Entering edit mode
spsp9987
•
0
@spsp9987-11762
Last seen 6.1 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 ?
> 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
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.
Um.. "RcppExamples" is installed. but it occurs still.
Does anybody know what the fail happens?
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
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.
Have you resolved the issue? I got similar problem recently and setting CXX1X environment variable for C++ compiler did help me.