Question: problem installing 'GLAD' package
0
gravatar for Shenglin Zheng
8.6 years ago by
Shenglin Zheng20 wrote:
Dear Colleagues:  I have problem in installing GLAD package. Please give us some advice.  --------------------- My step1 ------------------------------------------------ First, I installed gsl-1.7 locally : /mypath/bin/gsl-1.7 ./configure –prefix=/mypath/bin/gsl-1.7 Make Make install  -------------------My step2 -------------------------------------------- Second, I changed my .bash_profile as:  export PATH=/mypath/bin/gsl-1.7/bin:$PATH export  LD_LIBRARY_PATH=/mypath/bin/gsl-1.7/lib export GSL_LIB=/mypath/bin/gsl-1.7/lib export GSL_INC=/mypath/bin/gsl-1.7/include   -----------------My step3 ------------------------------------------------- Third, I install GLAD package. I got the following  error message:  > source("http://bioconductor.org/biocLite.R") BioC_mirror = http://www.bioconductor.org Change using chooseBioCmirror(). > biocLite("GLAD") Using R version 2.12.0, biocinstall version 2.7.4. Installing Bioconductor version 2.7 packages: [1] "GLAD" Please wait...  trying URL 'http://www.bioconductor.org/packages/2.7/bioc/src/contrib/ GLAD_2.12.0.tar.gz' Content type 'application/x-gzip' length 1293485 bytes (1.2 Mb) opened URL ================================================== downloaded 1.2 Mb  * installing *source* package âGLADâ ... checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for GSL... no checking for gcc... gcc -std=gnu99 checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc -std=gnu99 accepts -g... yes checking for gcc -std=gnu99 option to accept ISO C89... none needed checking for gsl-config... /usr/local/xiaosong/bin/gsl-1.7/bin/gsl- config checking for GSL - version >= 1.6... yes operating system: Linux configure: creating ./config.status config.status: creating src/Makevars  src/Makevars file  PKG_LIBS =  -lgsl -lgslcblas -lm PKG_CPPFLAGS +=  ** libs g++ -I/usr/local/xiaosong/bin/R-2.12.0/include  -I/usr/local/include    -fpic  -g -O2 -c BkpInfo.cpp -o BkpInfo.o g++ -I/usr/local/xiaosong/bin/R-2.12.0/include  -I/usr/local/include    -fpic  -g -O2 -c HaarSeg.cpp -o HaarSeg.o HaarSeg.cpp:20:25: error: gsl/gsl_cdf.h: No such file or directory HaarSeg.cpp: In function âdouble FDRThres(const double*, double, double, int)â: HaarSeg.cpp:573: error: âgsl_cdf_gaussian_Pâ was not declared in this scope make: *** [HaarSeg.o] Error 1 ERROR: compilation failed for package âGLADâ * removing â/usr/local/xiaosong/bin/R-2.12.0/library/GLADâ  The downloaded packages are in         â/tmp/RtmpbZT2rJ/downloaded_packagesâ Updating HTML index of packages in '.Library' Warning message: In install.packages(pkgs = pkgs, repos = repos, ...) :   installation of package 'GLAD' had non-zero exit status [[alternative HTML version deleted]]
cdf glad • 1.4k views
ADD COMMENTlink modified 8.6 years ago • written 8.6 years ago by Shenglin Zheng20
Answer: problem installing 'GLAD' package
0
gravatar for Shenglin Zheng
8.6 years ago by
Shenglin Zheng20 wrote:
Dear Colleagues:  I have problem in installing GLAD package. Please give us some advice.  --------------------- My step1 ------------------------------------------------ First, I installed gsl-1.7 locally : /mypath/bin/gsl-1.7 ./configure –prefix=/mypath/bin/gsl-1.7 Make Make install  -------------------My step2 -------------------------------------------- Second, I changed my .bash_profile as:  export PATH=/mypath/bin/gsl-1.7/bin:$PATH export  LD_LIBRARY_PATH=/mypath/bin/gsl-1.7/lib export GSL_LIB=/mypath/bin/gsl-1.7/lib export GSL_INC=/mypath/bin/gsl-1.7/include   -----------------My step3 ------------------------------------------------- Third, I install GLAD package. I got the following  error message:  > source("http://bioconductor.org/biocLite.R") BioC_mirror = http://www.bioconductor.org Change using chooseBioCmirror(). > biocLite("GLAD") Using R version 2.12.0, biocinstall version 2.7.4. Installing Bioconductor version 2.7 packages: [1] "GLAD" Please wait...  trying URL 'http://www.bioconductor.org/packages/2.7/bioc/src/contrib/ GLAD_2.12.0.tar.gz' Content type 'application/x-gzip' length 1293485 bytes (1.2 Mb) opened URL ================================================== downloaded 1.2 Mb  * installing *source* package âGLADâ ... checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for GSL... no checking for gcc... gcc -std=gnu99 checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc -std=gnu99 accepts -g... yes checking for gcc -std=gnu99 option to accept ISO C89... none needed checking for gsl-config... /usr/local/xiaosong/bin/gsl-1.7/bin/gsl- config checking for GSL - version >= 1.6... yes operating system: Linux configure: creating ./config.status config.status: creating src/Makevars  src/Makevars file  PKG_LIBS =  -lgsl -lgslcblas -lm PKG_CPPFLAGS +=  ** libs g++ -I/usr/local/xiaosong/bin/R-2.12.0/include  -I/usr/local/include    -fpic  -g -O2 -c BkpInfo.cpp -o BkpInfo.o g++ -I/usr/local/xiaosong/bin/R-2.12.0/include  -I/usr/local/include    -fpic  -g -O2 -c HaarSeg.cpp -o HaarSeg.o HaarSeg.cpp:20:25: error: gsl/gsl_cdf.h: No such file or directory HaarSeg.cpp: In function âdouble FDRThres(const double*, double, double, int)â: HaarSeg.cpp:573: error: âgsl_cdf_gaussian_Pâ was not declared in this scope make: *** [HaarSeg.o] Error 1 ERROR: compilation failed for package âGLADâ * removing â/usr/local/xiaosong/bin/R-2.12.0/library/GLADâ  The downloaded packages are in         â/tmp/RtmpbZT2rJ/downloaded_packagesâ Updating HTML index of packages in '.Library' Warning message: In install.packages(pkgs = pkgs, repos = repos, ...) :   installation of package 'GLAD' had non-zero exit status [[alternative HTML version deleted]]
ADD COMMENTlink written 8.6 years ago by Shenglin Zheng20

Years later, the question still remains unanswered.

ADD REPLYlink written 8 months ago by 26246994660
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