[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]]
>>>>
>>>> _______________________________________________
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