[Bioc-devel] R CMD SHLIB throwing error on zin1 (linux) BioC nightly build

Brad Friedman friedman.brad at gene.com
Thu Dec 17 17:58:57 CET 2015


Thank YOU!!! Bioconductor is fantastic.

Brad Friedman
617-230-7055 

> On Dec 17, 2015, at 8:47 AM, "Obenchain, Valerie" <Valerie.Obenchain at RoswellPark.org> wrote:
> 
> Thanks!
> 
> Valerie
> 
>> On 12/17/2015 08:32 AM, Brad Friedman wrote:
>> Thanks, I've made the corresponding change to release version, and
>> bumped minor version there.
>> 
>> I previously only made it to devel.
>> 
>> Brad 
>> 
>> On Thu, Dec 17, 2015 at 8:21 AM, Obenchain, Valerie
>> <Valerie.Obenchain at roswellpark.org
>> <mailto:Valerie.Obenchain at roswellpark.org>> wrote:
>> 
>>    Hi Brad,
>> 
>>    Following up on this because AnalysisPageServer is still broken in
>>    release. Can you please fix?
>> 
>>    Thanks.
>>    Valerie
>> 
>> 
>>>    On 12/14/2015 01:36 PM, Morgan, Martin wrote:
>>> At least for the R package side of things, I think the question
>>    of how to invoke R CMD in a Makefile is moot for
>>    AnalysisPageServer -- remove the Makefile, and the shared object
>>    is created automatically when the package is built with R CMD
>>    build AnalysisPageServer.
>>> 
>>> But for the record the format for referring to R in Writing R
>>    Extensions in a Makefile is
>>> 
>>>    "${R_HOME}/bin/R" ...
>>> 
>>> ${R_HOME} is an environment variable, quotes allow for spaces in
>>    the path. A more cross-platform version is  I think
>>> 
>>>    "${R_HOME}/bin${R_ARCH_BIN}/R"
>>> 
>>> where on single-architecture platforms ${R_ARCH_BIN} is
>>    undefined hence harmless.
>>> 
>>> Somewhat circularly, R_HOME is set by R CMD
>>> 
>>> $ env|grep R_HOME
>>> $ R CMD env|grep R_HOME
>>> R_HOME=/home/mtmorgan/bin/R-devel
>>> $ Rrel CMD env|grep R_HOME
>>> R_HOME=/home/mtmorgan/bin/R-3-2-branch
>>> 
>>> ________________________________________
>>> From: Bioc-devel [bioc-devel-bounces at r-project.org
>>    <mailto:bioc-devel-bounces at r-project.org>] on behalf of Dan
>>    Tenenbaum [dtenenba at fredhutch.org <mailto:dtenenba at fredhutch.org>]
>>> Sent: Monday, December 14, 2015 4:06 PM
>>> To: Brad Friedman
>>> Cc: bioc-devel
>>> Subject: Re: [Bioc-devel] R CMD SHLIB throwing error on zin1
>>    (linux)    BioC    nightly build
>>> 
>>> ----- Original Message -----
>>>> From: "Brad Friedman" <friedman.brad at gene.com
>>    <mailto:friedman.brad at gene.com>>
>>>> To: "bioc-devel" <bioc-devel at r-project.org
>>    <mailto:bioc-devel at r-project.org>>
>>>> Sent: Monday, December 14, 2015 1:01:24 PM
>>>> Subject: [Bioc-devel] R CMD SHLIB throwing error on zin1
>>    (linux) BioC nightly build
>>>> I’m getting an error that R cannot be found on the nightly
>>    build server.
>>>> Obviously it can be found at some point, since R CMD build
>>    started, but at
>>>> the moment of calling R CMD SHLIB it can’t be found again.
>>>> 
>>>> I was wondering if anything had changed on the server, or maybe
>>    I’m doing
>>>> my Makefile wrong.
>>> 
>>> Probably both. We made a change, removing R from the PATH on the
>>    linux and windows machines (on Mac R is in /usr/bin so it's a bad
>>    idea to remove that directory from the PATH) because we realized
>>    that there are packages that fail when R is not in the PATH, and
>>    one can't assume that R will always be in the path, so we wanted
>>    to make sure those packages failed so that we'd find the problems.
>>    That seems to be what is happening in your case.
>>> 
>>> I'm not sure what the exact syntax is, but your makefile should
>>    reference R as $R_HOME/bin/R.
>>> 
>>> Dan
>>> 
>>> 
>>>> The error only happens on the linux server: mac (oaxaca)
>>>> and windows (moscato1) build fine. And I can’t reproduce this
>>    on my local
>>>> linux server with a fresh checkout.
>>>> 
>>>> Nightly build
>>    <http://bioconductor.org/checkResults/release/bioc-LATEST/AnalysisPageServer/zin1-buildsrc.html>
>>>> results:
>>    ##############################################################################
>>    ##############################################################################
>>>> ###
>>>> ### Running command:
>>>> ###
>>>> ###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD build
>>    --keep-empty-dirs
>>>> --no-resave-data AnalysisPageServer
>>>> ###
>>    ##############################################################################
>>    ##############################################################################
>>>> 
>>>> * checking for file ‘AnalysisPageServer/DESCRIPTION’ ... OK
>>>> * preparing ‘AnalysisPageServer’:
>>>> * checking DESCRIPTION meta-information ... OK
>>>> * cleaning src
>>>> * installing the package to build vignettes
>>>>     -----------------------------------
>>>> * installing *source* package ‘AnalysisPageServer’ ...
>>>> ** libs
>>>> ** arch -
>>>> R CMD SHLIB AnalysisPageSVG.cpp tinyxml2.cpp cor.cpp catch.c
>>>> SearchReplace2.cpp R_init_AnalysisPageServer.cpp -o
>>>> AnalysisPageServer.so
>>>> /bin/bash: R: command not found
>>>> make: *** [AnalysisPageServer] Error 127
>>>> ERROR: compilation failed for package ‘AnalysisPageServer’
>>>> * removing ‘/tmp/RtmpREgK1P/Rinst3e5828c9cd0f/AnalysisPageServer’
>>>>     -----------------------------------
>>>> ERROR: package installation failed
>>>> 
>>>> and the contents of src/Makefile:
>>>> 
>>>> AnalysisPageServer: AnalysisPageSVG.cpp tinyxml2.cpp cor.cpp
>>>> AnalysisPageSVG.h tinyxml2.h cor.h catch.c SearchReplace2.cpp
>>>> SearchReplace2.h catch.h
>>>>   R CMD SHLIB AnalysisPageSVG.cpp tinyxml2.cpp cor.cpp catch.c
>>>> SearchReplace2.cpp R_init_AnalysisPageServer.cpp -o
>>>> AnalysisPageServer.so
>>>> clean:
>>>>   rm *.o *.so
>>>> 
>>>> 
>>>> 
>>>>      [[alternative HTML version deleted]]
>>>> 
>>>> _______________________________________________
>>>> Bioc-devel at r-project.org <mailto:Bioc-devel at r-project.org>
>>    mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>    <https://stat.ethz.ch/mailman/listinfo/bioc-devel>
>>> _______________________________________________
>>> Bioc-devel at r-project.org <mailto:Bioc-devel at r-project.org>
>>    mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>    <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.
>>> _______________________________________________
>>> Bioc-devel at r-project.org <mailto:Bioc-devel at r-project.org>
>>    mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>    <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.
> 
> 
> 
> 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.



More information about the Bioc-devel mailing list