Question: Issue of installing the GLAD package
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6.5 years ago by
Guest User12k
Guest User12k wrote:
I have trouble in installing the GLAD package. I know before installing it , I have to get GSL installed first. I installed it according to the install guide line on the GSL web site. I believe I installed it successfully. Then, when I tried to install GLAD. I input the following command: source("http://bioconductor.org/biocLite.R") biocLite("GLAD") I got the following error msg: BioC_mirror: http://bioconductor.org Using Bioconductor version 2.12 (BiocInstaller 1.10.1), R version 3.0.1. Installing package(s) 'GLAD' trying URL 'http://bioconductor.org/packages/2.12/bioc/src/contrib/GLA D_2.24.0.tar.gz' Content type 'application/x-gzip' length 812778 bytes (793 Kb) opened URL ================================================== downloaded 793 Kb * installing *source* package ???GLAD??? ... checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for GSL... yes GSL has been found on the operating system operating system: Linux configure: creating ./config.status config.status: creating src/Makevars src/Makevars file PKG_LIBS = -L/usr/local/lib -lgsl -lgslcblas -lm PKG_CPPFLAGS += ** libs g++ -I/usr/share/R/include -DNDEBUG -fpic -O2 -pipe -g -c BkpInfo.cpp -o BkpInfo.o g++ -I/usr/share/R/include -DNDEBUG -fpic -O2 -pipe -g -c HaarSeg.cpp -o HaarSeg.o g++ -I/usr/share/R/include -DNDEBUG -fpic -O2 -pipe -g -c MoveBkp.cpp -o MoveBkp.o g++ -I/usr/share/R/include -DNDEBUG -fpic -O2 -pipe -g -c OutliersGNL.cpp -o OutliersGNL.o g++ -I/usr/share/R/include -DNDEBUG -fpic -O2 -pipe -g -c chrBreakpoints.cpp -o chrBreakpoints.o g++ -I/usr/share/R/include -DNDEBUG -fpic -O2 -pipe -g -c cutree.cpp -o cutree.o g++ -I/usr/share/R/include -DNDEBUG -fpic -O2 -pipe -g -c daglad.cpp -o daglad.o g++ -I/usr/share/R/include -DNDEBUG -fpic -O2 -pipe -g -c distance.cpp -o distance.o g++ -I/usr/share/R/include -DNDEBUG -fpic -O2 -pipe -g -c filterBkp.cpp -o filterBkp.o g++ -I/usr/share/R/include -DNDEBUG -fpic -O2 -pipe -g -c findCluster.cpp -o findCluster.o g++ -I/usr/share/R/include -DNDEBUG -fpic -O2 -pipe -g -c glad- utils.cpp -o glad-utils.o g++ -I/usr/share/R/include -DNDEBUG -fpic -O2 -pipe -g -c hclust.cpp -o hclust.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O2 -pipe -g -c laws.c -o laws.o g++ -I/usr/share/R/include -DNDEBUG -fpic -O2 -pipe -g -c loopRemove.cpp -o loopRemove.o g++ -shared -o GLAD.so BkpInfo.o HaarSeg.o MoveBkp.o OutliersGNL.o chrBreakpoints.o cutree.o daglad.o distance.o filterBkp.o findCluster.o glad-utils.o hclust.o laws.o loopRemove.o -L/usr/local/lib -lgsl -lgslcblas -lm -L/usr/lib/R/lib -lR installing to /home/zhoujiayi/R/x86_64-pc-linux-gnu- library/3.0/GLAD/libs ** R ** data ** demo ** inst ** preparing package for lazy loading ** 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 '/home/zhoujiayi/R/x86_64-pc-linux-gnu- library/3.0/GLAD/libs/GLAD.so': libgsl.so.0: cannot open shared object file: No such file or directory Error: loading failed Execution halted ERROR: loading failed * removing ???/home/zhoujiayi/R/x86_64-pc-linux-gnu- library/3.0/GLAD??? The downloaded source packages are in ???/tmp/RtmpvMaBRk/downloaded_packages??? Warning message: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : installation of package ???GLAD??? had non-zero exit status > Do you know how to solve this problem? -- output of sessionInfo(): R version 3.0.1 (2013-05-16) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_CA.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_CA.UTF-8 LC_COLLATE=en_CA.UTF-8 [5] LC_MONETARY=en_CA.UTF-8 LC_MESSAGES=en_CA.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base > -- Sent via the guest posting facility at bioconductor.org.
glad • 1.0k views
ADD COMMENTlink modified 6.5 years ago by Laurent Gatto1.2k • written 6.5 years ago by Guest User12k
Answer: Issue of installing the GLAD package
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gravatar for Laurent Gatto
6.5 years ago by
Laurent Gatto1.2k
Belgium
Laurent Gatto1.2k wrote:
On 7 June 2013 19:12, Aiden [guest] <guest at="" bioconductor.org=""> wrote: > > I have trouble in installing the GLAD package. I know before installing it , I have to get GSL installed first. I installed it according to the install guide line on the GSL web site. I believe I installed it successfully. > Then, when I tried to install GLAD. I input the following command: > source("http://bioconductor.org/biocLite.R") > biocLite("GLAD") > > I got the following error msg: > > BioC_mirror: http://bioconductor.org > Using Bioconductor version 2.12 (BiocInstaller 1.10.1), R version 3.0.1. > Installing package(s) 'GLAD' > > trying URL 'http://bioconductor.org/packages/2.12/bioc/src/contrib/G LAD_2.24.0.tar.gz' > > > Content type 'application/x-gzip' length 812778 bytes (793 Kb) > opened URL > ================================================== > downloaded 793 Kb > > * installing *source* package ???GLAD??? ... > > checking for pkg-config... /usr/bin/pkg-config > checking pkg-config is at least version 0.9.0... yes > checking for GSL... yes > GSL has been found on the operating system > operating system: Linux > configure: creating ./config.status > config.status: creating src/Makevars > > src/Makevars file > > PKG_LIBS = -L/usr/local/lib -lgsl -lgslcblas -lm > PKG_CPPFLAGS += > > ** libs > g++ -I/usr/share/R/include -DNDEBUG -fpic -O2 -pipe -g -c BkpInfo.cpp -o BkpInfo.o > > g++ -I/usr/share/R/include -DNDEBUG -fpic -O2 -pipe -g -c HaarSeg.cpp -o HaarSeg.o > g++ -I/usr/share/R/include -DNDEBUG -fpic -O2 -pipe -g -c MoveBkp.cpp -o MoveBkp.o > > g++ -I/usr/share/R/include -DNDEBUG -fpic -O2 -pipe -g -c OutliersGNL.cpp -o OutliersGNL.o > g++ -I/usr/share/R/include -DNDEBUG -fpic -O2 -pipe -g -c chrBreakpoints.cpp -o chrBreakpoints.o > g++ -I/usr/share/R/include -DNDEBUG -fpic -O2 -pipe -g -c cutree.cpp -o cutree.o > > > g++ -I/usr/share/R/include -DNDEBUG -fpic -O2 -pipe -g -c daglad.cpp -o daglad.o > g++ -I/usr/share/R/include -DNDEBUG -fpic -O2 -pipe -g -c distance.cpp -o distance.o > g++ -I/usr/share/R/include -DNDEBUG -fpic -O2 -pipe -g -c filterBkp.cpp -o filterBkp.o > > > g++ -I/usr/share/R/include -DNDEBUG -fpic -O2 -pipe -g -c findCluster.cpp -o findCluster.o > g++ -I/usr/share/R/include -DNDEBUG -fpic -O2 -pipe -g -c glad-utils.cpp -o glad-utils.o > g++ -I/usr/share/R/include -DNDEBUG -fpic -O2 -pipe -g -c hclust.cpp -o hclust.o > > > gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O2 -pipe -g -c laws.c -o laws.o > g++ -I/usr/share/R/include -DNDEBUG -fpic -O2 -pipe -g -c loopRemove.cpp -o loopRemove.o > g++ -shared -o GLAD.so BkpInfo.o HaarSeg.o MoveBkp.o OutliersGNL.o chrBreakpoints.o cutree.o daglad.o distance.o filterBkp.o findCluster.o glad-utils.o hclust.o laws.o loopRemove.o -L/usr/local/lib -lgsl -lgslcblas -lm -L/usr/lib/R/lib -lR > > > installing to /home/zhoujiayi/R/x86_64-pc-linux-gnu- library/3.0/GLAD/libs > ** R > ** data > ** demo > ** inst > ** preparing package for lazy loading > ** 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 '/home/zhoujiayi/R/x86_64-pc-linux- gnu-library/3.0/GLAD/libs/GLAD.so': > > libgsl.so.0: cannot open shared object file: No such file or directory > Error: loading failed > Execution halted > ERROR: loading failed > > * removing ???/home/zhoujiayi/R/x86_64-pc-linux-gnu- library/3.0/GLAD??? > > The downloaded source packages are in > ???/tmp/RtmpvMaBRk/downloaded_packages??? > Warning message: > In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > installation of package ???GLAD??? had non-zero exit status > >> > Do you know how to solve this problem? On ubuntu sudo apt-get install libgsl0-dev should fix the issue. Laurent > > -- output of sessionInfo(): > > R version 3.0.1 (2013-05-16) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_CA.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_CA.UTF-8 LC_COLLATE=en_CA.UTF-8 > [5] LC_MONETARY=en_CA.UTF-8 LC_MESSAGES=en_CA.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base >> > > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > 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
ADD COMMENTlink written 6.5 years ago by Laurent Gatto1.2k
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