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Question: error when installing package oligo
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gravatar for Wolfgang Raffelsberger
4.5 years ago by
Wolfgang Raffelsberger60 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). 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.ta r.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]]
ADD COMMENTlink modified 4.5 years ago by Martin Morgan ♦♦ 20k • written 4.5 years ago by Wolfgang Raffelsberger60
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gravatar for Martin Morgan
4.5 years ago by
Martin Morgan ♦♦ 20k
United States
Martin Morgan ♦♦ 20k wrote:
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/l ib/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 ?pm<-? with signature > ?object="TilingFeatureSet",subset="ANY",target="ANY",value="array"?: > expanding the signature to include omitted arguments in definition: = > "missing" > Note: in method for ?mm<-? with signature > ?object="TilingFeatureSet",subset="ANY",target="ANY",value="array"?: > 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 ?/linux/biolo/R_surf/R-3.0.0/lib64/R/library/oligo? > > The downloaded source packages are in > ?/tmp/RtmpVY9MBm/downloaded_packages? > Warning message: > In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > installation of package ?oligo? 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]] > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793
ADD COMMENTlink written 4.5 years ago by Martin Morgan ♦♦ 20k
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