Chipseeker is unavabile on Linux CentOS7 ?
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spsp9987 • 0
@spsp9987-11762
Last seen 3.3 years ago

 

I tried to install "Chipseeker" on Linux CentOS7.

but the problem occured. it said that "fgsea, DOSE, chipseeker had non-zero status exit".

 

is the package, Chipseeker undecent on Linux ?

Bioconduct or Chipseeker CentOS7 Linux installation • 1.3k views
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Guangchuang Yu ★ 1.2k
@guangchuang-yu-5419
Last seen 5 months ago
China/Guangzhou/Southern Medical Univer…

you need to provide more detail information

Base on your msg, the issue is actually due to fail of fgsea installation.

 

you need to try `biocLite("fgsea")` and provide us the error msg.

 

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> biocLite("fgsea")                           
BioC_mirror: http://bioconductor.org
Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.1 (2016-06-21).
Installing package(s) ‘fgsea’
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100  653k  100  653k    0     0   502k      0  0:00:01  0:00:01 --:--:--  502k
* installing *source* package ‘fgsea’ ...
** libs
I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG  -DU_STATIC_IMPLEMENTATION -I"/usr/lib64/microsoft-r/3.3/lib64/R/library/Rcpp/include"      -c RcppExports.cpp -o RcppExports.o
sh: I/usr/lib64/microsoft-r/3.3/lib64/R/include: no such file or directory
make: [RcppExports.o] 오류 127 (ignored)
I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG  -DU_STATIC_IMPLEMENTATION -I"/usr/lib64/microsoft-r/3.3/lib64/R/library/Rcpp/include"      -c fastGSEA.cpp -o fastGSEA.o
sh: I/usr/lib64/microsoft-r/3.3/lib64/R/include: no such file or directory
make: [fastGSEA.o] error 127 (ignored)
gcc -std=gnu99 -I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG  -DU_STATIC_IMPLEMENTATION -I"/usr/lib64/microsoft-r/3.3/lib64/R/library/Rcpp/include"   -fpic  -DU_STATIC_IMPLEMENTATION -O2 -g  -c fgsea_init.c -o fgsea_init.o
-shared -L/usr/lib64/microsoft-r/3.3/lib64/R/lib -o fgsea.so RcppExports.o fastGSEA.o fgsea_init.o -L/usr/lib64/microsoft-r/3.3/lib64/R/lib -lR
sh: line 2: -shared: command not found
make: *** [fgsea.so] error 127
ERROR: compilation failed for package ‘fgsea’
* removing ‘/usr/lib64/microsoft-r/3.3/lib64/R/library/fgsea’

The downloaded source packages are in
    ‘/tmp/RtmpKeb92o/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
warnings(): 
In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘fgsea’ had non-zero exit status

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It seem like something eats up compiler command line: the line "I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG  -DU_STATIC_IMPLEMENTATION -I"/usr/lib64/microsoft-r/3.3/lib64/R/library/Rcpp/include"      -c RcppExports.cpp -o RcppExports.o` should start with "g++ -I/usr/lib/..." or something like that.

I found a similar month-old report here: https://social.technet.microsoft.com/Forums/scriptcenter/en-US/3ad8896c-e88c-4e98-bc55-64f5a26c4fe1/failing-to-install-boom-on-centos-7-with-mro-331?forum=ropen but  it wasn't resolved.

Can you try to install package RcppExamples? This sholud check whethere you have working C++ integration or not. It could be Mircosoft-R bug, so you can also try to switch to standard R.

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Um.. "RcppExamples" is installed. but it occurs still. 

Does anybody know what the fail happens?

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The suggestion was 'can you installl...' not 'is it installed...' because it looks like from your output that your R does not know what C++ compiler to use. As another way to get the same information, look at the output of R CMD config run at the command line, particularly

R CMD config CC
R CMD config CXX

These should indicate a C and C++ compiler that is available to your system. It looks from the output above that the CXX will be empty -- you've managed to configure your R to think that it does not have a C++ compiler. If that's the case, then it will help to know how you installed R.

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Have you resolved the issue? I got similar problem recently and setting CXX1X environment variable for C++ compiler did help me.

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