[Bioc-devel] " Error in serialize(data, node$con, xdr = FALSE)" during Vignette build (ChIC)

2018-04-16 Thread Carmen M. Livi 

Hi all,

my package recently got accepted and moved to the Bioconductor repository.

Suddenly I get an error during the package build for Linux and OS (the 
INSTALL is working). The error occurs during the creation of the 
vignette in a chunk. The error was not there before and I can't 
reproduce it on my local machine:


" Error in serialize(data, node$con, xdr = FALSE) :
error writing to connection
Execution halted "

Interestingly I get the same error in totally different points for Linux 
and OS.


I am using BiocParallel with BPPARAM = 
BiocParallel::MulticoreParam(workers = 5) and requested 5 CPUs.
Can it be that I am not supposed to use that many CPUs? Did anyone 
encounter a similar issue?
Should I avoid parallelization in the vignette or should I just reduce 
the number?
The dataset I use in the vignette is a small one, so I suppose it is not 
a memory issue.


Thanks for any suggestion,

Carmen

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Re: [Bioc-devel] Can not push to bioconductor! please help me!

2018-04-16 Thread Shepherd, Lori 
Dear BioMedR maintainer,

Unfortunately BioMedR was removed from Bioconductor as of Release 3.6 (last
Oct).  We reached out several times before the 3.6 release as your package had
been failing since early July 2017. Part of the Bioconductor guidelines require
that packages are actively maintained and fixed in a timely manner. Packages are
built daily indicating if there are ERROR's or WARNING's and should be
occasionally checked:

http://bioconductor.org/checkResults/

Besides emailing you privately several times,  it was also posted before the
release on the support site and devel mailing list (bioc-devel@r-project.org)
links given below - giving time to respond before officially being
deprecated. And you would have recieved email notifications from
bbs-nore...@bioconductor.org indicating build failures.

https://support.bioconductor.org/p/100984/
https://support.bioconductor.org/p/100199/

https://stat.ethz.ch/pipermail/bioc-devel/2017-September/011522.html

As you remained unresponsive and the package remained broken it began the
deprecation and end-of-life process.

If you would like to revive the package, it would need to go through
the package review process again and at this point is too late to be included in
the Bioc 3.7 release.  You can have it reviewed and accepted to be re-included 
in
Bioc 3.8 later this year.



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 Zhu MF 

Sent: Monday, April 16, 2018 12:32:10 PM
To: bioc-devel@r-project.org
Subject: [Bioc-devel] Can not push to bioconductor! please help me!

dear sir:


contents in GitHub and that in bioconductor are not the same. I want to update 
the package to follow the contents in github, but falied:


git remote -v
origin  g...@github.com:wind22zhu/BioMedR.git (fetch)
origin  g...@github.com:wind22zhu/BioMedR.git (push)
upstream  g...@git.bioconductor.org:packages/BioMedR.git (fetch)
upstream  g...@git.bioconductor.org:packages/BioMedR.git (push)




$ git push upstream master
Enter passphrase for key '/c/Users/ifyoung/.ssh/id_rsa':
FATAL: W any packages/BioMedR wind22zhu 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.






$ ssh -T g...@git.bioconductor.org




 R  packages/BioMedR


No WRITE(W) permissions?
Why?
Can you help me ? I have been stucked here  for several days!
[[alternative HTML version deleted]]

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Re: [Bioc-devel] Can not push to bioconductor! please help me!

2018-04-16 Thread Turaga, Nitesh 
Hi Zhu,

You submitted your keys with the wrong username. Please use your SVN ID “m.zhu” 
and resubmit

Best,

Nitesh 
> On Apr 16, 2018, at 12:32 PM, Zhu MF  wrote:
> 
> dear sir:
> 
> 
> contents in GitHub and that in bioconductor are not the same. I want to 
> update the package to follow the contents in github, but falied:
> 
> 
> git remote -v
> origin  g...@github.com:wind22zhu/BioMedR.git (fetch)
> origin  g...@github.com:wind22zhu/BioMedR.git (push)
> upstream  g...@git.bioconductor.org:packages/BioMedR.git (fetch) 
> upstream  g...@git.bioconductor.org:packages/BioMedR.git (push)
> 
> 
> 
> 
> $ git push upstream master
> Enter passphrase for key '/c/Users/ifyoung/.ssh/id_rsa':
> FATAL: W any packages/BioMedR wind22zhu 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.
> 
> 
> 
> 
> 
> 
> $ ssh -T g...@git.bioconductor.org
> 
> 
> 
> 
> R  packages/BioMedR
> 
> 
> No WRITE(W) permissions?
> Why?
> Can you help me ? I have been stucked here  for several days!
>   [[alternative HTML version deleted]]
> 
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[Bioc-devel] Can not push to bioconductor! please help me!

2018-04-16 Thread Zhu MF 
dear sir:


contents in GitHub and that in bioconductor are not the same. I want to update 
the package to follow the contents in github, but falied:


git remote -v
origin  g...@github.com:wind22zhu/BioMedR.git (fetch)
origin  g...@github.com:wind22zhu/BioMedR.git (push)
upstream  g...@git.bioconductor.org:packages/BioMedR.git (fetch) 
upstream  g...@git.bioconductor.org:packages/BioMedR.git (push)




$ git push upstream master
Enter passphrase for key '/c/Users/ifyoung/.ssh/id_rsa':
FATAL: W any packages/BioMedR wind22zhu 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.






$ ssh -T g...@git.bioconductor.org




 R  packages/BioMedR


No WRITE(W) permissions?
Why?
Can you help me ? I have been stucked here  for several days!
[[alternative HTML version deleted]]

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Re: [Bioc-devel] Windows

2018-04-16 Thread Ramon Diaz-Uriarte 

And I have now asked this in R-pkg-devel
(https://stat.ethz.ch/pipermail/r-package-devel/2018q2/002617.html), as
suggested by Martin Maechler
(https://stat.ethz.ch/pipermail/bioc-devel/2018-April/013169.html) in the
thread linked by Lori.

But if you can use \link{foo} (instead of \link[pkg]{foo} and
\link[pkg:bar]{foo}), as also suggested by Håkon Tjeldnes, then you should
have no problems.


Best,

R.

On Mon, 16-April-2018, at 13:16:54, Shepherd, Lori 
 wrote:
> This was also discussed in this thread a few weeks ago
>
> https://stat.ethz.ch/pipermail/bioc-devel/2018-April/013156.html
>
>
>
> 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 Mike Smith 
> 
> Sent: Monday, April 16, 2018 6:13:38 AM
> To: Rainer Johannes; bioc-devel
> Subject: Re: [Bioc-devel] Windows  on Tokay2>
>
> Martin mentioned that he changed the wording in
> https://github.com/wch/r-source/commit/cbd7ca1b1aedf0405e11ee2440fbde891cba524e
> , so more recently than your version of R-devel.
>
> Mike
>
> On 16 April 2018 at 11:57, Rainer Johannes 
> wrote:
>
>> Thanks Mike,
>>
>> I somehow missed the discussion you mentioned. I would really not like to
>> include the name of the Rd file I want to link to. The *default* way that
>> works on Linux and macOS should also work on Windows - otherwise what's the
>> matter of the alias? Interestingly, on my Windows test machine (Windows 7)
>> I don't get these warnings (R-devel from 2018-01-07 r74091).
>>
>> jo
>>
>> > On 16 Apr 2018, at 10:49, Mike Smith  wrote:
>> >
>> > Hi Johannes,
>> >
>> > xcms is certainly not alone with the warning, and it was discussed in
>> https://stat.ethz.ch/pipermail/bioc-devel/2018-April/013156.html
>> >
>> > I think you should be able to get round it by including the name of Rd
>> file you're linking to e.g.  
>> \code{\link[MSnbase:pickpeaks-method]{pickPeaks}}
>> (I haven't actually tested this though).
>> >
>> > Mike
>> >
>> > On 16 April 2018 at 09:06, Rainer Johannes 
>> wrote:
>> > Dear all,
>> >
>> > we're experiencing WARNINGS in xcms on Tokay2 that are all related to
>> links in Rd files to functions and methods in other packages.
>> > Example:
>> > we have \code{\link[MSnbase]{pickPeaks}} in
>> XCMSnExp-inherited-methods.Rd that links to the method in MSnbase, that
>> works nicely on Linux and macOS build machines, but on tokay2 we get:
>> >
>> >   Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpw7qeJw/R.
>> INSTALL1e704df56ca9/xcms/man/XCMSnExp-inherited-methods.Rd:59: file link
>> 'pickPeaks' in package 'MSnbase' does not exist and so has been treated as
>> a topic
>> >
>> > is there any other solution to removing all links to external packages?
>> >
>> > thanks, jo
>> >
>> > ___
>> > Bioc-devel@r-project.org mailing list
>> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> >
>>
>>
>
> [[alternative HTML version deleted]]
>
> ___
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>
>
> This email message may contain legally privileged and/or confidential 
> information.  If you are not the intended recipient(s), or the employee or 
> agent responsible for the delivery of this message to the intended 
> recipient(s), you are hereby notified that any disclosure, copying, 
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--
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 3.7 Windows check warning "file link zz in package yy does not exist "

2018-04-16 Thread Ramon Diaz-Uriarte 

Dear Martin,


On Mon, 09-April-2018, at 17:35:47, Martin Maechler 
 wrote:
>> Ramon Diaz-Uriarte 
>> on Mon, 9 Apr 2018 16:51:38 +0200 writes:
>
> > Dear Martin,
>
> > On Fri, 06-April-2018, at 18:59:00, Martin Morgan
> >  wrote:
> >> On 04/06/2018 10:44 AM, Lluís Revilla wrote:
> >>> I have recently faced a similar warning.  This is when a
> >>> link to a help page of another package is broken (there
> >>> is not such help page). Although those could be false
> >>> positives: mclapply help page does exists in parallel
> >>> package.  as.MAList does exists in devel limma
> >> 
> >> when \link-ing to another package, from
> >> RShowDoc("R-exts") section 2.5 the [] has to name the
> >> html help page, not the name of the function. For
> >> instance, `mclapply` is documented on a man page called
> >> mcdummies.Rd (!), so '\link[parallel:mcdummies]{nearest}
> >> would presumably not
>
> > I am confused here: as far as I can tell, there is an
> > mclapply.html file:
>
> > http://stat.ethz.ch/R-manual/R-devel/library/parallel/html/mclapply.html
>
> > In addition, when I use the \link[parallel:mcdummies] I
> > get a warning when testing under Linux.
>
>
> > On rereading section 2.5, I think \link[pkg]{foo} should
> > work too (if there is a foo.html file.)
>
> > Nevertheless, section 2.5 indicates that \link[pkg]{foo}
> > and \link[pkg:bar]{foo} are rarely needed, so I'll try to
> > remove them (except in those cases, covered in section
> > 2.5, where "more than one package offers help on a topic")
>
> Only on Windows, indeed,
> mclapply() is just a dummy function, calling lapply() IIRC.
>
> It is unfortunate that given the above you would be lead to use
> different \link{}s if you are on Windows than on non-Win...
>
> This would be a good question on the   R-package-devel   mailing
> list.
>

Done (https://stat.ethz.ch/pipermail/r-package-devel/2018q2/002617.html).

Thanks,

R.


> Martin
>
>
> >> generate the warning. Similarly
> >> \link[limma:asmalist]{as.MAList}.
> >> 
> >> There are several things that still need exploration.
> >> 
> >> - platform-specific (I have a vague understanding that
> >> Windows is special, but that might be outdated... [at
> >> least in this context...])
> >> 
>
> > I am only getting the warnings under Windows (which lead
> > me to think it was windows misbehaving).
>
>
> >> - recent. I have to admit to changing the text of the
> >> warning with this commit
> >> 
> >> 
> >> 
> https://github.com/wch/r-source/commit/cbd7ca1b1aedf0405e11ee2440fbde891cba524e
> >> 
> >> but what I was intending to do was to change what it
> >> says, from the warning in release ('missing file link')
> >> to what it says, correctly, in devel 'file link ... does
> >> not exist and so has been treated as a topic'.  The old
> >> text appears in release, and the new in devel, as
> >> anticipated.  If I messed up somehow please let me
> >> know...
> >> 
> >> - even with the warning, the link isn't broken in the
> >> dynamic help system (it might have been broken prior to
> >> my commit...).
>
> > OK, thanks.
>
> > Best,
>
>
> > R.
>
>
> >> 
> >> Martin
> >> 
> >>> 
> >>> HTH
> >>> 
> >>> On 6 April 2018 at 16:35, Vincent Carey
> >>>  wrote:
> >>> 
>  ive seen this too apropos bigrquery on windows
>  
>  On Fri, Apr 6, 2018 at 10:22 AM Ramon Diaz-Uriarte
>   wrote:
>  
> > 
> > Dear All,
> > 
> > Two packages I maintain are showing, in Windows, a
> > warning during check with messages like
> > 
> > Rd warning:
> > 
> C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp21WlQD/R.INSTALL23343f935731/
>  OncoSimulR/man/oncoSimulIndiv.Rd:570:
> > file link 'mclapply' in package 'parallel' does not
> > exist and so has been treated as a topic
> > 
> > or
> > 
> > Rd warning:
> > C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQfQaA1/R.
>  INSTALL1ec81d5b6233/ADaCGH2/man/inputToADaCGH.Rd:45:
> > file link 'as.MAList' in package 'limma' does not
> > exist and so has been treated as a topic
> > 
> > 
> > 
> > that I cannot reproduce under Linux and that I think
> > are false positives. Is there a way to avoid this
> > warning? As far as I can tell, those links really
> > exist.
> > 
> > Best,
> > 
> > 
> > R.
> > 
> > --
> > Ramon Diaz-Uriarte Department of Biochemistry, Lab
> > B-25 Facultad de Medicina Universidad

Re: [Bioc-devel] repository change after package acceptance

2018-04-16 Thread Shepherd, Lori 
Yes Bioconductor utilizes the copy on 
git.bioconductor.org:packages/PowerExplorer.git  so as long as changes are 
pushed there - your github repository doesn't matter -


You may have to submit additional ssh-keys to Bioconductor for access; by 
default we use ssh keys from the github account that it was submitted under.



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 Xu Qiao 

Sent: Monday, April 16, 2018 7:55:40 AM
To: Llu�s Revilla
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] repository change after package acceptance

Thanks for your help, Llu�s.

-Xu

From: Llu�s Revilla [mailto:lluis.revi...@gmail.com]
Sent: maanantai 16. huhtikuuta 2018 13.48
To: Xu Qiao 
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] repository change after package acceptance

Dear Xu,

While you, with your ssh key, keep pushing to the 
git.bioconductor.org it doesn't matter where else 
is stored.
To move a repository within github you need to follow this tutorial: 
https://help.github.com/articles/transferring-a-repository-owned-by-your-personal-account/#transferring-to-an-organization
Regards,
Llu�s


On 16 April 2018 at 12:05, Xu Qiao > 
wrote:
Hi everyone,

I am the developer of package "PowerExplorer",  it has been accepted last week, 
and now it is visible on Bioconductor git server. However, the package was 
developed in my own personal GitHub repository, now I need to move it into our 
lab repository. Does anyone have any idea how to do this smoothly? Since the 
Bioconductor is expecting to be associated with my original GitHub-id.

Kind regards,
Xu
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Re: [Bioc-devel] repository change after package acceptance

2018-04-16 Thread Xu Qiao 
Thanks for your help, Lluís.

-Xu

From: Lluís Revilla [mailto:lluis.revi...@gmail.com]
Sent: maanantai 16. huhtikuuta 2018 13.48
To: Xu Qiao 
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] repository change after package acceptance

Dear Xu,

While you, with your ssh key, keep pushing to the 
git.bioconductor.org it doesn't matter where else 
is stored.
To move a repository within github you need to follow this tutorial: 
https://help.github.com/articles/transferring-a-repository-owned-by-your-personal-account/#transferring-to-an-organization
Regards,
Lluís


On 16 April 2018 at 12:05, Xu Qiao > 
wrote:
Hi everyone,

I am the developer of package "PowerExplorer",  it has been accepted last week, 
and now it is visible on Bioconductor git server. However, the package was 
developed in my own personal GitHub repository, now I need to move it into our 
lab repository. Does anyone have any idea how to do this smoothly? Since the 
Bioconductor is expecting to be associated with my original GitHub-id.

Kind regards,
Xu
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Re: [Bioc-devel] Need some help to submit a R package.

2018-04-16 Thread Martin Morgan 
If you are still having problems understanding warnings, it is probably 
better to use the github issue -- it may take some time to get an 
answer, because the reviewers have many responsibilities.


It looks like your 'webhook' is not correct, and that you are not 
changing the version of your package (from 0.99.0 to 0.99.1, 0.99.2, 
...) when you wish to generate another build report. @grimbough 
indicated in the github issue how to address these problems.


Martin

On 04/16/2018 03:58 AM, Pijush Das wrote:

Dear  Ruqian,


Yes sir, I have opened the build report which is a link to an HTML page
with details.
But I unable to understand why the WARNING massages are showing.

Three days before the other reviewers had made some comments and asked me
to address
those issues and also told me to solve the NOTEs produced by BioCheck.

Presently I am working on the sigFeature package to address those issues.
I shall communicate soon after solving those issues.


Thank you


Regards
Pijush



On Mon, Apr 16, 2018 at 4:06 AM, Ruqian Lyu 
wrote:


Hi Pijush,

Did you open the build report which is a link to an HTML page with details
of the warning?


Regards,
Ruqian



On Fri, Apr 13, 2018 at 4:54 PM, Pijush Das  wrote:


Dear Sir,


I have submitted an R package named "sigFeature" in Github and also
Bioconductor 9 days before.
The reviewers only said that there is some WARNING problem in the package
in different platform.

But after that they are not communicating any thing regarding the package.
I have checked the package
windows and Ubuntu it is working fine.

I unable to understand what actually the problem is ?
And the reviewers are not communicating about the problem. Though I am
getting lots of email from bioc-devel dealing with others package
problem .

Please suggest me what should I do now ?




Thank you



Regards
Pijush




On Mon, Apr 2, 2018 at 4:26 PM, Turaga, Nitesh <
nitesh.tur...@roswellpark.org> wrote:


Hi,

Please read through this documentation.

http://bioconductor.org/developers/package-submission/


Nitesh


On Apr 2, 2018, at 2:00 AM, Pijush Das  wrote:

Dear Sir,



I have developed an R package. I want to submit this package in
Bioconductor.
Please help me to submit the R package.









regards
Pijush Das

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Re: [Bioc-devel] Windows

2018-04-16 Thread Shepherd, Lori 
This was also discussed in this thread a few weeks ago

https://stat.ethz.ch/pipermail/bioc-devel/2018-April/013156.html



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 Mike Smith 

Sent: Monday, April 16, 2018 6:13:38 AM
To: Rainer Johannes; bioc-devel
Subject: Re: [Bioc-devel] Windows 

Martin mentioned that he changed the wording in
https://github.com/wch/r-source/commit/cbd7ca1b1aedf0405e11ee2440fbde891cba524e
, so more recently than your version of R-devel.

Mike

On 16 April 2018 at 11:57, Rainer Johannes 
wrote:

> Thanks Mike,
>
> I somehow missed the discussion you mentioned. I would really not like to
> include the name of the Rd file I want to link to. The *default* way that
> works on Linux and macOS should also work on Windows - otherwise what's the
> matter of the alias? Interestingly, on my Windows test machine (Windows 7)
> I don't get these warnings (R-devel from 2018-01-07 r74091).
>
> jo
>
> > On 16 Apr 2018, at 10:49, Mike Smith  wrote:
> >
> > Hi Johannes,
> >
> > xcms is certainly not alone with the warning, and it was discussed in
> https://stat.ethz.ch/pipermail/bioc-devel/2018-April/013156.html
> >
> > I think you should be able to get round it by including the name of Rd
> file you're linking to e.g.  \code{\link[MSnbase:pickpeaks-method]{pickPeaks}}
> (I haven't actually tested this though).
> >
> > Mike
> >
> > On 16 April 2018 at 09:06, Rainer Johannes 
> wrote:
> > Dear all,
> >
> > we're experiencing WARNINGS in xcms on Tokay2 that are all related to
> links in Rd files to functions and methods in other packages.
> > Example:
> > we have \code{\link[MSnbase]{pickPeaks}} in
> XCMSnExp-inherited-methods.Rd that links to the method in MSnbase, that
> works nicely on Linux and macOS build machines, but on tokay2 we get:
> >
> >   Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpw7qeJw/R.
> INSTALL1e704df56ca9/xcms/man/XCMSnExp-inherited-methods.Rd:59: file link
> 'pickPeaks' in package 'MSnbase' does not exist and so has been treated as
> a topic
> >
> > is there any other solution to removing all links to external packages?
> >
> > thanks, jo
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
>

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Re: [Bioc-devel] repository change after package acceptance

2018-04-16 Thread Lluís Revilla 
Dear Xu,

While you, with your ssh key, keep pushing to the git.bioconductor.org it
doesn't matter where else is stored.
To move a repository within github you need to follow this tutorial:
https://help.github.com/articles/transferring-a-repository-owned-by-your-personal-account/#transferring-to-an-organization

Regards,

Lluís


On 16 April 2018 at 12:05, Xu Qiao  wrote:

> Hi everyone,
>
> I am the developer of package "PowerExplorer",  it has been accepted last
> week, and now it is visible on Bioconductor git server. However, the
> package was developed in my own personal GitHub repository, now I need to
> move it into our lab repository. Does anyone have any idea how to do this
> smoothly? Since the Bioconductor is expecting to be associated with my
> original GitHub-id.
>
> Kind regards,
> Xu
> ___
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>

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Re: [Bioc-devel] Windows

2018-04-16 Thread Mike Smith 
Martin mentioned that he changed the wording in
https://github.com/wch/r-source/commit/cbd7ca1b1aedf0405e11ee2440fbde891cba524e
, so more recently than your version of R-devel.

Mike

On 16 April 2018 at 11:57, Rainer Johannes 
wrote:

> Thanks Mike,
>
> I somehow missed the discussion you mentioned. I would really not like to
> include the name of the Rd file I want to link to. The *default* way that
> works on Linux and macOS should also work on Windows - otherwise what's the
> matter of the alias? Interestingly, on my Windows test machine (Windows 7)
> I don't get these warnings (R-devel from 2018-01-07 r74091).
>
> jo
>
> > On 16 Apr 2018, at 10:49, Mike Smith  wrote:
> >
> > Hi Johannes,
> >
> > xcms is certainly not alone with the warning, and it was discussed in
> https://stat.ethz.ch/pipermail/bioc-devel/2018-April/013156.html
> >
> > I think you should be able to get round it by including the name of Rd
> file you're linking to e.g.  \code{\link[MSnbase:pickpeaks-method]{pickPeaks}}
> (I haven't actually tested this though).
> >
> > Mike
> >
> > On 16 April 2018 at 09:06, Rainer Johannes 
> wrote:
> > Dear all,
> >
> > we're experiencing WARNINGS in xcms on Tokay2 that are all related to
> links in Rd files to functions and methods in other packages.
> > Example:
> > we have \code{\link[MSnbase]{pickPeaks}} in
> XCMSnExp-inherited-methods.Rd that links to the method in MSnbase, that
> works nicely on Linux and macOS build machines, but on tokay2 we get:
> >
> >   Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpw7qeJw/R.
> INSTALL1e704df56ca9/xcms/man/XCMSnExp-inherited-methods.Rd:59: file link
> 'pickPeaks' in package 'MSnbase' does not exist and so has been treated as
> a topic
> >
> > is there any other solution to removing all links to external packages?
> >
> > thanks, jo
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
>

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[Bioc-devel] repository change after package acceptance

2018-04-16 Thread Xu Qiao 
Hi everyone,

I am the developer of package "PowerExplorer",  it has been accepted last week, 
and now it is visible on Bioconductor git server. However, the package was 
developed in my own personal GitHub repository, now I need to move it into our 
lab repository. Does anyone have any idea how to do this smoothly? Since the 
Bioconductor is expecting to be associated with my original GitHub-id.

Kind regards,
Xu
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Re: [Bioc-devel] Windows

2018-04-16 Thread Rainer Johannes 
Thanks Mike,

I somehow missed the discussion you mentioned. I would really not like to 
include the name of the Rd file I want to link to. The *default* way that works 
on Linux and macOS should also work on Windows - otherwise what's the matter of 
the alias? Interestingly, on my Windows test machine (Windows 7) I don't get 
these warnings (R-devel from 2018-01-07 r74091).

jo

> On 16 Apr 2018, at 10:49, Mike Smith  wrote:
> 
> Hi Johannes,
> 
> xcms is certainly not alone with the warning, and it was discussed in 
> https://stat.ethz.ch/pipermail/bioc-devel/2018-April/013156.html
> 
> I think you should be able to get round it by including the name of Rd file 
> you're linking to e.g.  \code{\link[MSnbase:pickpeaks-method]{pickPeaks}} (I 
> haven't actually tested this though).
> 
> Mike
> 
> On 16 April 2018 at 09:06, Rainer Johannes  wrote:
> Dear all,
> 
> we're experiencing WARNINGS in xcms on Tokay2 that are all related to links 
> in Rd files to functions and methods in other packages.
> Example:
> we have \code{\link[MSnbase]{pickPeaks}} in XCMSnExp-inherited-methods.Rd 
> that links to the method in MSnbase, that works nicely on Linux and macOS 
> build machines, but on tokay2 we get:
> 
>   Rd warning: 
> C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpw7qeJw/R.INSTALL1e704df56ca9/xcms/man/XCMSnExp-inherited-methods.Rd:59:
>  file link 'pickPeaks' in package 'MSnbase' does not exist and so has been 
> treated as a topic
> 
> is there any other solution to removing all links to external packages?
> 
> thanks, jo
> 
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> 

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Re: [Bioc-devel] Windows

2018-04-16 Thread Mike Smith 
Hi Johannes,

xcms is certainly not alone with the warning, and it was discussed in
https://stat.ethz.ch/pipermail/bioc-devel/2018-April/013156.html

I think you should be able to get round it by including the name of Rd file
you're linking to e.g.  \code{\link[MSnbase:pickpeaks-method]{pickPeaks}}
(I haven't actually tested this though).

Mike

On 16 April 2018 at 09:06, Rainer Johannes 
wrote:

> Dear all,
>
> we're experiencing WARNINGS in xcms on Tokay2 that are all related to
> links in Rd files to functions and methods in other packages.
> Example:
> we have \code{\link[MSnbase]{pickPeaks}} in XCMSnExp-inherited-methods.Rd
> that links to the method in MSnbase, that works nicely on Linux and macOS
> build machines, but on tokay2 we get:
>
>   Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpw7qeJw/R.
> INSTALL1e704df56ca9/xcms/man/XCMSnExp-inherited-methods.Rd:59: file link
> 'pickPeaks' in package 'MSnbase' does not exist and so has been treated as
> a topic
>
> is there any other solution to removing all links to external packages?
>
> thanks, jo
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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Re: [Bioc-devel] Need some help to submit a R package.

2018-04-16 Thread Pijush Das 
Dear  Ruqian,


Yes sir, I have opened the build report which is a link to an HTML page
with details.
But I unable to understand why the WARNING massages are showing.

Three days before the other reviewers had made some comments and asked me
to address
those issues and also told me to solve the NOTEs produced by BioCheck.

Presently I am working on the sigFeature package to address those issues.
I shall communicate soon after solving those issues.


Thank you


Regards
Pijush



On Mon, Apr 16, 2018 at 4:06 AM, Ruqian Lyu 
wrote:

> Hi Pijush,
>
> Did you open the build report which is a link to an HTML page with details
> of the warning?
>
>
> Regards,
> Ruqian
>
>
>
> On Fri, Apr 13, 2018 at 4:54 PM, Pijush Das  wrote:
>
>> Dear Sir,
>>
>>
>> I have submitted an R package named "sigFeature" in Github and also
>> Bioconductor 9 days before.
>> The reviewers only said that there is some WARNING problem in the package
>> in different platform.
>>
>> But after that they are not communicating any thing regarding the package.
>> I have checked the package
>> windows and Ubuntu it is working fine.
>>
>> I unable to understand what actually the problem is ?
>> And the reviewers are not communicating about the problem. Though I am
>> getting lots of email from bioc-devel dealing with others package
>> problem .
>>
>> Please suggest me what should I do now ?
>>
>>
>>
>>
>> Thank you
>>
>>
>>
>> Regards
>> Pijush
>>
>>
>>
>>
>> On Mon, Apr 2, 2018 at 4:26 PM, Turaga, Nitesh <
>> nitesh.tur...@roswellpark.org> wrote:
>>
>> > Hi,
>> >
>> > Please read through this documentation.
>> >
>> > http://bioconductor.org/developers/package-submission/
>> >
>> >
>> > Nitesh
>> >
>> > > On Apr 2, 2018, at 2:00 AM, Pijush Das  wrote:
>> > >
>> > > Dear Sir,
>> > >
>> > >
>> > >
>> > > I have developed an R package. I want to submit this package in
>> > > Bioconductor.
>> > > Please help me to submit the R package.
>> > >
>> > >
>> > >
>> > >
>> > >
>> > >
>> > >
>> > >
>> > >
>> > > regards
>> > > Pijush Das
>> > >
>> > >   [[alternative HTML version deleted]]
>> > >
>> > > ___
>> > > Bioc-devel@r-project.org mailing list
>> > > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> >
>> >
>> >
>> > 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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[Bioc-devel] Windows

2018-04-16 Thread Rainer Johannes 
Dear all,

we're experiencing WARNINGS in xcms on Tokay2 that are all related to links in 
Rd files to functions and methods in other packages.
Example:
we have \code{\link[MSnbase]{pickPeaks}} in XCMSnExp-inherited-methods.Rd that 
links to the method in MSnbase, that works nicely on Linux and macOS build 
machines, but on tokay2 we get:

  Rd warning: 
C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpw7qeJw/R.INSTALL1e704df56ca9/xcms/man/XCMSnExp-inherited-methods.Rd:59:
 file link 'pickPeaks' in package 'MSnbase' does not exist and so has been 
treated as a topic

is there any other solution to removing all links to external packages?

thanks, jo

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