Re: [Bioc-devel] Package not being built on Windows or Mac

2017-03-20 Thread Dan Tenenbaum 
As I recall, there were issues building RCytoscape (and packages that depend on 
it) on Mac and Windows. Mostly because this requires a running instance of 
Cytoscape for each platform (and double that for release + devel). That used 
too much infrastructure so we disabled building on those platforms. However, 
since RCytoscape contains no native (C/C++/Fortran) code, it will still be 
available on all platforms and should install just fine.

As long as the same is true of categoryCompare then Mac/Windows users should be 
able to use it.

Dan


- Original Message -
> From: "James W. MacDonald" 
> To: "Robert M. Flight" 
> Cc: "bioc-devel" 
> Sent: Monday, March 20, 2017 2:22:36 PM
> Subject: Re: [Bioc-devel] Package not being built on Windows or Mac

> It's probably because you depend on RCytoscape, which isn't supported on
> Windows or MacOS. And maybe this has something to do with XMLRPC?
> 
> Jim
> 
> 
> 
> On Mon, Mar 20, 2017 at 4:59 PM, Robert M. Flight 
> wrote:
> 
>> As per the exhortation to check the build status on Devel prior to next
>> version of Bioconductor release, I just noticed that my package
>> categoryCompare has a "not supported" on Windows and Mac.
>>
>> Looking at release history, this seems to  I have changed at Bioc v 3.4,
>> and I'm curious why that would be the case.
>>
>> Regards,
>>
>> Robert
>>
>> Robert M Flight, PhD
>> Bioinformatics Research Associate
>> Puller of Rabbits from Hats
>> Resource Center for Stable Isotope Resolved Metabolomics
>> Manager, Systems Biology and Omics Integration Journal Club
>> Markey Cancer Center
>> CC434 Roach Building
>> University of Kentucky
>> Lexington, KY
>>
>> Twitter: @rmflight
>> Web: rmflight.github.io
>> ORCID:
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__orcid.org_-2D0001-2D8141-2D7788=DwICAg=eRAMFD45gAfqt84VtBcfhQ=TF6f93hjWmgMzjqP9F3thRifibmFvfjc5Ae-bzNwDGo=KPLsJPHGh_SklfKfn_epC0AQwKR8K6yNDv7cVLAJ1FQ=n-q_ynuSgrWSRqpLP4_jtAcjUUkBkQS47cGcISvMTH8=
>> EM rfligh...@gmail.com
>> PH 502-509-1827
>>
>> To call in the statistician after the experiment is done may be no more
>> than asking him to perform a post-mortem examination: he may be able to say
>> what the experiment died of. - Ronald Fisher
>>
>> [[alternative HTML version deleted]]
>>
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwICAg=eRAMFD45gAfqt84VtBcfhQ=TF6f93hjWmgMzjqP9F3thRifibmFvfjc5Ae-bzNwDGo=KPLsJPHGh_SklfKfn_epC0AQwKR8K6yNDv7cVLAJ1FQ=s4b92CENsDvGb5LJKA-xyg2pTKm6kJHUNfyOrk_ySY4=
>>
> 
> 
> 
> --
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099
> 
>   [[alternative HTML version deleted]]
> 
> ___
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Re: [Bioc-devel] Package not being built on Windows or Mac

2017-03-20 Thread James W. MacDonald 
It's probably because you depend on RCytoscape, which isn't supported on
Windows or MacOS. And maybe this has something to do with XMLRPC?

Jim



On Mon, Mar 20, 2017 at 4:59 PM, Robert M. Flight 
wrote:

> As per the exhortation to check the build status on Devel prior to next
> version of Bioconductor release, I just noticed that my package
> categoryCompare has a "not supported" on Windows and Mac.
>
> Looking at release history, this seems to  I have changed at Bioc v 3.4,
> and I'm curious why that would be the case.
>
> Regards,
>
> Robert
>
> Robert M Flight, PhD
> Bioinformatics Research Associate
> Puller of Rabbits from Hats
> Resource Center for Stable Isotope Resolved Metabolomics
> Manager, Systems Biology and Omics Integration Journal Club
> Markey Cancer Center
> CC434 Roach Building
> University of Kentucky
> Lexington, KY
>
> Twitter: @rmflight
> Web: rmflight.github.io
> ORCID: http://orcid.org/-0001-8141-7788
> EM rfligh...@gmail.com
> PH 502-509-1827
>
> To call in the statistician after the experiment is done may be no more
> than asking him to perform a post-mortem examination: he may be able to say
> what the experiment died of. - Ronald Fisher
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>



-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099

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[Bioc-devel] Package not being built on Windows or Mac

2017-03-20 Thread Robert M. Flight 
As per the exhortation to check the build status on Devel prior to next
version of Bioconductor release, I just noticed that my package
categoryCompare has a "not supported" on Windows and Mac.

Looking at release history, this seems to  I have changed at Bioc v 3.4,
and I'm curious why that would be the case.

Regards,

Robert

Robert M Flight, PhD
Bioinformatics Research Associate
Puller of Rabbits from Hats
Resource Center for Stable Isotope Resolved Metabolomics
Manager, Systems Biology and Omics Integration Journal Club
Markey Cancer Center
CC434 Roach Building
University of Kentucky
Lexington, KY

Twitter: @rmflight
Web: rmflight.github.io
ORCID: http://orcid.org/-0001-8141-7788
EM rfligh...@gmail.com
PH 502-509-1827

To call in the statistician after the experiment is done may be no more
than asking him to perform a post-mortem examination: he may be able to say
what the experiment died of. - Ronald Fisher

[[alternative HTML version deleted]]

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[Bioc-devel] tximport fails to build on Windows

2017-03-20 Thread Michael Love 
Anyone have any ideas for how to debug this?

I get an error from the tximport vignette on tokay2, but I can't
figure out what could be the issue:

...
1 Quitting from lines 185-189 (tximport.Rmd)
Error: processing vignette 'tximport.Rmd' failed with diagnostics:
cannot open the connection
Execution halted

http://master.bioconductor.org/checkResults/devel/bioc-LATEST/tximport/tokay2-buildsrc.html

Those lines look innocuous to me, and work fine on Linux and Mac:

184 ```{r}
185 files <- file.path(dir,"sailfish", samples$run, "quant.sf")
186 names(files) <- paste0("sample",1:6)
187 txi.sailfish <- tximport(files, type="sailfish", tx2gene=tx2gene)
188 head(txi.sailfish$counts)
189 ```

I tried bumping the version and I still get the error from tokay2.

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[Bioc-devel] Bioconductor 3.5 release

2017-03-20 Thread Obenchain, Valerie 
Hi all,

The release of Bioconductor 3.5 will be Tuesday, April 25. Please see
the schedule for details:

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

Over the next month we'll announce the key deadlines on bioc-devel. Lori
sent the first one last week and it's important for anyone planning to
submit a new package:

  https://stat.ethz.ch/pipermail/bioc-devel/2017-March/010594.html

As you know, part of preparing for the release is cleaning up the
software and experimental data build reports. It would be greatly
appreciated if you could proactively look at your packages and help us
get them "in the green" with a clean build and check.

  http://www.bioconductor.org/checkResults/


Thanks.

Valerie




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Re: [Bioc-devel] Perl version issue with building Rhtslib

2017-03-20 Thread Martin Morgan 
Hi Dinakar -- your patch didn't make it through the mailing list; can 
you forward it to me directly? Thanks, Martin


On 03/17/2017 12:45 PM, Dinakar Kulkarni wrote:

Hello,

The following error was generated while attempting to install the "Rhtslib"
package in R v3.3.2:

/usr/bin/perl: symbol lookup error: /perl-modules/5.18.2/1.142660/x86_64-
linux-2.6-rhel6/lib/perl5/x86_64-linux-thread-multi/auto/List/Util/Util.so:
undefined symbol: Perl_xs_apiversion_bootcheck

WARNING: 'autoconf' is missing on your system.

 You should only need it if you modified 'configure.ac',

 or m4 files included by it.

 The 'autoconf' program is part of the GNU Autoconf package:

 

 It also requires GNU m4 and Perl in order to run:

 

 

make[1]: *** [configure] Error 127

make[1]: Leaving directory `/tmp/Rtmpn6FFZH/R.INSTALL671e
4ed4c86d/Rhtslib/src/htslib'

make: *** [htslib/libhts.la] Error 2

ERROR: compilation failed for package ‘Rhtslib’

On further investigation, I was able to determine that the default Perl
version on the OS (RHEL 6.6) was v5.10.1, so it turned out to be an
incompatibility issue.

I looked into the source for Rhtslib and see that it use these 3 Perl
scripts:

Rhtslib/src/htslib/test/compare_sam.pl
Rhtslib/src/htslib/test/test.pl
Rhtslib/src/htslib/test/test_view.pl

and they use the default env Perl. I believe that it would be better to
specify the Perl version within these scripts(i.e. use v5.18.2) for
compiling/building the package. I've attached suggested patch files here
for the same.

Thanks,
Dinakar.




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Re: [Bioc-devel] developing R package for new release

2017-03-20 Thread James W. MacDonald 
On Fri, Mar 17, 2017 at 3:45 PM, Nicholas Clark 
wrote:

> I’m planning on adding some new features to my package (GRmetrics) before
> this upcoming release and I have a few development questions.
>
>
> 1) Which version of R should I be using? I looked at this page (
> http://bioconductor.org/developers/how-to/useDevel/
> ), but I was still confused as to whether I should use the recently
> released R 3.3.3 or the R-devel 3.4.0 at http://r.research.att.com/


For the spring release you should use R-devel. For the fall release you
should use the most current version of R. This is because we release twice
a year, but R is only released in spring.

Looking at the useDevel page I see that I am simply repeating (almost
verbatim) what is written there. Is there something unclear about this that
we should address? It seems clear enough to me, but I've been doing this a
long time.


>
> .
>
>
> 2) What is the best/easiest way to work with github? Should I fork the
> repository from the read-only Bioconductor repo and work on that or
> maintain a separate repo? Or does it not matter?
>

I believe you should fork the repo from the Bioconductor mirror and use
that. There is some info here (
http://bioconductor.org/developers/how-to/git-mirrors/). But there are some
considerations to be made. Right now, we are using subversion for version
control, and anything you do in github has to be 'subversionized' in order
for your commits to be checked into the main version control repository.
It's far easier IMO to just use subversion to do all your version control,
because you don't have to worry about getting git to talk to subversion.

That said, after the April release we are transitioning to git, so we will
be using git soon enough. But for now I am still using SVN because it's a
direct commit to the main repo. My advice is to use whatever the main repo
is based on, because mixing and matching adds an extra level of complexity
that doesn't appear to have much to offer in return.


>
> 3) Should I make a “release-3.5” branch and commit changes there, or
> should it be “devel”, or just the “master” branch? http://bioconductor.
> org/developers/how-to/git-mirrors/
>  talks about this, but again, it’s not clear to me.
>

You never make your own branches. That's controlled by BioC core. Unless
you are fixing a bug in the release version of your package you should be
using the master branch (or if you use SVN, you should just be checking out
of the trunk,
https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GRmetrics).


>
> 4) It looks like my package is failing the Windows build because it
> requires “SummarizedExperiment”, which is failing the Windows build. Is
> there anything I can do to fix this? Apologies if this has already been
> addressed. The error is: ERROR: dependency ‘SummarizedExperiment’ is not
> available for package ‘GRmetrics' (http://bioconductor.org/
> checkResults/release/bioc-LATEST/GRmetrics/tokay1-buildsrc.html
> )
>

If one of your dependencies is failing, and in particular if the dependency
is maintained by Bioc core, then the best thing to do is wait. If you are
relying on somebody else's package and they are consistently failing you
might contact them and find out if you can help.

Jim



>
> Best,
> Nick Clark
>
>
>
> [[alternative HTML version deleted]]
>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099

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[Bioc-devel] developing R package for new release

2017-03-20 Thread Nicholas Clark 
I’m planning on adding some new features to my package (GRmetrics) before this 
upcoming release and I have a few development questions.


1) Which version of R should I be using? I looked at this page 
(http://bioconductor.org/developers/how-to/useDevel/
), but I was still confused as to whether I should use the recently released R 
3.3.3 or the R-devel 3.4.0 at http://r.research.att.com/
.


2) What is the best/easiest way to work with github? Should I fork the 
repository from the read-only Bioconductor repo and work on that or maintain a 
separate repo? Or does it not matter?


3) Should I make a “release-3.5” branch and commit changes there, or should it 
be “devel”, or just the “master” branch? 
http://bioconductor.org/developers/how-to/git-mirrors/
 talks about this, but again, it’s not clear to me.


4) It looks like my package is failing the Windows build because it requires 
“SummarizedExperiment”, which is failing the Windows build. Is there anything I 
can do to fix this? Apologies if this has already been addressed. The error is: 
ERROR: dependency ‘SummarizedExperiment’ is not available for package 
‘GRmetrics' 
(http://bioconductor.org/checkResults/release/bioc-LATEST/GRmetrics/tokay1-buildsrc.html
)


Best,
Nick Clark



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