[Bioc-devel] libRblas and libRlapack are broken dependencies for packages in R 3.1.0 on Fedora 20
Martin Morgan
mtmorgan at fhcrc.org
Tue May 6 21:45:09 CEST 2014
On 05/06/2014 12:29 PM, E N wrote:
>> Date: Tue, 6 May 2014 09:44:16 -0700
>> From: mtmorgan at fhcrc.org
>> To: gifi2007 at hotmail.com
>> Subject: Re: [Bioc-devel] libRblas and libRlapack are broken dependencies for packages in R 3.1.0 on Fedora 20
>>
>> On 05/06/2014 09:28 AM, E N wrote:
>>>> From: mtmorgan at fhcrc.org
>>>> To: gifi2007 at hotmail.com; bioc-devel at r-project.org
>>>> Subject: Re: [Bioc-devel] libRblas and libRlapack are broken dependencies for packages in R 3.1.0 on Fedora 20
>>>>
>>>> Let's focus on preprocessCore, which does not have any additional dependencies.
>>>>
>>>> Also, I assume you mean that you are using R that comes with the fedora package
>>>> manager, rather than the R that is redistributed by Rstudio.
>>>
>>> Yes, I'm using the very R packaged by Fedora, this one to be more accurate: <https://stat.ethz.ch/pipermail/bioc-devel/2014-May/005706.html>
>>>
>>>
>>>>
>>>> If you could provide the output of
>>>>
>>>> R CMD config BLAS_LIBS
>>>>
>>>> and the full output of
>>>>
>>>> R -e "library(BiocInstaller); biocLite('preprocessCore')"
>>>>
>>>> again using the R that is installed with the fedora package manager, then that
>>>> would help to understand your problem.
>>>>
>>>> If your problem is only with the version of R distributed by Rstudio, then as I
>>>> understand it the solution is in the hands of Rstudio, and I am sure they will
>>>> respond promptly.
>>>>
>>>> Martin
>>>>
>>>
>>> Please find provided below the commands outputs:
>>> =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
>>> [@localhost ...]$ R CMD config BLAS_LIBS
>>> -lblas
>>>
>>> [@localhost ...]$ R -e "library(BiocInstaller); biocLite('preprocessCore')"
>>>
>>> R version 3.1.0 (2014-04-10) -- "Spring Dance"
>>> Copyright (C) 2014 The R Foundation for Statistical Computing
>>> Platform: x86_64-redhat-linux-gnu (64-bit)
>>>
>>> R is free software and comes with ABSOLUTELY NO WARRANTY.
>>> You are welcome to redistribute it under certain conditions.
>>> Type 'license()' or 'licence()' for distribution details.
>>>
>>> Natural language support but running in an English locale
>>>
>>> R is a collaborative project with many contributors.
>>> Type 'contributors()' for more information and
>>> 'citation()' on how to cite R or R packages in publications.
>>>
>>> Type 'demo()' for some demos, 'help()' for on-line help, or
>>> 'help.start()' for an HTML browser interface to help.
>>> Type 'q()' to quit R.
>>>
>>>> library(BiocInstaller); biocLite('preprocessCore')
>>> Bioconductor version 2.14 (BiocInstaller 1.14.2), ?biocLite for help
>>> BioC_mirror: http://bioconductor.org
>>> Using Bioconductor version 2.14 (BiocInstaller 1.14.2), R version
>>> 3.1.0.
>>> Installing package(s) 'preprocessCore'
>>> trying URL 'http://bioconductor.org/packages/2.14/bioc/src/contrib/preprocessCore_1.26.0.tar.gz'
>>> Content type 'application/x-gzip' length 120387 bytes (117 Kb)
>>> opened URL
>>> ==================================================
>>> downloaded 117 Kb
>>>
>>> * installing *source* package ‘preprocessCore’ ...
>>> checking for gcc... gcc -m64 -std=gnu99
>>> checking whether the C compiler works... yes
>>> checking for C compiler default output file name... a.out
>>> checking for suffix of executables...
>>> checking whether we are cross compiling... no
>>> checking for suffix of object files... o
>>> checking whether we are using the GNU C compiler... yes
>>> checking whether gcc -m64 -std=gnu99 accepts -g... yes
>>> checking for gcc -m64 -std=gnu99 option to accept ISO C89... none needed
>>> checking how to run the C preprocessor... gcc -m64 -std=gnu99 -E
>>> checking for library containing pthread_create... -lpthread
>>> checking for grep that handles long lines and -e... /usr/bin/grep
>>> checking for egrep... /usr/bin/grep -E
>>> checking for ANSI C header files... yes
>>> checking for sys/types.h... yes
>>> checking for sys/stat.h... yes
>>> checking for stdlib.h... yes
>>> checking for string.h... yes
>>> checking for memory.h... yes
>>> checking for strings.h... yes
>>> checking for inttypes.h... yes
>>> checking for stdint.h... yes
>>> checking for unistd.h... yes
>>> checking for stdlib.h... (cached) yes
>>> checking if PTHREAD_STACK_MIN is defined... yes
>>> configure: creating ./config.status
>>> config.status: creating src/Makevars
>>>
>>> [...]
>>>
>>> gcc -m64 -std=gnu99 -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -flto -fpic -Wl,-z,relro -o preprocessCore.so R_colSummarize.o R_plmd_interfaces.o R_plmr_interfaces.o R_rlm_interfaces.o R_subColSummarize.o R_subrcModel_interfaces.o avg.o avg_log.o biweight.o init_package.o lm.o log_avg.o log_median.o matrix_functions.o median.o median_log.o medianpolish.o plmd.o plmr.o psi_fns.o qnorm.o rlm.o rlm_anova.o rlm_se.o rma_background4.o rma_common.o weightedkerneldensity.o -lpthread -llapack -lblas -lgfortran -lm -lquadmath -L/usr/lib64/R/lib -lR
>>>
>>> /usr/bin/ld: cannot find -llapack
>>> /usr/bin/ld: cannot find -lblas
>>
>> This is really about fedora system configuration; R has been built by linking to
>> system-provided lapack and blas, but now R cannot find those libraries. Do they
>> exist ?
>>
>> locate liblapack
>> locate libblas
>> R CMD locate liblapack
>> R CMD locate libblas
>>
>> if not then there is somehow a missing dependency (on system-provided rather
>> than R-provided lapack and blas) in the fedora R package. Presumably you can
>> work around this by installing the lapack / blas dependency manually (i.e.,
>> through the fedora package manager), and getting Tom Callaway to update the
>> dependencies in R-3.1.0-4.fc20.src.rpm (although I see there that bals-devel>=
>> 3.0 is already require'd.
>>
>> Partly I am 'shooting in the dark', so if I am missing something please excuse
>> my errors.
>>
>> Martin
>>
>>>
>>> collect2: error: ld returned 1 exit status
>>> make: *** [preprocessCore.so] Error 1
>>> ERROR: compilation failed for package ‘preprocessCore’
>>> =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
>>>
>>> The full compilation output is the enclosed file. Errors come from the way R was builf for Fedora 20 and the previously mentioned Tom seems to be steady on the library dependencies management: "This is because we're building R with the system blas/lapack instead of their bundled copy (something we should have done a while ago)."
>>> ***something we should have done a while ago***
>>>
>>> Regards,
>>> Eric.
>
>
> [@localhost ~]$ locate liblapack
> /usr/lib64/atlas/liblapack.so.3
> /usr/lib64/atlas/liblapack.so.3.0
>
> [@localhost ~]$ locate libblas
> /usr/lib64/libblas.so.3
> /usr/lib64/libblas.so.3.4
> /usr/lib64/libblas.so.3.4.2
>
> [@localhost ~]$ R CMD locate liblapack
> /usr/lib64/atlas/liblapack.so.3
> /usr/lib64/atlas/liblapack.so.3.0
>
> [@localhost ~]$ R CMD locate libblas
> /usr/lib64/libblas.so.3
> /usr/lib64/libblas.so.3.4
> /usr/lib64/libblas.so.3.4.2
>
> R finds its BLAS and LAPACK dependencies, but packages can't. I'm neither a system packager nor an R package writer, but from the Tom Callaway's message I understood the following:
> +prior R-3.1.0 on Fedora, packages could link to BLAS & LAPACK bundled with R regardless the system (un)provided similar libraries;
> +since that R release, packages can no more search dependencies within R shared lib, they ought use the system ones.
>
> Let's reuse 'preprocessCore' as an example. When <grep -nri 'lapack'> is applied to its sources, there are outputs for "matrix_functions.c" and "matrix_functions.c". Both files carry the following includes:
> #include <R_ext/Rdynload.h>
> #include <R.h>
> #include <Rdefines.h>
> #include <Rmath.h>
> #include <Rinternals.h>
>
> I suspect the problems stem from there. If I didn't miss Tom Callaway's point so far, such includes should be replaced by system's (i.e. Fedora).
>
Those are the headers, and are relevant to the part of the compilation that you
elided out [...]. The problem you see
>>> gcc -m64 -std=gnu99 -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
-fexceptions -fstack-protector-strong --param=ssp-buffer-size=4
-grecord-gcc-switches -m64 -mtune=generic -flto -fpic -Wl,-z,relro -o
preprocessCore.so R_colSummarize.o R_plmd_interfaces.o R_plmr_interfaces.o
R_rlm_interfaces.o R_subColSummarize.o R_subrcModel_interfaces.o avg.o avg_log.o
biweight.o init_package.o lm.o log_avg.o log_median.o matrix_functions.o
median.o median_log.o medianpolish.o plmd.o plmr.o psi_fns.o qnorm.o rlm.o
rlm_anova.o rlm_se.o rma_background4.o rma_common.o weightedkerneldensity.o
-lpthread -llapack -lblas -lgfortran -lm -lquadmath -L/usr/lib64/R/lib -lR
>>>
>>> /usr/bin/ld: cannot find -llapack
>>> /usr/bin/ld: cannot find -lblas
is with linking; R is not able to find your blas and lapack libraries. I guess
the following simple commands fail for you -- create a simple C source code file
$ cat > tmp.c
int main(int argc, const char **argv) {}
(press cntrl-D after typing the above, so you have a file 'tmp.c' with that
single line of code) and try to
$ gcc -m64 -lblas tmp.c
$ ./a.out
$
For me gcc finds libblas, and creates an executable file a.out, which actually
does nothing. For you I guess you'll see something like the following, where
I've replaced '-lblas' with a reference to some imaginary library that my system
knows nothing about
$ gcc -m64 -limaginary tmp.c
/usr/bin/ld: cannot find -limaginary
collect2: error: ld returned 1 exit status
$
If this is the case, then somehow your package manager has installed the lapack
and blas packages without making their location known to other programs.
Libraries are usually discovered via ldconfig, and I have for instance
$ ldconfig -p|grep blas
libgslcblas.so.0 (libc6,x86-64) => /usr/lib/libgslcblas.so.0
libgslcblas.so (libc6,x86-64) => /usr/lib/libgslcblas.so
libf77blas.so.3 (libc6,x86-64) => /usr/lib/libf77blas.so.3
libcblas.so.3 (libc6,x86-64) => /usr/lib/libcblas.so.3
libblas.so.3 (libc6,x86-64) => /usr/lib/libblas.so.3
libblas.so (libc6,x86-64) => /usr/lib/libblas.so
You might have success with
$ sudo ldconfig
but after this I'll let someone with access to a fedora system step in.
Martin
> Eric.
>
> P.S. I left the whole conversation history in this mail to make it visible on the mailing list, which I should have done in my previous messages, sorry for my inadvertence.
>
>
>
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