Entering edit mode
Shenglin Zheng
▴
20
@shenglin-zheng-4375
Last seen 10.0 years ago
Dear Colleagues:
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I have problem in installing GLAD package. Please give us some advice.
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--------------------- My step1
------------------------------------------------
First, I installed gsl-1.7 locally : /mypath/bin/gsl-1.7
./configure âprefix=/mypath/bin/gsl-1.7
Make
Make install
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-------------------My step2
--------------------------------------------
Second, I changed my .bash_profile as:
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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
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-----------------My step3
-------------------------------------------------
Third, I install GLAD package. I got the following error message:
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> 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...
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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
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* 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
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src/Makevars file
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PKG_LIBS =Â -lgsl -lgslcblas -lm
PKG_CPPFLAGS +=
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** libs
g++ -I/usr/local/xiaosong/bin/R-2.12.0/include -I/usr/local/includeÂ
  -fpic -g -O2 -c BkpInfo.cpp -o BkpInfo.o
g++ -I/usr/local/xiaosong/bin/R-2.12.0/include -I/usr/local/includeÂ
  -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
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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]]
Years later, the question still remains unanswered.