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
>>
>> 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>
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