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Last seen 10.5 years ago
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
>
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