[R] Help....package "GPLOTS" will not install. Linux
Uwe Ligges
ligges at statistik.tu-dortmund.de
Thu Feb 4 16:50:16 CET 2010
After some update of gdata the package needs the Compress::Raw::Zlib
perl module and tries to build it but fails.
Please report the issue you found to the package maintainer.
Please note that you are using a really outdated version of R .
Uwe Ligges
On 04.02.2010 01:29, Laurence Cooke wrote:
> 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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