[R] installing Contfrac package gives a gcc error

[Yeroslaviz, Assa]

Hi everyone,

I am trying to install the contra package on my Ubuntu server.

Ich bekomme aber die folgende Fehlermeldung:

But I keep getting this error:

Installing contfrac
'/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet  \
  CMD INSTALL '/tmp/Rtmp0ZStmN/devtools84a45d407429/contfrac'  \
  --library='/home/yeroslaviz/R/x86_64-pc-linux-gnu-library/3.3'  \
  --install-tests

* installing *source* package ‘contfrac’ ...
** package ‘contfrac’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c contfrac.c -o contfrac.o
gcc: error: unrecognized command line option ‘-fstack-protector-strong’
gcc: error: unrecognized command line option ‘-Wdate-time’
/usr/lib/R/etc/Makeconf:132: recipe for target 'contfrac.o' failed
make: *** [contfrac.o] Error 1
ERROR: compilation failed for package ‘contfrac’
* removing ‘/home/yeroslaviz/R/x86_64-pc-linux-gnu-library/3.3/contfrac’
Error: Command failed (1)


is this a known problem?

my server has the following gcc version installed- 5.4.0.

BUT when typing which gcc I get the following path - /home/yeroslaviz/anaconda_ete/bin/gcc
the version of this gcc is though -  4.8.5.

the gcc version of  /usr/bin/gcc -v  is

Using built-in specs.
COLLECT_GCC=/usr/bin/gcc
COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/5/lto-wrapper
Target: x86_64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Ubuntu 5.4.0-6ubuntu1~16.04.4' --with-bugurl=file:///usr/share/doc/gcc-5/README.Bugs --enable-languages=c,ada,c++,java,go,d,fortran,objc,obj-c++ --prefix=/usr --program-suffix=-5 --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --with-sysroot=/ --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-libmpx --enable-plugin --with-system-zlib --disable-browser-plugin --enable-java-awt=gtk --enable-gtk-cairo --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-5-amd64/jre --enable-java-home --with-jvm-root-dir=/usr/lib/jvm/java-1.5.0-gcj-5-amd64 --with-jvm-jar-dir=/usr/lib/jvm-exports/java-1.5.0-gcj-5-amd64 --with-arch-directory=amd64 --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --enable-objc-gc --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu
Thread model: posix
gcc version 5.4.0 20160609 (Ubuntu 5.4.0-6ubuntu1~16.04.4)

I will appreciate any help.

danke
Assa


> sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.1 LTS

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

loaded via a namespace (and not attached):
[1] tools_3.3.2 tcltk_3.3.2


——

Assa Yeroslaviz, PhD
Application service, Bioinformatics group
Max Planck Institute for Biochemistry
Am Klopferspitz 18, 82152 Martinsried
Germany
Tel:     +49 89 8578 2427
Email: yeroslaviz at biochem.mpg.de<mailto:yeroslaviz at biochem.mpg.de>


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