> biocLite("xps", type="source")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.12 (BiocInstaller 1.10.4), R version 3.1.3.
Installing package(s) 'xps'
trying URL 'http://bioconductor.org/packages/2.12/bioc/src/contrib/xps_1.20.3.tar.gz'
Content type 'application/x-gzip' length 6622799 bytes (6.3 MB)
opened URL
==================================================
downloaded 6.3 MB
* installing *source* package ‘xps’ ...
checking for gcc... gcc -m64 -std=gnu99
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -m64 -std=gnu99 accepts -g... yes
checking for gcc -m64 -std=gnu99 option to accept ANSI C... none needed
checking how to run the C preprocessor... gcc -m64 -std=gnu99 -E
checking for gcc... (cached) gcc -m64 -std=gnu99
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc -m64 -std=gnu99 accepts -g... (cached) yes
checking for gcc -m64 -std=gnu99 option to accept ANSI C... (cached) none needed
found ROOT version 6.02/05 in directory /home/dhwani/Desktop/root/root-6.02.05
** libs
** arch -
Unknown argument "--dicttype"!
Usage: root-config [--prefix[=DIR]] [--exec-prefix[=DIR]] [--version] [--cflags] [--auxcflags] [--ldflags] [--new] [--nonew] [--libs] [--glibs] [--evelibs] [--bindir] [--libdir] [--incdir] [--etcdir] [--noauxcflags] [--noauxlibs] [--noldflags] [--has-<feature>] [--arch] [--platform] [--config] [--features] [--ncpu] [--git-revision] [--python-version] [--cc] [--cxx] [--f77] [--ld ] [--help]
g++ -I/home/dhwani/Desktop/root/root-6.02.05/include -O2 -Wall -fPIC -pthread -std=c++11 -Wno-deprecated-declarations -m64 -I/home/dhwani/Desktop/root/root-6.02.05/include -c TMLMath.cxx
TMLMath.cxx:1109:0: warning: "xmax" redefined [enabled by default]
#define xmax 2.5327372760800758e+305
^
TMLMath.cxx:1060:0: note: this is the location of the previous definition
# define xmax 3.745194030963158e306
^
TMLMath.cxx: In static member function ‘static Double_t TMLMath::Expm1(Double_t)’:
TMLMath.cxx:123:13: error: ‘cout’ was not declared in this scope
if(kCSa) cout << "------TMLMath::Expm1------" << endl;
^
TMLMath.cxx:123:13: note: suggested alternative:
In file included from /home/dhwani/Desktop/root/root-6.02.05/include/Riostream.h:25:0,
from TMLMath.h:52,
from TMLMath.cxx:58:
/opt/rh/devtoolset-2/root/usr/include/c++/4.8.2/iostream:61:18: note: ‘std::cout’
extern ostream cout; /// Linked to standard output
^
TMLMath.cxx:1434:57: error: ‘endl’ was not declared in this scope
if(kCSa) cout << "------TMLMath::PNormBoth------" << endl;
^
TMLMath.cxx:1434:57: note: suggested alternative:
In file included from /opt/rh/devtoolset-2/root/usr/include/c++/4.8.2/iterator:64:0,
from /home/dhwani/Desktop/root/root-6.02.05/include/TList.h:32,
from TMLMath.cxx:53:
/opt/rh/devtoolset-2/root/usr/include/c++/4.8.2/ostream:564:5: note: ‘std::endl’
endl(basic_ostream<_CharT, _Traits>& __os)
^
make: *** [TMLMath.o] Error 1
ERROR: compilation failed for package ‘xps’
* removing ‘/usr/lib64/R/library/xps’
The downloaded source packages are in
‘/tmp/RtmpB90UjX/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
sessioninfo
R version 3.1.3 (2015-03-09)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: CentOS release 6.6 (Final)
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
other attached packages:
[1] BiocInstaller_1.10.4
loaded via a namespace (and not attached):
[1] tools_3.1.3
The error was huge and couldn't upload the whole