ATACseqQC
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jianhong
error when install ATACseqQC
Dear,
When I install ATACseqQC, the following error occurred: RandPSSMGen.cpp:32:31: fatal error: gsl/gsl_histogram.h: No such file or directory #include <gsl/gsl_histogram.h> The reason is that I have install gsl (GNU scientific library) at a non-standard position. I am not an root user, So I couldn't install it in the default path /usr/local/include/gsl. I have added the path of gsl to my environmental variables. However, I still can't install ATACseqQC. May be I need to change the header of ATACseqQC source file. Could you help me?
Best regards
Hi Wangjiawen,
This is a issue in package MotIV. You can add link path in ~/.R/Makevars like this: LDFLAGS: -L/path/to/you/local/lib
see details at https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Using-Makevars or google: Makevars.
Let me know if you still have any issues.
Jianhong.
On Fri, Dec 7, 2018 at 9:12 AM wangjiawen2013 [email protected] wrote:
Dear,
When I install ATACseqQC, the following error occurred: RandPSSMGen.cpp:32:31: fatal error: gsl/gsl_histogram.h: No such file or directory #include <gsl/gsl_histogram.h> The reason is that I have install gsl (GNU scientific library) at a non-standard position. I am not an root user, So I couldn't install it in the default path /usr/local/include/gsl. I have added the path of gsl to my environmental variables. However, I still can't install ATACseqQC. May be I need to change the header of ATACseqQC source file. Could you help me?
Best regards
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-- Yours sincerely, Jianhong Ou
I cannot find .R in my home directory. I made a new directory ~/.R/Makevars and added new line "LDFLAGS: -L/path/to/you/local/lib". It didn't work at all. Then I downloaded MotIV package and modified Makevars (add new line LDFLAGS: -L/path/to/you/local/lib) in its src directory, then installed it with R CMD INSTALL. However, the Makevers.in file in src made new Makevars file and overlapped the old one. So this attempt failed again.
In .bashrc: export PATH=/home/wangjw/bin/gsl/bin:$PATH export LD_LIBRARY_PATH=/home/wangjw/bin/gsl/lib:$LD_LIBRARY_PATH
I cannot find .R in my home directory. I made a new directory ~/.R/Makevars and added new line "LDFLAGS: -L/home/wangjw/bin/gsl/lib"
try to add one more line in your ~/.R/Makevars: CFLAGS=-I/path/to/your/gsl/include
It does not work. It seems that BiocManager cannot find my ~/.R/Makevars.
It works for me now, by setting ~/.R/Makevars
LDFLAGS=-L/path/to/your/gsl/lib -lgsl -lgslcblas CFLAGS=-I/path/to/your/gsl/include PKG_LIBS=-L/path/to/your/gsl/lib
Then add following to ~/.bashrc
export PATH=/path/to/your/gsl/bin:$PATH export LD_LIBRARY_PATH=/path/to/your/gsl/2.5/lib:/path/to/your/gsl/include:$LD_LIBRARY_PATH
