[BioC] Issue of installing the GLAD package

Aiden [guest] guest at bioconductor.org
Fri Jun 7 20:12:07 CEST 2013

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:

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/GLAD_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  

** 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
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)

 [1] LC_CTYPE=en_CA.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_CA.UTF-8        LC_COLLATE=en_CA.UTF-8    
 [7] LC_PAPER=C                 LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

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