[R] Help....package "GPLOTS" will not install. Linux
Gabor Grothendieck
ggrothendieck at gmail.com
Thu Feb 4 18:12:17 CET 2010
Several things to try:
1. install ActiveState perl. I believe that that perl distribution
already contains the offending perl module so you might be able to
avoid building it, or
2. just remove src/Makefile from gdata so it does not try to build
that perl module. You may lose some
functionality from gdata but it may be functionality you don't need.
2010/2/4 Uwe Ligges <ligges at statistik.tu-dortmund.de>:
> 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 Please note that you are using a really outdated version of R .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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> and provide commented, minimal, self-contained, reproducible code.
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