[BioC] Issue of installing the GLAD package

[Laurent Gatto]

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/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
> 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
>>
>
>
> --
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>
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