Question: Chipseeker is unavabile on Linux CentOS7 ?
0
gravatar for spsp9987
3.0 years ago by
spsp99870
spsp99870 wrote:

 

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 ?

ADD COMMENTlink modified 3.0 years ago by Guangchuang Yu1.1k • written 3.0 years ago by spsp99870
Answer: Chipseeker is unavabile on Linux CentOS7 ?
0
gravatar for Guangchuang Yu
3.0 years ago by
Guangchuang Yu1.1k
China/Guangzhou/Southern Medical University
Guangchuang Yu1.1k wrote:

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.

 

ADD COMMENTlink written 3.0 years ago by Guangchuang Yu1.1k

> 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

ADD REPLYlink written 3.0 years ago by spsp99870

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.

ADD REPLYlink written 3.0 years ago by assaron150

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

Does anybody know what the fail happens?

ADD REPLYlink modified 3.0 years ago • written 3.0 years ago by spsp99870

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.

ADD REPLYlink modified 3.0 years ago • written 3.0 years ago by Martin Morgan ♦♦ 23k

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

ADD REPLYlink written 2.9 years ago by assaron150
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