[Bioc-devel] Fwd: [Bioconductor/Contributions] GIGSEA (#720)

[Shijia Zhu]

Hi Everyone,

  My package just passed the check, without errors or warnings.

I am pretty new to Bioconductor. May I ask whether this is done? or
anything else I need to do for releasing my package?

Any help would be much appreciated.

Best
Shijia



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Subject: Re: [Bioconductor/Contributions] GIGSEA (#720)
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Re: [Bioc-devel] BioC 3.7 Windows check warning "file link zz in package yy does not exist "

[Martin Morgan]

On 04/18/2018 02:45 PM, Vincent Carey wrote:



On Mon, Apr 9, 2018 at 11:23 AM, Martin Morgan 
> 
wrote:




On 04/09/2018 10:51 AM, Ramon Diaz-Uriarte wrote:


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.


yeah, this is a pretty good one. If you look at

https://github.com/wch/r-source/tree/trunk/src/library/parallel/man


you'll see that there are different man pages for different
operating systems. On windows there is mcdummies, on unix mclapply &
friends. This seems like a bad idea (users comparing notes to work
through a problem get different help pages!). I don't really know
how to link explicitly to these in a conditional manner.


Does this mean that to cross-reference to MArrayLM-class, I need to find 
limma source and
determine that the topic is covered in marraylm.Rd and use 
\link[limma:marraylm]{MArrayLM-class} for
the cross-reference?  I don't see how this is good -- are the page names 
programmatically accessible

to developers who want to cross-reference?  here's the grep result:

marraylm.Rd:\alias{MArrayLM-class}


I agree that this is a bad idea.

I think the first solution is not to use \link[pkg]{foo} when it is not 
needed, which Writing R Extensions 
(https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Cross_002dreferences) 
says


  "These are rarely needed, perhaps to refer to not-yet-installed 
packages (but there the HTML help system will resolve the link at run 
time) or in the normally undesirable event that more than one package 
offers help on a topic"


Packages you depend / import and even suggest will be installed by the 
build system, so the only need is when two or more packages define the 
same topic.


But even then, when faced with a WARNING, and even Bioc core team 
members or reviewers for new packages hassling you about correcting 
WARNINGs, I personally would trade off sanity for perfection and stick 
with \link[limma]{MArrayLM-class} -- there is a WARNING, but the warning 
says that it's going to treat MArrayLM-class as a topic (alias) and 
it'll get resolved correctly.


Also, for what it's worth, the opinion expressed in 
https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Cross_002dreferences 
is that the fact that these WARNINGs are often Windows-specific is more 
likely that the linux check is wrong (i.e., the WARNING should also be 
generated there). I will try to investigate that further.


Martin





And in general it seems highly fragile to link to the name of the
help page, rather than to the alias. I'd treat the 'warning' as
(maybe bad) advice, rather than a requirement.

On rereading section 2.5, I think \link[pkg]{foo} should work
too (if there
is a foo.html file.)


it does (but on windows there is no mclapply.html). But also on
windows the '...treated as a topic' part of the warning actually
indicates that R has figured out where it should link, so you get
the warning but also a working link.

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")


yes the first pass should also be the simplest -- no fancy markup
unless necessary.

Martin




generate the warning. Similarly
\link[limma:asmalist]{as.MAList}.

There are several things that still need 

Re: [Bioc-devel] BioC 3.7 Windows check warning "file link zz in package yy does not exist "

[Vincent Carey]

yes, the [] is a habit i need to break.  ok, we'll get by.

On Wed, Apr 18, 2018 at 3:09 PM, Martin Morgan <
martin.mor...@roswellpark.org> wrote:

>
>
> On 04/18/2018 02:45 PM, Vincent Carey wrote:
>
>>
>>
>> On Mon, Apr 9, 2018 at 11:23 AM, Martin Morgan <
>> martin.mor...@roswellpark.org >
>> wrote:
>>
>>
>>
>> On 04/09/2018 10:51 AM, Ramon Diaz-Uriarte wrote:
>>
>>
>> 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/m
>> clapply.html
>> > mclapply.html>
>>
>> In addition, when I use the \link[parallel:mcdummies] I get a
>> warning when
>> testing under Linux.
>>
>>
>> yeah, this is a pretty good one. If you look at
>>
>> https://github.com/wch/r-source/tree/trunk/src/library/parallel/man
>> 
>>
>> you'll see that there are different man pages for different
>> operating systems. On windows there is mcdummies, on unix mclapply &
>> friends. This seems like a bad idea (users comparing notes to work
>> through a problem get different help pages!). I don't really know
>> how to link explicitly to these in a conditional manner.
>>
>>
>> Does this mean that to cross-reference to MArrayLM-class, I need to find
>> limma source and
>> determine that the topic is covered in marraylm.Rd and use
>> \link[limma:marraylm]{MArrayLM-class} for
>> the cross-reference?  I don't see how this is good -- are the page names
>> programmatically accessible
>> to developers who want to cross-reference?  here's the grep result:
>>
>> marraylm.Rd:\alias{MArrayLM-class}
>>
>
> I agree that this is a bad idea.
>
> I think the first solution is not to use \link[pkg]{foo} when it is not
> needed, which Writing R Extensions (https://cran.r-project.org/do
> c/manuals/r-release/R-exts.html#Cross_002dreferences) says
>
>   "These are rarely needed, perhaps to refer to not-yet-installed packages
> (but there the HTML help system will resolve the link at run time) or in
> the normally undesirable event that more than one package offers help on a
> topic"
>
> Packages you depend / import and even suggest will be installed by the
> build system, so the only need is when two or more packages define the same
> topic.
>
> But even then, when faced with a WARNING, and even Bioc core team members
> or reviewers for new packages hassling you about correcting WARNINGs, I
> personally would trade off sanity for perfection and stick with
> \link[limma]{MArrayLM-class} -- there is a WARNING, but the warning says
> that it's going to treat MArrayLM-class as a topic (alias) and it'll get
> resolved correctly.
>
> Also, for what it's worth, the opinion expressed in
> https://cran.r-project.org/doc/manuals/r-release/R-exts.html
> #Cross_002dreferences is that the fact that these WARNINGs are often
> Windows-specific is more likely that the linux check is wrong (i.e., the
> WARNING should also be generated there). I will try to investigate that
> further.
>
> Martin
>
>
>
>>
>> And in general it seems highly fragile to link to the name of the
>> help page, rather than to the alias. I'd treat the 'warning' as
>> (maybe bad) advice, rather than a requirement.
>>
>> On rereading section 2.5, I think \link[pkg]{foo} should work
>> too (if there
>> is a foo.html file.)
>>
>>
>> it does (but on windows there is no mclapply.html). But also on
>> windows the '...treated as a topic' part of the warning actually
>> indicates that R has figured out where it should link, so you get
>> the warning but also a working link.
>>
>> Nevertheless, section 2.5 indicates that \link[pkg]{foo} and
>> \link[pkg:bar]{foo} are rarely 

Re: [Bioc-devel] GateFinder: Windows Server Error

[Tony Culos]

Hi Lori,

Thanks for your assistance and helping me understand how to change the
supported platforms on a package, it's much appreciated. When might I know
whether these changes had the desired affect? Is there a way to have it
checked directly or will I have to wait for another set of tests to be ran
on your systems?

Thank You,
Tony C.

On Wed, Apr 18, 2018 at 4:19 AM, Shepherd, Lori <
lori.sheph...@roswellpark.org> wrote:

> Yes this is possible.
>
> If you add the file to the top level of your package
>
> ".BBSoptions"
>
>
> with the entry
>
> "UnsupportedPlatforms: win32"
>
>
>
>
>
> 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 Tony
> Culos 
> *Sent:* Tuesday, April 17, 2018 5:02 PM
> *To:* bioc-devel@r-project.org
> *Subject:* [Bioc-devel] GateFinder: Windows Server Error
>
> Hello,
>
> I'm working on resolving the error with the GateFinder package for Windows
> Server 2012 R2 Standard, it appears that the issue is a calculation
> difference between 32 and 64-bit systems. Is it possible to have the
> package be included in the next release only with support for 64-bit
> systems? I couldn't find any explicit reference to this sort of situation
> so any clarification would be greatly appreciated.
>
> Thank You,
> Tony C.
>
> [[alternative HTML version deleted]]
>
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> information. If you are not the intended recipient(s), or the employee or
> agent responsible for the delivery of this message to the intended
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Re: [Bioc-devel] BioC 3.7 Windows check warning "file link zz in package yy does not exist "

[Vincent Carey]

On Mon, Apr 9, 2018 at 11:23 AM, Martin Morgan <
martin.mor...@roswellpark.org> wrote:

>
>
> On 04/09/2018 10:51 AM, Ramon Diaz-Uriarte wrote:
>
>>
>> Dear Martin,
>>
>> On Fri, 06-April-2018, at 18:59:00, Martin Morgan <
>> martin.mor...@roswellpark.org> 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.
>>
>
> yeah, this is a pretty good one. If you look at
>
>   https://github.com/wch/r-source/tree/trunk/src/library/parallel/man
>
> you'll see that there are different man pages for different operating
> systems. On windows there is mcdummies, on unix mclapply & friends. This
> seems like a bad idea (users comparing notes to work through a problem get
> different help pages!). I don't really know how to link explicitly to these
> in a conditional manner.
>

Does this mean that to cross-reference to MArrayLM-class, I need to find
limma source and
determine that the topic is covered in marraylm.Rd and use
\link[limma:marraylm]{MArrayLM-class} for
the cross-reference?  I don't see how this is good -- are the page names
programmatically accessible
to developers who want to cross-reference?  here's the grep result:

marraylm.Rd:\alias{MArrayLM-class}


>
> And in general it seems highly fragile to link to the name of the help
> page, rather than to the alias. I'd treat the 'warning' as (maybe bad)
> advice, rather than a requirement.
>
> On rereading section 2.5, I think \link[pkg]{foo} should work too (if there
>> is a foo.html file.)
>>
>
> it does (but on windows there is no mclapply.html). But also on windows
> the '...treated as a topic' part of the warning actually indicates that R
> has figured out where it should link, so you get the warning but also a
> working link.
>
> 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")
>>
>
> yes the first pass should also be the simplest -- no fancy markup unless
> necessary.
>
> 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/cbd7ca1b1aedf0405e11e
>>> e2440fbde891cba524e
>>>
>>> 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.INSTALL2
>> 3343f935731/
>>
> 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 

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

[Shepherd, Lori]

This page

http://bioconductor.org/packages/3.7/bioc/html/coMET.html
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/
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

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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recipient(s), you are hereby notified that any disclosure, copying, 
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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
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/
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

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


[[alternative HTML version deleted]]

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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.

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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


[[alternative HTML version deleted]]

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Re: [Bioc-devel] ‘SOCKcluster’ cluster error with bplapply() under merida2

[Martin Morgan]

Also FWIW changing things like (there are a number of these changes)

sum(unlist(lapply(data, length)))/1e+06

to
sum(lengths(data)) / 1e6

actually has measurable effect on the speed of your code.

Martin

On 04/18/2018 10:47 AM, Carmen M. Livi wrote:

Dear Martin Morgan,

ok, I will switch back to parallel then. Thank you very much for your 
reply.


Kind regards,
Carmen

On 18/04/2018 15:30, Martin Morgan wrote:
I'm sorry not to respond to your first email. This is a problem in 
BiocParallel that I am working on. In your particular case, where you 
are relying on a third-party package that uses parallel::mclapply, I 
think you should revert to using that.


Martin

On 04/18/2018 09:22 AM, Carmen M. Livi wrote:

Hi all,

I was using parallel::mclapply() but have been encouraged to substitute
it with BiocParallel::bplapply().

BiocParallel::bplapply(data,
      BPPARAM = BiocParallel::MulticoreParam(workers =x ),
      FUN  =...)

I never had problems with the code. Now the package got accepted and
moved to the bioconductor-repository and suddenly I am getting errors in
the vignette build when asking for 5 workers:

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

After reducing the number of requested workers to 3 my package passed
under linux (malbec2 and malbec1) but still fails under OS X (merida2):

"Error : failed to stop ‘SOCKcluster’ cluster: error writing to 
connection"
https://master.bioconductor.org/checkResults/3.7/bioc-LATEST/ChIC/merida2-buildsrc.html 



Does anyone have an idea what is going on? Am I not supposed to ask for
more then 1 worker in the vignette?

What if I just switch back to parallel::mclapply?

Thank you,
Carmen
//

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information.  If you are not the intended recipient(s), or the 
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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 
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Re: [Bioc-devel] ‘SOCKcluster’ cluster error with bplapply() under merida2

[Carmen M. Livi]

Dear Martin Morgan,

ok, I will switch back to parallel then. Thank you very much for your reply.

Kind regards,
Carmen

On 18/04/2018 15:30, Martin Morgan wrote:
I'm sorry not to respond to your first email. This is a problem in 
BiocParallel that I am working on. In your particular case, where you 
are relying on a third-party package that uses parallel::mclapply, I 
think you should revert to using that.


Martin

On 04/18/2018 09:22 AM, Carmen M. Livi wrote:

Hi all,

I was using parallel::mclapply() but have been encouraged to substitute
it with BiocParallel::bplapply().

BiocParallel::bplapply(data,
      BPPARAM = BiocParallel::MulticoreParam(workers =x ),
      FUN  =...)

I never had problems with the code. Now the package got accepted and
moved to the bioconductor-repository and suddenly I am getting errors in
the vignette build when asking for 5 workers:

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

After reducing the number of requested workers to 3 my package passed
under linux (malbec2 and malbec1) but still fails under OS X (merida2):

"Error : failed to stop ‘SOCKcluster’ cluster: error writing to 
connection"
https://master.bioconductor.org/checkResults/3.7/bioc-LATEST/ChIC/merida2-buildsrc.html 



Does anyone have an idea what is going on? Am I not supposed to ask for
more then 1 worker in the vignette?

What if I just switch back to parallel::mclapply?

Thank you,
Carmen
//

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

[Shepherd, Lori]

Dear BioMedR Maintainer


I'm sorry that you never responded to our many earlier emails and 
notifications. I recommend checking your email systems to make sure emails from 
Bioconductor and RoswellPark are not being blocked or spammed.

To address your first point:

Your github repository is not what we use at Bioconductor as the canonical 
location. That is your personal local repository. When the package was accepted 
you received instructions for updating the package in Bioconductor using svn.  
Since then,  Bioconductor has moved to git version control, which was announced 
multiple times with instructions on how to update package.   We posed FAQs and 
instructions for git on the website.
http://bioconductor.org/developers/how-to/git/

It is your responsibilty to make sure your package works with any dependencies
you required and that it builds on our Bioconductor systems (not your 
independent systems)
http://bioconductor.org/checkResults/ .

Your package has already been removed from Bioconductor following the end of
life procedure for packages found at
https://www.bioconductor.org/developers/package-end-of-life/

Please resubmit to the tracker for re-review and inclusion in Bioc 3.8
https://github.com/Bioconductor/Contributions/issues



Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Zhu MF 
Sent: Wednesday, April 18, 2018 2:04:40 AM
To: Shepherd, Lori
Cc: bioc-devel@r-project.org
Subject: Re:Re: [Bioc-devel] Can not push to bioconductor! please help me!


Dear sir,

Thank you for your letter.

Firstly, Actually, I don't know why does the content in GitHub and Bioconductor 
are not the same when the package was firstly releaed in bioconductor?  In the 
GitHub we have removed the error file since the first release.

Then, the tips of the checked error was caused by the  expired function of rcdk 
not BioMedR.

The error is in the unitest that actually worked well in other cases, so in our 
local machine, this error have not been triggerd in the past one year, so we 
don't know what happened.

So, could you help us simple the review process and include in the  Bioc 3.7 
release?

Thank you very much!




At 2018-04-17 01:47:51, "Shepherd, Lori" 
> wrote:

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 

Re: [Bioc-devel] ‘SOCKcluster’ cluster error with bplapply() under merida2

[Martin Morgan]

I'm sorry not to respond to your first email. This is a problem in 
BiocParallel that I am working on. In your particular case, where you 
are relying on a third-party package that uses parallel::mclapply, I 
think you should revert to using that.


Martin

On 04/18/2018 09:22 AM, Carmen M. Livi wrote:

Hi all,

I was using parallel::mclapply() but have been encouraged to substitute
it with BiocParallel::bplapply().

BiocParallel::bplapply(data,
      BPPARAM = BiocParallel::MulticoreParam(workers =x ),
      FUN  =...)

I never had problems with the code. Now the package got accepted and
moved to the bioconductor-repository and suddenly I am getting errors in
the vignette build when asking for 5 workers:

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

After reducing the number of requested workers to 3 my package passed
under linux (malbec2 and malbec1) but still fails under OS X (merida2):

"Error : failed to stop ‘SOCKcluster’ cluster: error writing to connection"
https://master.bioconductor.org/checkResults/3.7/bioc-LATEST/ChIC/merida2-buildsrc.html

Does anyone have an idea what is going on? Am I not supposed to ask for
more then 1 worker in the vignette?

What if I just switch back to parallel::mclapply?

Thank you,
Carmen
//

[[alternative HTML version deleted]]

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[Bioc-devel] ‘SOCKcluster’ cluster error with bplapply() under merida2

[Carmen M. Livi]

Hi all,

I was using parallel::mclapply() but have been encouraged to substitute 
it with BiocParallel::bplapply().

BiocParallel::bplapply(data,
     BPPARAM = BiocParallel::MulticoreParam(workers =x ),
     FUN  =...)

I never had problems with the code. Now the package got accepted and 
moved to the bioconductor-repository and suddenly I am getting errors in 
the vignette build when asking for 5 workers:

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

After reducing the number of requested workers to 3 my package passed 
under linux (malbec2 and malbec1) but still fails under OS X (merida2):

"Error : failed to stop ‘SOCKcluster’ cluster: error writing to connection "
https://master.bioconductor.org/checkResults/3.7/bioc-LATEST/ChIC/merida2-buildsrc.html

Does anyone have an idea what is going on? Am I not supposed to ask for 
more then 1 worker in the vignette?

What if I just switch back to parallel::mclapply?

Thank you,
Carmen
//

[[alternative HTML version deleted]]

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Re: [Bioc-devel] Transition from Google Sheet to Web App

[Obenchain, Valerie]

This transition will start at 9am EST today. We'll post back when it's done.

Valerie


On 04/17/2018 10:27 AM, Obenchain, Valerie wrote:

Hi developers,

Tomorrow we are bringing a web app online to help with the management of SSH 
keys. The app will replace the Google Sheet currently used to add keys. Through 
the web interface you'll be able to add keys and change your email or github 
username. There is also an option to see what packages you have access to.

Using the app is not a requirement. It's intended to help package authors get 
setup with keys and access to their package in the Bioconductor git repository. 
Those of you already set up with keys and access may never need to use it.

Tomorrow, April 18, we'll have downtime from 9-11am EST while we take down the 
Google Sheet and bring up the app.

Thanks.

Valerie and Nitesh


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 
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Re: [Bioc-devel] GateFinder: Windows Server Error

[Shepherd, Lori]

Yes this is possible.

If you add the file to the top level of your package

".BBSoptions"


with the entry

"UnsupportedPlatforms: win32"





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 Tony Culos 

Sent: Tuesday, April 17, 2018 5:02 PM
To: bioc-devel@r-project.org
Subject: [Bioc-devel] GateFinder: Windows Server Error

Hello,

I'm working on resolving the error with the GateFinder package for Windows
Server 2012 R2 Standard, it appears that the issue is a calculation
difference between 32 and 64-bit systems. Is it possible to have the
package be included in the next release only with support for 64-bit
systems? I couldn't find any explicit reference to this sort of situation
so any clarification would be greatly appreciated.

Thank You,
Tony C.

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

[Zhu MF]

Dear sir,
 
Thank you for your letter. 


Firstly, Actually, I don't know why does the content in GitHub and Bioconductor 
are not the same when the package was firstly releaed in bioconductor?  In the 
GitHub we have removed the error file since the first release.


Then, the tips of the checked error was caused by the  expired function of rcdk 
not BioMedR.


The error is in the unitest that actually worked well in other cases, so in our 
local machine, this error have not been triggerd in the past one year, so we 
don't know what happened.


So, could you help us simple the review process and include in the  Bioc 3.7 
release?


Thank you very much!





At 2018-04-17 01:47:51, "Shepherd, Lori"  wrote:


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!
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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 
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