1.6   knitr_1.17  stringr_1.2.0   digest_0.6.12   
evaluate_0.10.1?

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Re: [Bioc-devel] Organism.dplyr::supportedFilters warning

[Van Twisk, Daniel]

A recent change that was made to GSEABase seems to be the source of the 
problem.  We're looking at it now.


From: Bioc-devel  on behalf of Lucas Schiffer 

Sent: Tuesday, October 3, 2017 2:29:51 PM
To: Ludwig Geistlinger
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Organism.dplyr::supportedFilters warning

Hello,

I think this is related to GSEABase, I noticed this warning when updating 
packages today.

* installing *source* package 'GSEABase' ...
** R
** inst
** preparing package for lazy loading
Warning: no function found corresponding to methods exports from 
'Organism.dplyr' for: 'supportedFilters'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: no function found corresponding to methods exports from 
'Organism.dplyr' for: 'supportedFilters'
* DONE (GSEABase)

Perhaps GSEABase or Organism.dplyr needs a patch.

Thanks,

Lucas

> On Oct 3, 2017, at 10:54, Ludwig Geistlinger 
>  wrote:
>
> Hi,
>
> R CMD check of the devel version of my package lately started to trigger a
> warning:
>
> http://bioconductor.org/checkResults/devel/bioc-LATEST/EnrichmentBrowser/malbec1-checksrc.html
>
>
> * checking whether package �EnrichmentBrowser� can be installed ... WARNING
> Found the following significant warnings:
>
> Warning: no function found corresponding to methods exports from
> �Organism.dplyr� for: �supportedFilters�
>
> See
> �/home/biocbuild/bbs-3.6-bioc/meat/EnrichmentBrowser.Rcheck/00install.out�
> for details.
>
> I am not quite sure how to deal with that.
> Any advice?
>
> Thanks,
> Ludwig
>
> --
> Dr. Ludwig Geistlinger
> eMail: ludwig.geistlin...@bio.ifi.lmu.de
>
>> Hi,
>>
>> This Friday, October 6, is the last day to submit new packages for
>> inclusion in BioC 3.6. Packages submitted by Friday still need to complete
>> the review process before the release but we'll do our best to get them
>> in. Packages submitted after the deadline will be included in the new
>> devel, BioC 3.7.
>>
>>  http://www.bioconductor.org/developers/release-schedule/
>>
>> Valerie
>>
>>
>> This email message may contain legally privileged and/or confidential
>> information.  If you are not the intended recipient(s), or the employee or
>> agent responsible for the delivery of this message to the intended
>> recipient(s), you are hereby notified that any disclosure, copying,
>> distribution, or use of this email message is prohibited.  If you have
>> received this message in error, please notify the sender immediately by
>> e-mail and delete this email message from your computer. Thank you.
>>   [[alternative HTML version deleted]]
>>
>> ___
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>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
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Re: [Bioc-devel] Organism.dplyr::supportedFilters warning

[Lucas Schiffer]

Hello,

I think this is related to GSEABase, I noticed this warning when updating 
packages today.

* installing *source* package 'GSEABase' ...
** R
** inst
** preparing package for lazy loading
Warning: no function found corresponding to methods exports from 
'Organism.dplyr' for: 'supportedFilters'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: no function found corresponding to methods exports from 
'Organism.dplyr' for: 'supportedFilters'
* DONE (GSEABase)

Perhaps GSEABase or Organism.dplyr needs a patch.

Thanks,

Lucas

> On Oct 3, 2017, at 10:54, Ludwig Geistlinger 
>  wrote:
> 
> Hi,
> 
> R CMD check of the devel version of my package lately started to trigger a
> warning:
> 
> http://bioconductor.org/checkResults/devel/bioc-LATEST/EnrichmentBrowser/malbec1-checksrc.html
> 
> 
> * checking whether package ‘EnrichmentBrowser’ can be installed ... WARNING
> Found the following significant warnings:
> 
> Warning: no function found corresponding to methods exports from
> ‘Organism.dplyr’ for: ‘supportedFilters’
> 
> See
> ‘/home/biocbuild/bbs-3.6-bioc/meat/EnrichmentBrowser.Rcheck/00install.out’
> for details.
> 
> I am not quite sure how to deal with that.
> Any advice?
> 
> Thanks,
> Ludwig
> 
> -- 
> Dr. Ludwig Geistlinger
> eMail: ludwig.geistlin...@bio.ifi.lmu.de
> 
>> Hi,
>> 
>> This Friday, October 6, is the last day to submit new packages for
>> inclusion in BioC 3.6. Packages submitted by Friday still need to complete
>> the review process before the release but we'll do our best to get them
>> in. Packages submitted after the deadline will be included in the new
>> devel, BioC 3.7.
>> 
>>  http://www.bioconductor.org/developers/release-schedule/
>> 
>> Valerie
>> 
>> 
>> This email message may contain legally privileged and/or confidential
>> information.  If you are not the intended recipient(s), or the employee or
>> agent responsible for the delivery of this message to the intended
>> recipient(s), you are hereby notified that any disclosure, copying,
>> distribution, or use of this email message is prohibited.  If you have
>> received this message in error, please notify the sender immediately by
>> e-mail and delete this email message from your computer. Thank you.
>>  [[alternative HTML version deleted]]
>> 
>> ___
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>> 
> 
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Re: [Bioc-devel] cherry picking fixes to release

[Turaga, Nitesh]

Thanks for the heads up. I will fix the documentation on the website. 

Best,

Nitesh 

> On Oct 3, 2017, at 2:17 PM, Michael Lawrence  
> wrote:
> 
> Yes, that seems to have fixed it. Thanks for your help.
> 
> I guess the guide on the Bioc website needs to be tweaked.
> 
> Michael
> 
> On Tue, Oct 3, 2017 at 11:15 AM, Turaga, Nitesh
>  wrote:
>> I’m just guessing, but I think “git” is trying to work on the upstream 
>> RELEASE_3_5 directly.
>> 
>> Maybe try,
>> 
>>git fetch —all
>>git checkout -b RELASE_3_5 upstream/RELEASE_3_5   ## This will create 
>> a local branch RELEASE_3_5 which follows your upstream/RELEASE_3_5
>> 
>> This should not have that detached head state.
>> 
>> Nitesh
>> 
>> 
>> 
>>> On Oct 3, 2017, at 2:11 PM, Turaga, Nitesh  
>>> wrote:
>>> 
>>> Hi Micheal,
>>> 
>>> This is very interesting, I’m never run across it.
>>> 
>>> Can you tell me what package you are working on, and I’ll try your commands 
>>> as a user. (I won’t push anything, just want to reproduce the error)
>>> 
>>> Best,
>>> 
>>> Nitesh
 On Oct 3, 2017, at 1:51 PM, Michael Lawrence  
 wrote:
 
 Hi Nitesh,
 
 I tried following your guide to fixing bugs in devel and release, but
 I hit a hurdle.
 
 I did a git fetch --all. Then a git branch RELEASE_3_5.
 
 But I end up in a weird detached head state.
 
 bash-3.2$ git branch
 * (HEAD detached from origin/RELEASE_3_5)
 master
 
 Do you have any ideas?
 
 Thanks,
 Michael
>>> 
>> 
>> 
>> 
>> This email message may contain legally privileged and/or confidential 
>> information.  If you are not the intended recipient(s), or the employee or 
>> agent responsible for the delivery of this message to the intended 
>> recipient(s), you are hereby notified that any disclosure, copying, 
>> distribution, or use of this email message is prohibited.  If you have 
>> received this message in error, please notify the sender immediately by 
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[Bioc-devel] Fwd: git svn permissions

[Turaga, Nitesh]

Begin forwarded message:

From: Thomas Lawson 
>
Subject: Re: [Bioc-devel] git svn permissions
Date: October 3, 2017 at 12:37:14 PM EDT
To: "Turaga, Nitesh" 
>

Great! Seems to work now.

Thanks Nitesh,

Tom

On Tue, Oct 3, 2017 at 4:35 PM, Turaga, Nitesh 
> wrote:
Hi Thomas,

As far the password goes, that is happening from your “origin” i.e Github. You 
set a password for your SSH key there, and we have no way of knowing what it 
is. It is prompting for a password because you are using your HTTPS protocol 
for GitHub, i.e it is not using you SSH key.  This would be your GitHub 
password.

The second attempt you have another issue, you seem to have submitted keys 
again under t.lawson. I just processed the form, and added the keys to 
Bioconductor.

See if that fixes your “fetch upstream” issue.

Best,

Nitesh


> On Oct 3, 2017, at 11:04 AM, Thomas Lawson 
> > wrote:
>
> Hi all,
>
> I have been trying to link my existing github repository to my bioconductor
> repository but I am having a bit of trouble...
>
> I have been following: 
> https://master.bioconductor
> .org/developers/how-to/git/sync-existing-repositories/
>
> I have the an existing github repository 
> (github.com/viant-metabolomics/
> msPurity) that I would like to use maintain my bioconductor repository
> (https://bioconductor.org/packages/release/bioc/html/msPurity.html)
>
> I have created a SSH key with github and used the git /svn form
> https://docs.google.com/forms/d/e/1FAIpQLSdlTbNjsQJDp0BA480vo4tNufs0ziNyNmexegNZgNieIovbAA/
> viewform
>
>   - Using my old svn account username (t.lawson) for the "enter your SVN
>   user id" section
>
>
>   - Using a my github username (tomnl) for the "SSH public key or your
>   GitHub id" section
>
> I can then run the following command OK "git remote add upstream git@git.
> bioconductor.org:packages/msPurity.git"
>
> And when I run "git remote -v" I get:
>
> # originhttps://github.com/Viant-Metabolomics/msPurity (fetch)
> # originhttps://github.com/Viant-Metabolomics/msPurity (push)
> # upstream
> g...@git.bioconductor.org:packages/msPurity.git
>  (fetch)
> # upstream
> g...@git.bioconductor.org:packages/msPurity.git
>  (push)
>
> But when I run "git fetch --all" I get a prompt for a password for thomas.
> nigel.law...@gmail.com
>
> I tried the password that I set for the SSH key but I couldn't get access.
>
>
>
> In case I made a mistake somewhere, I have just repeated the process. I
> have just created a new SSH key following 
> https://help.github
> .com/articles/generating-a-new-ssh-key-and-adding-it-to-the-ssh-agent/
>
> The resubmitted the new SSH public key with Github and resubmitted the git/
> svn form (03/10/2017  approx 14:00).
>
> I now get another error when I run 'git fetch upstram':
>
> # Permission denied (publickey).
> # fatal: Could not read from remote repository.
>
> # Please make sure you have the correct access rights and the repository
> exists.
>
>
> Apologies if I have missed something straightforward
>
> Kind regards,
>
> Tom
>
>   [[alternative HTML version deleted]]
>
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[Bioc-devel] git svn permissions

[Thomas Lawson]

Hi all,

I have been trying to link my existing github repository to my bioconductor
repository but I am having a bit of trouble...

I have been following: https://master.bioconductor
.org/developers/how-to/git/sync-existing-repositories/

I have the an existing github repository (github.com/viant-metabolomics/
msPurity) that I would like to use maintain my bioconductor repository
(https://bioconductor.org/packages/release/bioc/html/msPurity.html)

I have created a SSH key with github and used the git /svn form
https://docs.google.com/forms/d/e/1FAIpQLSdlTbNjsQJDp0BA480vo4tNufs0ziNyNmexegNZgNieIovbAA/
viewform

   - Using my old svn account username (t.lawson) for the "enter your SVN
   user id" section


   - Using a my github username (tomnl) for the "SSH public key or your
   GitHub id" section

I can then run the following command OK "git remote add upstream git@git.
bioconductor.org:packages/msPurity.git"

And when I run "git remote -v" I get:

# originhttps://github.com/Viant-Metabolomics/msPurity (fetch)
# originhttps://github.com/Viant-Metabolomics/msPurity (push)
# upstreamg...@git.bioconductor.org:packages/msPurity.git (fetch)
# upstreamg...@git.bioconductor.org:packages/msPurity.git (push)

But when I run "git fetch --all" I get a prompt for a password for thomas.
nigel.law...@gmail.com

I tried the password that I set for the SSH key but I couldn't get access.



In case I made a mistake somewhere, I have just repeated the process. I
have just created a new SSH key following https://help.github
.com/articles/generating-a-new-ssh-key-and-adding-it-to-the-ssh-agent/

The resubmitted the new SSH public key with Github and resubmitted the git/
svn form (03/10/2017  approx 14:00).

I now get another error when I run 'git fetch upstram':

# Permission denied (publickey).
# fatal: Could not read from remote repository.

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


Apologies if I have missed something straightforward

Kind regards,

Tom

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[Bioc-devel] Organism.dplyr::supportedFilters warning

[Ludwig Geistlinger]

Hi,

R CMD check of the devel version of my package lately started to trigger a
warning:

http://bioconductor.org/checkResults/devel/bioc-LATEST/EnrichmentBrowser/malbec1-checksrc.html


* checking whether package ‘EnrichmentBrowser’ can be installed ... WARNING
Found the following significant warnings:

Warning: no function found corresponding to methods exports from
‘Organism.dplyr’ for: ‘supportedFilters’

See
‘/home/biocbuild/bbs-3.6-bioc/meat/EnrichmentBrowser.Rcheck/00install.out’
for details.

I am not quite sure how to deal with that.
Any advice?

Thanks,
Ludwig

-- 
Dr. Ludwig Geistlinger
eMail: ludwig.geistlin...@bio.ifi.lmu.de

> Hi,
>
> This Friday, October 6, is the last day to submit new packages for
> inclusion in BioC 3.6. Packages submitted by Friday still need to complete
> the review process before the release but we'll do our best to get them
> in. Packages submitted after the deadline will be included in the new
> devel, BioC 3.7.
>
>   http://www.bioconductor.org/developers/release-schedule/
>
> Valerie
>
>
> This email message may contain legally privileged and/or confidential
> information.  If you are not the intended recipient(s), or the employee or
> agent responsible for the delivery of this message to the intended
> recipient(s), you are hereby notified that any disclosure, copying,
> distribution, or use of this email message is prohibited.  If you have
> received this message in error, please notify the sender immediately by
> e-mail and delete this email message from your computer. Thank you.
>   [[alternative HTML version deleted]]
>
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[Bioc-devel] Bioconductor 3.6 release: deadline for new packages

[Obenchain, Valerie]

Hi,

This Friday, October 6, is the last day to submit new packages for inclusion in 
BioC 3.6. Packages submitted by Friday still need to complete the review 
process before the release but we'll do our best to get them in. Packages 
submitted after the deadline will be included in the new devel, BioC 3.7.

  http://www.bioconductor.org/developers/release-schedule/

Valerie


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