[BioC] error when installing package oligo
Martin Morgan
mtmorgan at fhcrc.org
Tue May 28 15:20:10 CEST 2013
On 05/28/2013 02:33 AM, Wolfgang Raffelsberger wrote:
> Dear list,
>
> I've encountered the following problem when trying to install the package
> "oligo" on R-3.0.0 :
> On Ubuntu the installation stalls with the message "unable to load shared
> object '/linux/biolo/R_surf/R-3.0.0/lib64/R/library/oligo/libs/oligo.so':"
> (see details below).
Hi Wolfgang --
This sounds similar to this thread
https://stat.ethz.ch/pipermail/bioc-sig-sequencing/2010-August/001427.html
basically, that you have two zlib installations. You're finding one during
compile time, and the other during load time.
Resolution probably requires some detective work. The output
> #include "..." search starts here:
> #include <...> search starts here:
> /biolo/R_surf/R-3.0.0/lib64/R/include
> /linux/biolo/R_surf/R-3.0.0/lib64/R/library/preprocessCore/include
> /usr/local/include
> /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include
> /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include-fixed
> /usr/include
in conjunction with
locate libz.h
probably points to the header libz.h found during compilation (I'd bet a
non-standard version installed by third party software in /usr/local/include).
locate libz.so
R CMD env|grep LD_LIBRARY_PATH
ldconfig -p
might be helpful for understanding load time resolution.
Maybe this kind of issue is also at the root of
https://stat.ethz.ch/pipermail/bioconductor/2011-November/042142.html
?
Martin
> Also, on Windows XP I couldn't install sucessfully, XP tells me that it
> can't find the procedure "sprintf_s" in "msvcrt.dll". However, this might
> rather be an issue of (my?) WinXP installation. So I'd prefer to get "oligo
> working" on Ubuntu first. "affxparser" seems to be installed correctly.
> Any hints ?
>
> Here the procedure on Ubuntu (some special/quotation characters in the
> message(s) don't show up well on the screen, but this should not have any
> functional consequences):
>
>> source("http://www.bioconductor.org/biocLite.R")
>> biocLite("oligo")
> BioC_mirror: http://bioconductor.org
> Using Bioconductor version 2.12 (BiocInstaller 1.10.1), R version 3.0.0.
> Installing package(s) 'oligo'
> trying URL '
> http://bioconductor.org/packages/2.12/bioc/src/contrib/oligo_1.24.0.tar.gz'
> Content type 'application/x-gzip' length 5431248 bytes (5.2 Mb)
> opened URL
> ===================================
>
> [[ ... lots of text on screen, only the end is shown here ...]]
>
> Thread model: posix
> gcc version 4.4.3 (Ubuntu 4.4.3-4ubuntu5.1)
> COLLECT_GCC_OPTIONS='-std=gnu99' '-I/biolo/R_surf/R-3.0.0/lib64/R/include'
> '-DNDEBUG' '-I/usr/local/include'
> '-I/linux/biolo/R_surf/R-3.0.0/lib64/R/library/preprocessCore/include'
> '-fpic' '-v' '-c' '-o' 'trimmed.o' '-mtune=generic'
> /usr/lib/gcc/x86_64-linux-gnu/4.4.3/cc1 -quiet -v
> -I/biolo/R_surf/R-3.0.0/lib64/R/include -I/usr/local/include
> -I/linux/biolo/R_surf/R-3.0.0/lib64/R/library/preprocessCore/include
> -DNDEBUG trimmed.c -D_FORTIFY_SOURCE=2 -quiet -dumpbase trimmed.c
> -mtune=generic -auxbase-strip trimmed.o -std=gnu99 -version -fpic
> -fstack-protector -o /tmp/ccNLIIAr.s
> GNU C (Ubuntu 4.4.3-4ubuntu5.1) version 4.4.3 (x86_64-linux-gnu)
> compiled by GNU C version 4.4.3, GMP version 4.3.2, MPFR version
> 2.4.2-p1.
> GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
> ignoring nonexistent directory "/usr/local/include/x86_64-linux-gnu"
> ignoring nonexistent directory
> "/usr/lib/gcc/x86_64-linux-gnu/4.4.3/../../../../x86_64-linux-gnu/include"
> ignoring nonexistent directory "/usr/include/x86_64-linux-gnu"
> ignoring duplicate directory "/usr/local/include"
> as it is a non-system directory that duplicates a system directory
> #include "..." search starts here:
> #include <...> search starts here:
> /biolo/R_surf/R-3.0.0/lib64/R/include
> /linux/biolo/R_surf/R-3.0.0/lib64/R/library/preprocessCore/include
> /usr/local/include
> /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include
> /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include-fixed
> /usr/include
> End of search list.
> GNU C (Ubuntu 4.4.3-4ubuntu5.1) version 4.4.3 (x86_64-linux-gnu)
> compiled by GNU C version 4.4.3, GMP version 4.3.2, MPFR version
> 2.4.2-p1.
> GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
> Compiler executable checksum: 462394bb0ac77cba16b6fb6b32589358
> COLLECT_GCC_OPTIONS='-std=gnu99' '-I/biolo/R_surf/R-3.0.0/lib64/R/include'
> '-DNDEBUG' '-I/usr/local/include'
> '-I/linux/biolo/R_surf/R-3.0.0/lib64/R/library/preprocessCore/include'
> '-fpic' '-v' '-c' '-o' 'trimmed.o' '-mtune=generic'
> as -V -Qy -o trimmed.o /tmp/ccNLIIAr.s
> GNU assembler version 2.20.1 (x86_64-linux-gnu) using BFD version (GNU
> Binutils for Ubuntu) 2.20.1-system.20100303
> COMPILER_PATH=/usr/lib/gcc/x86_64-linux-gnu/4.4.3/:/usr/lib/gcc/x86_64-linux-gnu/4.4.3/:/usr/lib/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/4.4.3/:/usr/lib/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/4.4.3/:/usr/lib/gcc/x86_64-linux-gnu/
> LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/4.4.3/:/usr/lib/gcc/x86_64-linux-gnu/4.4.3/:/usr/lib/gcc/x86_64-linux-gnu/4.4.3/../../../../lib/:/lib/../lib/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/4.4.3/../../../:/lib/:/usr/lib/:/usr/lib/x86_64-linux-gnu/
> COLLECT_GCC_OPTIONS='-std=gnu99' '-I/biolo/R_surf/R-3.0.0/lib64/R/include'
> '-DNDEBUG' '-I/usr/local/include'
> '-I/linux/biolo/R_surf/R-3.0.0/lib64/R/library/preprocessCore/include'
> '-fpic' '-v' '-c' '-o' 'trimmed.o' '-mtune=generic'
> gcc -std=gnu99 -shared -L/usr/local/lib64 -o oligo.so DABG.o ParserGzXYS.o
> ParserXYS.o baseProfile.o basecontent.o chipbackground.o mas5calls.o rma2.o
> rma_common.o trimmed.o -lz -lgfortran -lm
> -L/biolo/R_surf/R-3.0.0/lib64/R/lib -lRlapack
> -L/biolo/R_surf/R-3.0.0/lib64/R/lib -lRblas
> -L/biolo/R_surf/R-3.0.0/lib64/R/lib -lR
> installing to /linux/biolo/R_surf/R-3.0.0/lib64/R/library/oligo/libs
> ** R
> ** inst
> ** preparing package for lazy loading
> Note: in method for âpm<-â with signature
> âobject="TilingFeatureSet",subset="ANY",target="ANY",value="array"â:
> expanding the signature to include omitted arguments in definition: =
> "missing"
> Note: in method for âmm<-â with signature
> âobject="TilingFeatureSet",subset="ANY",target="ANY",value="array"â:
> expanding the signature to include omitted arguments in definition: =
> "missing"
> ** help
> *** installing help indices
> ** building package indices
> ** installing vignettes
> ** testing if installed package can be loaded
> Error in dyn.load(file, DLLpath = DLLpath, ...) :
> unable to load shared object
> '/linux/biolo/R_surf/R-3.0.0/lib64/R/library/oligo/libs/oligo.so':
> /linux/biolo/R_surf/R-3.0.0/lib64/R/library/oligo/libs/oligo.so:
> undefined symbol: gzgetc_
> Error: loading failed
> Execution halted
> ERROR: loading failed
> * removing â/linux/biolo/R_surf/R-3.0.0/lib64/R/library/oligoâ
>
> The downloaded source packages are in
> â/tmp/RtmpVY9MBm/downloaded_packagesâ
> Warning message:
> In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
> installation of package âoligoâ had non-zero exit status
>>
>> # for completeness
>>
>> sessionInfo()
> R version 3.0.0 (2013-04-03)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
> [7] LC_PAPER=C LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] affxparser_1.32.1 BiocInstaller_1.10.1
>
> loaded via a namespace (and not attached):
>
> [1] tools_3.0.0
>>
>
>
> Thank's in advance,
> Wolfgang
>
> . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
> Wolfgang Raffelsberger, PhD
> IGBMC,
> 1 rue Laurent Fries, 67404 Illkirch Strasbourg, France
> Tel (+33) 388 65 3300 Fax (+33) 388 65 3201
> wolfgang.raffelsberger (at) igbmc.fr
>
> [[alternative HTML version deleted]]
>
>
>
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