Trouble compiling flowCore v1.36.7 on RHEL 6.7
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@brian-d-peyser-phd-6106
Last seen 5.9 years ago

I get an error with flowCore when trying to update my Bioconductor packages (as root):

> library(BiocInstaller)
Bioconductor version 3.2 (BiocInstaller 1.20.1), ?biocLite for help
> biocLite()
BioC_mirror: http://bioconductor.org
Using Bioconductor 3.2 (BiocInstaller 1.20.1), R 3.2.3 (2015-12-10).
Old packages: 'flowCore'
Update all/some/none? [a/s/n]: a
trying URL 'http://bioconductor.org/packages/3.2/bioc/src/contrib/flowCore_1.36.7.tar.gz'
Content type 'application/x-gzip' length 12940912 bytes (12.3 MB)
==================================================
downloaded 12.3 MB

* installing *source* package ‘flowCore’ ...
** libs
g++ -m64 -std=c++0x -I/usr/include/R -DNDEBUG -I../inst/include/  -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/BH/include"   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c FastLogicle.cpp -o FastLogicle.o
g++ -m64 -std=c++0x -I/usr/include/R -DNDEBUG -I../inst/include/  -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/BH/include"   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c Hyperlog.cpp -o Hyperlog.o
g++ -m64 -std=c++0x -I/usr/include/R -DNDEBUG -I../inst/include/  -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/BH/include"   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c Logicle.cpp -o Logicle.o
g++ -m64 -std=c++0x -I/usr/include/R -DNDEBUG -I../inst/include/  -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/BH/include"   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c RcppExports.cpp -o RcppExports.o
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I../inst/include/  -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/BH/include"   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic  -c biexponential.c -o biexponential.o
g++ -m64 -std=c++0x -I/usr/include/R -DNDEBUG -I../inst/include/  -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/BH/include"   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c convertRawBytes.cpp -o convertRawBytes.o
convertRawBytes.cpp: In function ‘std::vector<double, std::allocator<double> > convertRawBytes(BYTES, bool, std::vector<short unsigned int, std::allocator<short unsigned int> >, short unsigned int, bool)’:
convertRawBytes.cpp:48: error: expected initializer before ‘:’ token
convertRawBytes.cpp:53: error: expected primary-expression before ‘auto’
convertRawBytes.cpp:53: error: expected ‘)’ before ‘auto’
convertRawBytes.cpp:53: warning: unused variable ‘nElement’
convertRawBytes.cpp:56: error: ‘nElement’ was not declared in this scope
convertRawBytes.cpp:61: error: ‘nrow’ was not declared in this scope
make: *** [convertRawBytes.o] Error 1
ERROR: compilation failed for package ‘flowCore’
* removing ‘/usr/lib64/R/library/flowCore’
* restoring previous ‘/usr/lib64/R/library/flowCore’

The downloaded source packages are in
    ‘/tmp/RtmpvHYgO6/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl,  :
  installation of package ‘flowCore’ had non-zero exit status

My sessionInfo:

> sessionInfo()
R version 3.2.3 (2015-12-10)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Workstation release 6.7 (Santiago)

locale:
 [1] LC_CTYPE=en_US.utf8       LC_NUMERIC=C             
 [3] LC_TIME=en_US.utf8        LC_COLLATE=en_US.utf8    
 [5] LC_MONETARY=en_US.utf8    LC_MESSAGES=en_US.utf8   
 [7] LC_PAPER=en_US.utf8       LC_NAME=C                
 [9] LC_ADDRESS=C              LC_TELEPHONE=C           
[11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C      

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] BiocInstaller_1.20.1

loaded via a namespace (and not attached):
[1] tools_3.2.3

I have also tried:

# R CMD INSTALL flowCore_1.36.7.tar.gz

with the same result. As indicated at http://bioconductor.org/checkResults/release/bioc-LATEST/flowCore/ compilation was OK on Ubuntu 14.04.2 LTS, and I had no problem building on Ubuntu 14.04.3 LTS. Any hints for Red Hat 6?

 
flowcore • 1.2k views
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0
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What version off gcc are you using on RH6?  I seem to remember that it can be a bit outdated by default.

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I'm using Red Hat's default:

$ gcc --version
gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-16)
Copyright (C) 2010 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
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I'm pretty sure the Ubuntu versions you mentioned us gcc 4.8 or greater.  Maybe try updating the version on RH using the devtoolset-3-toolchain here.

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Will try with the devtoolset-3-toolchain. Unfortunately, I'm only seeing beta repositories for rhscl; not sure what's wrong with Red Hat, but without those I can't install devtoolset-3 and I'm not keen on using beta repos. I have a support request in with Red Hat to ask why the repo is missing.

Thanks for the hint!

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Jiang, Mike ★ 1.3k
@jiang-mike-4886
Last seen 8 weeks ago
(Private Address)

Your gcc is too old and it failed at some c++11 code in flowCore. Bioconductor release uses gcc 4.8.4.

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@brian-d-peyser-phd-6106
Last seen 5.9 years ago

Getting the RHEL devtools-3 version of gcc (v4.9.2) fixed it for me.

Thanks for the help!

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