[R] Help....package "GPLOTS" will not install. Linux
Laurence Cooke
lcooke at azcc.arizona.edu
Thu Feb 4 01:29:59 CET 2010
Hello,
Apologies in advance if this is not the appropriate forum for this post.
My problem is I'm not able to install the package "GPLOTS". Below are
the outputs for the commands: sessionInfo() and
install.packages("gplots",dependencies=TRUE).
It seems the package "GDATA" is part of the problem but I'm not an
expert in this. The "GDATA" package will not install if I try
installing it separately.
In case the "GPLOTS" package from one repository might be corrupted, I
did try installing from 2 different repositories and got the same
errors.
Any help would be greatly appreciated.
Thank you,
Larry
> sessionInfo()
R version 2.8.0 (2008-10-20)
i686-redhat-linux-gnu
locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;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] tcltk_2.8.0 tools_2.8.0
> install.packages("gplots",dependencies=TRUE)
--- Please select a CRAN mirror for use in this session ---
Loading Tcl/Tk interface ... done
also installing the dependency ‘gdata’
trying URL 'http://cran.cnr.Berkeley.edu/src/contrib/gdata_2.7.1.tar.gz'
Content type 'application/x-gzip' length 903888 bytes (882 Kb)
opened URL
==================================================
downloaded 882 Kb
trying URL
'http://cran.cnr.Berkeley.edu/src/contrib/gplots_2.7.4.tar.gz'
Content type 'application/x-gzip' length 252885 bytes (246 Kb)
opened URL
==================================================
downloaded 246 Kb
* Installing *source* package 'gdata' ...
** libs
** arch -
tar xzf Compress-Raw-Zlib-2.024.tar.gz
cd Compress-Raw-Zlib-2.024 ; \
perl Makefile.PL
PREFIX=/tmp/R.INSTALL.Q18057/gdata/src/../inst/perl
LIB=/tmp/R.INSTALL.Q18057/gdata/src/../inst/perl ; \
make; \
make install
Parsing config.in...
Building Zlib enabled
Auto Detect Gzip OS Code..
Setting Gzip OS Code to 3 [Unix/Default]
Looks Good.
Up/Downgrade not needed.
Checking if your kit is complete...
Looks good
Writing Makefile for Compress::Raw::Zlib
make[1]: Entering directory
`/tmp/R.INSTALL.Q18057/gdata/src/Compress-Raw-Zlib-2.024'
cp lib/Compress/Raw/Zlib.pm blib/lib/Compress/Raw/Zlib.pm
AutoSplitting blib/lib/Compress/Raw/Zlib.pm
(blib/lib/auto/Compress/Raw/Zlib)
/usr/bin/perl /usr/lib/perl5/5.8.8/ExtUtils/xsubpp
-typemap /usr/lib/perl5/5.8.8/ExtUtils/typemap -typemap typemap Zlib.xs
> Zlib.xsc && mv Zlib.xsc Zlib.c
gcc -c -I./zlib-src -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing
-pipe -Wdeclaration-after-statement -I/usr/local/include
-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g
-pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic
-fasynchronous-unwind-tables -DVERSION=\"2.024\" -DXS_VERSION=\"2.024
\" -fPIC "-I/usr/lib/perl5/5.8.8/i386-linux-thread-multi/CORE"
-DGZIP_OS_CODE=3 -DUSE_PPPORT_H Zlib.c
Zlib.xs: In function ‘deRef_l’:
Zlib.xs:593: warning: value computed is not used
gcc -c -I./zlib-src -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing
-pipe -Wdeclaration-after-statement -I/usr/local/include
-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g
-pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic
-fasynchronous-unwind-tables -DVERSION=\"2.024\" -DXS_VERSION=\"2.024
\" -fPIC "-I/usr/lib/perl5/5.8.8/i386-linux-thread-multi/CORE"
-DGZIP_OS_CODE=3 -DUSE_PPPORT_H adler32.c
gcc -c -I./zlib-src -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing
-pipe -Wdeclaration-after-statement -I/usr/local/include
-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g
-pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic
-fasynchronous-unwind-tables -DVERSION=\"2.024\" -DXS_VERSION=\"2.024
\" -fPIC "-I/usr/lib/perl5/5.8.8/i386-linux-thread-multi/CORE"
-DGZIP_OS_CODE=3 -DUSE_PPPORT_H crc32.c
gcc -c -I./zlib-src -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing
-pipe -Wdeclaration-after-statement -I/usr/local/include
-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g
-pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic
-fasynchronous-unwind-tables -DVERSION=\"2.024\" -DXS_VERSION=\"2.024
\" -fPIC "-I/usr/lib/perl5/5.8.8/i386-linux-thread-multi/CORE"
-DGZIP_OS_CODE=3 -DUSE_PPPORT_H infback.c
gcc -c -I./zlib-src -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing
-pipe -Wdeclaration-after-statement -I/usr/local/include
-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g
-pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic
-fasynchronous-unwind-tables -DVERSION=\"2.024\" -DXS_VERSION=\"2.024
\" -fPIC "-I/usr/lib/perl5/5.8.8/i386-linux-thread-multi/CORE"
-DGZIP_OS_CODE=3 -DUSE_PPPORT_H inflate.c
gcc -c -I./zlib-src -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing
-pipe -Wdeclaration-after-statement -I/usr/local/include
-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g
-pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic
-fasynchronous-unwind-tables -DVERSION=\"2.024\" -DXS_VERSION=\"2.024
\" -fPIC "-I/usr/lib/perl5/5.8.8/i386-linux-thread-multi/CORE"
-DGZIP_OS_CODE=3 -DUSE_PPPORT_H uncompr.c
gcc -c -I./zlib-src -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing
-pipe -Wdeclaration-after-statement -I/usr/local/include
-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g
-pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic
-fasynchronous-unwind-tables -DVERSION=\"2.024\" -DXS_VERSION=\"2.024
\" -fPIC "-I/usr/lib/perl5/5.8.8/i386-linux-thread-multi/CORE"
-DGZIP_OS_CODE=3 -DUSE_PPPORT_H compress.c
gcc -c -I./zlib-src -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing
-pipe -Wdeclaration-after-statement -I/usr/local/include
-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g
-pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic
-fasynchronous-unwind-tables -DVERSION=\"2.024\" -DXS_VERSION=\"2.024
\" -fPIC "-I/usr/lib/perl5/5.8.8/i386-linux-thread-multi/CORE"
-DGZIP_OS_CODE=3 -DUSE_PPPORT_H deflate.c
gcc -c -I./zlib-src -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing
-pipe -Wdeclaration-after-statement -I/usr/local/include
-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g
-pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic
-fasynchronous-unwind-tables -DVERSION=\"2.024\" -DXS_VERSION=\"2.024
\" -fPIC "-I/usr/lib/perl5/5.8.8/i386-linux-thread-multi/CORE"
-DGZIP_OS_CODE=3 -DUSE_PPPORT_H inffast.c
gcc -c -I./zlib-src -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing
-pipe -Wdeclaration-after-statement -I/usr/local/include
-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g
-pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic
-fasynchronous-unwind-tables -DVERSION=\"2.024\" -DXS_VERSION=\"2.024
\" -fPIC "-I/usr/lib/perl5/5.8.8/i386-linux-thread-multi/CORE"
-DGZIP_OS_CODE=3 -DUSE_PPPORT_H inftrees.c
gcc -c -I./zlib-src -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing
-pipe -Wdeclaration-after-statement -I/usr/local/include
-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g
-pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic
-fasynchronous-unwind-tables -DVERSION=\"2.024\" -DXS_VERSION=\"2.024
\" -fPIC "-I/usr/lib/perl5/5.8.8/i386-linux-thread-multi/CORE"
-DGZIP_OS_CODE=3 -DUSE_PPPORT_H trees.c
gcc -c -I./zlib-src -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing
-pipe -Wdeclaration-after-statement -I/usr/local/include
-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g
-pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic
-fasynchronous-unwind-tables -DVERSION=\"2.024\" -DXS_VERSION=\"2.024
\" -fPIC "-I/usr/lib/perl5/5.8.8/i386-linux-thread-multi/CORE"
-DGZIP_OS_CODE=3 -DUSE_PPPORT_H zutil.c
Running Mkbootstrap for Compress::Raw::Zlib ()
chmod 644 Zlib.bs
rm -f blib/arch/auto/Compress/Raw/Zlib/Zlib.so
gcc -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386
-mtune=generic -fasynchronous-unwind-tables -L/usr/local/lib Zlib.o
adler32.o crc32.o infback.o inflate.o uncompr.o compress.o deflate.o
inffast.o inftrees.o trees.o zutil.o -o
blib/arch/auto/Compress/Raw/Zlib/Zlib.so \
\
chmod 755 blib/arch/auto/Compress/Raw/Zlib/Zlib.so
cp Zlib.bs blib/arch/auto/Compress/Raw/Zlib/Zlib.bs
chmod 644 blib/arch/auto/Compress/Raw/Zlib/Zlib.bs
Manifying blib/man3/Compress::Raw::Zlib.3pm
make[1]: Leaving directory
`/tmp/R.INSTALL.Q18057/gdata/src/Compress-Raw-Zlib-2.024'
make[1]: Entering directory
`/tmp/R.INSTALL.Q18057/gdata/src/Compress-Raw-Zlib-2.024'
Installing /tmp/R.INSTALL.Q18057/gdata/src/../inst/perl/i386-linux-thread-multi/auto/Compress/Raw/Zlib/Zlib.so
Installing /tmp/R.INSTALL.Q18057/gdata/src/../inst/perl/i386-linux-thread-multi/auto/Compress/Raw/Zlib/Zlib.bs
Files found in blib/arch: installing files in blib/lib into architecture
dependent library tree
Installing /tmp/R.INSTALL.Q18057/gdata/src/../inst/perl/i386-linux-thread-multi/Compress/Raw/Zlib.pm
Installing /tmp/R.INSTALL.Q18057/gdata/src/../inst/perl/i386-linux-thread-multi/auto/Compress/Raw/Zlib/autosplit.ix
Installing /tmp/R.INSTALL.Q18057/gdata/src/../inst/perl/share/man/man3/Compress::Raw::Zlib.3pm
Writing /tmp/R.INSTALL.Q18057/gdata/src/../inst/perl/i386-linux-thread-multi/auto/Compress/Raw/Zlib/.packlist
Appending installation info
to /tmp/R.INSTALL.Q18057/gdata/src/../inst/perl/i386-linux-thread-multi/perllocal.pod
make[1]: Leaving directory
`/tmp/R.INSTALL.Q18057/gdata/src/Compress-Raw-Zlib-2.024'
#
make clean
make[1]: Entering directory `/tmp/R.INSTALL.Q18057/gdata/src'
rm -rf Compress-Raw-Zlib-2.024
rm -rf ../inst/perl/share
make[1]: Leaving directory `/tmp/R.INSTALL.Q18057/gdata/src'
cp: cannot stat `*.so': No such file or directory
ERROR: compilation failed for package 'gdata'
** Removing '/usr/lib/R/library/gdata'
* Installing *source* package 'gplots' ...
** R
** data
** inst
** preparing package for lazy loading
Loading required package: gtools
Loading required package: gdata
Warning in library(pkg, character.only = TRUE, logical.return = TRUE,
lib.loc = lib.loc) :
there is no package called 'gdata'
Error: package 'gdata' could not be loaded
Execution halted
ERROR: lazy loading failed for package 'gplots'
** Removing '/usr/lib/R/library/gplots'
The downloaded packages are in
/tmp/RtmpwbpMJ3/downloaded_packages
Updating HTML index of packages in '.Library'
Warning messages:
1: In install.packages("gplots", dependencies = TRUE) :
installation of package 'gdata' had non-zero exit status
2: In install.packages("gplots", dependencies = TRUE) :
installation of package 'gplots' had non-zero exit status
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