error when install ATACseqQC about atacseqqc

[jianhong]

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.

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On Fri, Dec 7, 2018 at 9:12 AM wangjiawen2013 ***@***.***> 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 — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#13>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AFYSAxsPqxBFqxAJWtpWBa2gi3V7uEXNks5u2ndRgaJpZM4ZIg3C> .

-- Yours sincerely, Jianhong Ou

[wangjiawen2013]

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.

[jianhong]

how do you set /path/to/you/local/lib?

[wangjiawen2013]

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"

[jianhong]

try to add one more line in your ~/.R/Makevars:
CFLAGS=-I/path/to/your/gsl/include

[wangjiawen2013]

It does not work. It seems that BiocManager cannot find my ~/.R/Makevars.

[sckinta]

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