[BioC] installation problem
Weiming Zhang
Weiming.Zhang at uchsc.edu
Mon Oct 6 18:50:16 MEST 2003
Hi,
I am having some problems on installing bioconductor packages. I am
running R 1.7.1 on RH linux 7.2. I installed Graphviz by using RPM, but
not sure about HDF(I downloaded it and did what doc says I should do but
rhdf5 still could not find it). Could anybody give me some idea?
Thank you very much.
wz
> getBioC()
Running getBioC version 1.2.42....
If you encounter problems, first make sure that
you are running the latest version of getBioC()
which can be found at: www.bioconductor.org/getBioC.R
Please direct any concerns or questions to
bioconductor at stat.math.ethz.ch.
Loading required package: reposTools
Creating a new generic function for "summary" in package
reposTools
Synching your local package management information ...
Packages which have been removed:
Rgraphviz
RBGL
Ruuid
affy
genefilter
multtest
rhdf5
Synching your local package management information ...
Note: No specified download type, defaulting to Source
[1] "Attempting to download Rgraphviz from
http://www.bioconductor.org/repository/release1.2/package/Source"
[1] "Download complete."
[1] "Installing Rgraphviz"
* Installing *source* package 'Rgraphviz' ...
** libs
gcc -I/opt/math/R/lib/R/include `dotneato-config --cflags`
-I/usr/local/include -D__NO_MATH_INLINES -mieee-fp -Wall -fPIC -g -O2
-c Rgraphviz.c -o Rgraphviz.o
In file included from /usr/include/errno.h:36,
from /opt/math/R/lib/R/include/Rinternals.h:32,
from common.h:10,
from Rgraphviz.c:1:
/usr/include/bits/errno.h:25:26: linux/errno.h: No such file or
directory
In file included from /usr/include/bits/posix1_lim.h:126,
from /usr/include/limits.h:144,
from
/usr/lib/gcc-lib/i386-redhat-linux/2.96/include/limits.h:130,
from
/usr/lib/gcc-lib/i386-redhat-linux/2.96/include/syslimits.h:7,
from
/usr/lib/gcc-lib/i386-redhat-linux/2.96/include/limits.h:11,
from /opt/math/R/lib/R/include/Rinternals.h:38,
from common.h:10,
from Rgraphviz.c:1:
/usr/include/bits/local_lim.h:36:26: linux/limits.h: No such file or
directory
In file included from Rgraphviz.c:1:
common.h:19:20: render.h: No such file or directory
common.h:20:19: graph.h: No such file or directory
common.h:21:22: dotprocs.h: No such file or directory
common.h:22:24: neatoprocs.h: No such file or directory
common.h:23:20: adjust.h: No such file or directory
Rgraphviz.c:2:20: circle.h: No such file or directory
make: *** [Rgraphviz.o] Error 1
ERROR: compilation failed for package 'Rgraphviz'
[1] "Attempting to download RBGL from
http://www.bioconductor.org/repository/release1.2/package/Source"
[1] "Download complete."
[1] "Installing RBGL"
* Installing *source* package 'RBGL' ...
untarring boost include tree...
** libs
g++ -I/opt/math/R/lib/R/include -I/usr/local/include -mieee-fp
-IboostIncl -ftemplate-depth-30 -fPIC -g -O2 -c bfsBGL.cpp -o bfsBGL.o
In file included from /usr/include/bits/posix1_lim.h:126,
from /usr/include/limits.h:144,
from
/usr/lib/gcc-lib/i386-redhat-linux/2.96/include/limits.h:130,
from
/usr/lib/gcc-lib/i386-redhat-linux/2.96/include/syslimits.h:7,
from
/usr/lib/gcc-lib/i386-redhat-linux/2.96/include/limits.h:11,
from boostIncl/boost/config/suffix.hpp:26,
from boostIncl/boost/config.hpp:57,
from RBGL.h:4,
from bfsBGL.cpp:5:
/usr/include/bits/local_lim.h:36:26: linux/limits.h: No such file or
directory
In file included from /usr/include/errno.h:36,
from /opt/math/R/lib/R/include/Rmath.h:43,
from bfsBGL.cpp:26:
/usr/include/bits/errno.h:25:26: linux/errno.h: No such file or
directory
make: *** [bfsBGL.o] Error 1
ERROR: compilation failed for package 'RBGL'
[1] "Attempting to download Ruuid from
http://www.bioconductor.org/repository/release1.2/package/Source"
[1] "Download complete."
[1] "Installing Ruuid"
* Installing *source* package 'Ruuid' ...
creating cache ./config.cache
checking for glib-config... /usr/bin/glib-config
checking how to run the C preprocessor... cc -E
checking for /usr/include/unistd.h... yes
updating cache ./config.cache
creating ./config.status
creating src/Makevars
** libs
gcc -I/opt/math/R/lib/R/include -I/usr/include/glib-1.2
-I/usr/lib/glib/include -DHAVE_UNISTD_H=1 -I/usr/local/include
-D__NO_MATH_INLINES -mieee-fp -fPIC -g -O2 -c clear.c -o clear.o
In file included from /usr/include/bits/posix1_lim.h:126,
from /usr/include/limits.h:144,
from
/usr/lib/gcc-lib/i386-redhat-linux/2.96/include/limits.h:130,
from
/usr/lib/gcc-lib/i386-redhat-linux/2.96/include/syslimits.h:7,
from
/usr/lib/gcc-lib/i386-redhat-linux/2.96/include/limits.h:11,
from /usr/lib/glib/include/glibconfig.h:9,
from /usr/include/glib-1.2/glib.h:66,
from uuidP.h:24,
from clear.c:14:
/usr/include/bits/local_lim.h:36:26: linux/limits.h: No such file or
directory
make: *** [clear.o] Error 1
ERROR: compilation failed for package 'Ruuid'
[1] "Attempting to download affy from
http://www.bioconductor.org/repository/release1.2/package/Source"
[1] "Download complete."
[1] "Installing affy"
* Installing *source* package 'affy' ...
creating cache ./config.cache
checking how to run the C preprocessor... cc -E
checking for main in -lz... yes
checking for zlib.h... yes
checking if zlib version >= 1.1.3... yes
updating cache ./config.cache
creating ./config.status
creating src/Makevars
** libs
gcc -I/opt/math/R/lib/R/include -DHAVE_ZLIB=1 -I/usr/local/include
-D__NO_MATH_INLINES -mieee-fp -fPIC -g -O2 -c chipbackground.c -o
chipbackground.o
gcc -I/opt/math/R/lib/R/include -DHAVE_ZLIB=1 -I/usr/local/include
-D__NO_MATH_INLINES -mieee-fp -fPIC -g -O2 -c getall_locations.c -o
getall_locations.o
In file included from /usr/include/bits/posix1_lim.h:126,
from /usr/include/limits.h:144,
from
/usr/lib/gcc-lib/i386-redhat-linux/2.96/include/limits.h:130,
from
/usr/lib/gcc-lib/i386-redhat-linux/2.96/include/syslimits.h:7,
from
/usr/lib/gcc-lib/i386-redhat-linux/2.96/include/limits.h:11,
from /opt/math/R/lib/R/include/R.h:34,
from getall_locations.c:8:
/usr/include/bits/local_lim.h:36:26: linux/limits.h: No such file or
directory
In file included from /usr/include/errno.h:36,
from /opt/math/R/lib/R/include/Rinternals.h:32,
from /opt/math/R/lib/R/include/Rdefines.h:42,
from getall_locations.c:9:
/usr/include/bits/errno.h:25:26: linux/errno.h: No such file or
directory
make: *** [getall_locations.o] Error 1
ERROR: compilation failed for package 'affy'
[1] "Attempting to download genefilter from
http://www.bioconductor.org/repository/release1.2/package/Source"
[1] "Download complete."
[1] "Installing genefilter"
* Installing *source* package 'genefilter' ...
** libs
gcc -I/opt/math/R/lib/R/include -I/usr/local/include
-D__NO_MATH_INLINES -mieee-fp -fPIC -g -O2 -c genedist.c -o genedist.o
In file included from /usr/include/bits/posix1_lim.h:126,
from /usr/include/limits.h:144,
from
/usr/lib/gcc-lib/i386-redhat-linux/2.96/include/limits.h:130,
from
/usr/lib/gcc-lib/i386-redhat-linux/2.96/include/syslimits.h:7,
from
/usr/lib/gcc-lib/i386-redhat-linux/2.96/include/limits.h:11,
from /opt/math/R/lib/R/include/R.h:34,
from genedist.c:27:
/usr/include/bits/local_lim.h:36:26: linux/limits.h: No such file or
directory
In file included from /usr/include/errno.h:36,
from /opt/math/R/lib/R/include/Rinternals.h:32,
from genedist.c:28:
/usr/include/bits/errno.h:25:26: linux/errno.h: No such file or
directory
make: *** [genedist.o] Error 1
ERROR: compilation failed for package 'genefilter'
[1] "Attempting to download multtest from
http://www.bioconductor.org/repository/release1.2/package/Source"
[1] "Download complete."
[1] "Installing multtest"
* Installing *source* package 'multtest' ...
** libs
gcc -I/opt/math/R/lib/R/include -I/usr/local/include
-D__NO_MATH_INLINES -mieee-fp -O -Wall -DUSEDOUBLE -fPIC -g -O2 -c
block_sampling_fixed.c -o block_sampling_fixed.o
In file included from /usr/include/bits/posix1_lim.h:126,
from /usr/include/limits.h:144,
from
/usr/lib/gcc-lib/i386-redhat-linux/2.96/include/limits.h:130,
from
/usr/lib/gcc-lib/i386-redhat-linux/2.96/include/syslimits.h:7,
from
/usr/lib/gcc-lib/i386-redhat-linux/2.96/include/limits.h:11,
from /opt/math/R/lib/R/include/R.h:34,
from mt.h:8,
from block_sampling_fixed.c:7:
/usr/include/bits/local_lim.h:36:26: linux/limits.h: No such file or
directory
make: *** [block_sampling_fixed.o] Error 1
ERROR: compilation failed for package 'multtest'
[1] "Attempting to download rhdf5 from
http://www.bioconductor.org/repository/release1.2/package/Source"
[1] "Download complete."
[1] "Installing rhdf5"
* Installing *source* package 'rhdf5' ...
checking for gcc... gcc
checking for C compiler default output... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for executable suffix...
checking for object suffix... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking how to run the C preprocessor... gcc -E
checking for hdf5... yes
checking for H5Fopen in -lhdf5... no
checking for hdf5.h... no
checking hdf5 in /sw... failed
configure: error: please specify a valid hdf5 installation with
--with-hdf5=DIR
ERROR: configuration failed for package 'rhdf5'
>From URL:
http://www.bioconductor.org/repository/release1.2/package/Source
Rgraphviz version 1.0
RBGL version 1.0-0
Ruuid version 1.0
affy version 1.2.30
genefilter version 1.0.5
multtest version 1.0.2
rhdf5 version 1.0.1
Packages that were not updated:
AnnBuilder
Biobase
DynDoc
ROC
SAGElyzer
affycomp
affydata
annotate
edd
geneplotter
graph
hexbin
limma
makecdfenv
marrayClasses
marrayInput
marrayNorm
marrayPlots
marrayTools
reposTools
tkWidgets
vsn
widgetTools
Packages Rgraphviz and rhdf5 require special libraries to be installed.
Please see the URL http://www.bioconductor.org/faq.html#Other Notes for
more details on installing these packages if they fail
to install properly
Warning messages:
1: Installation of package Rgraphviz had non-zero exit status in:
installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce)
2: Installation of package RBGL had non-zero exit status in:
installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce)
3: Installation of package Ruuid had non-zero exit status in:
installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce)
4: Installation of package affy had non-zero exit status in:
installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce)
5: Installation of package genefilter had non-zero exit status in:
installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce)
6: Installation of package multtest had non-zero exit status in:
installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce)
7: Installation of package rhdf5 had non-zero exit status in:
installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce)
> getBioC()
Running getBioC version 1.2.42....
If you encounter problems, first make sure that
you are running the latest version of getBioC()
which can be found at: www.bioconductor.org/getBioC.R
Please direct any concerns or questions to
bioconductor at stat.math.ethz.ch.
Synching your local package management information ...
Packages which have been removed:
Rgraphviz
RBGL
Ruuid
affy
genefilter
multtest
rhdf5
Note: No specified download type, defaulting to Source
[1] "Attempting to download Rgraphviz from
http://www.bioconductor.org/repository/release1.2/package/Source"
[1] "Download complete."
[1] "Installing Rgraphviz"
* Installing *source* package 'Rgraphviz' ...
** libs
gcc -I/opt/math/R/lib/R/include `dotneato-config --cflags`
-I/usr/local/include -D__NO_MATH_INLINES -mieee-fp -Wall -fPIC -g -O2
-c Rgraphviz.c -o Rgraphviz.o
In file included from /usr/include/errno.h:36,
from /opt/math/R/lib/R/include/Rinternals.h:32,
from common.h:10,
from Rgraphviz.c:1:
/usr/include/bits/errno.h:25:26: linux/errno.h: No such file or
directory
In file included from /usr/include/bits/posix1_lim.h:126,
from /usr/include/limits.h:144,
from
/usr/lib/gcc-lib/i386-redhat-linux/2.96/include/limits.h:130,
from
/usr/lib/gcc-lib/i386-redhat-linux/2.96/include/syslimits.h:7,
from
/usr/lib/gcc-lib/i386-redhat-linux/2.96/include/limits.h:11,
from /opt/math/R/lib/R/include/Rinternals.h:38,
from common.h:10,
from Rgraphviz.c:1:
/usr/include/bits/local_lim.h:36:26: linux/limits.h: No such file or
directory
In file included from Rgraphviz.c:1:
common.h:19:20: render.h: No such file or directory
common.h:20:19: graph.h: No such file or directory
common.h:21:22: dotprocs.h: No such file or directory
common.h:22:24: neatoprocs.h: No such file or directory
common.h:23:20: adjust.h: No such file or directory
Rgraphviz.c:2:20: circle.h: No such file or directory
make: *** [Rgraphviz.o] Error 1
ERROR: compilation failed for package 'Rgraphviz'
[1] "Attempting to download RBGL from
http://www.bioconductor.org/repository/release1.2/package/Source"
[1] "Download complete."
[1] "Installing RBGL"
* Installing *source* package 'RBGL' ...
untarring boost include tree...
** libs
g++ -I/opt/math/R/lib/R/include -I/usr/local/include -mieee-fp
-IboostIncl -ftemplate-depth-30 -fPIC -g -O2 -c bfsBGL.cpp -o bfsBGL.o
In file included from /usr/include/bits/posix1_lim.h:126,
from /usr/include/limits.h:144,
from
/usr/lib/gcc-lib/i386-redhat-linux/2.96/include/limits.h:130,
from
/usr/lib/gcc-lib/i386-redhat-linux/2.96/include/syslimits.h:7,
from
/usr/lib/gcc-lib/i386-redhat-linux/2.96/include/limits.h:11,
from boostIncl/boost/config/suffix.hpp:26,
from boostIncl/boost/config.hpp:57,
from RBGL.h:4,
from bfsBGL.cpp:5:
/usr/include/bits/local_lim.h:36:26: linux/limits.h: No such file or
directory
In file included from /usr/include/errno.h:36,
from /opt/math/R/lib/R/include/Rmath.h:43,
from bfsBGL.cpp:26:
/usr/include/bits/errno.h:25:26: linux/errno.h: No such file or
directory
make: *** [bfsBGL.o] Error 1
ERROR: compilation failed for package 'RBGL'
[1] "Attempting to download Ruuid from
http://www.bioconductor.org/repository/release1.2/package/Source"
[1] "Download complete."
[1] "Installing Ruuid"
* Installing *source* package 'Ruuid' ...
creating cache ./config.cache
checking for glib-config... /usr/bin/glib-config
checking how to run the C preprocessor... cc -E
checking for /usr/include/unistd.h... yes
updating cache ./config.cache
creating ./config.status
creating src/Makevars
** libs
gcc -I/opt/math/R/lib/R/include -I/usr/include/glib-1.2
-I/usr/lib/glib/include -DHAVE_UNISTD_H=1 -I/usr/local/include
-D__NO_MATH_INLINES -mieee-fp -fPIC -g -O2 -c clear.c -o clear.o
In file included from /usr/include/bits/posix1_lim.h:126,
from /usr/include/limits.h:144,
from
/usr/lib/gcc-lib/i386-redhat-linux/2.96/include/limits.h:130,
from
/usr/lib/gcc-lib/i386-redhat-linux/2.96/include/syslimits.h:7,
from
/usr/lib/gcc-lib/i386-redhat-linux/2.96/include/limits.h:11,
from /usr/lib/glib/include/glibconfig.h:9,
from /usr/include/glib-1.2/glib.h:66,
from uuidP.h:24,
from clear.c:14:
/usr/include/bits/local_lim.h:36:26: linux/limits.h: No such file or
directory
make: *** [clear.o] Error 1
ERROR: compilation failed for package 'Ruuid'
[1] "Attempting to download affy from
http://www.bioconductor.org/repository/release1.2/package/Source"
[1] "Download complete."
[1] "Installing affy"
* Installing *source* package 'affy' ...
creating cache ./config.cache
checking how to run the C preprocessor... cc -E
checking for main in -lz... yes
checking for zlib.h... yes
checking if zlib version >= 1.1.3... yes
updating cache ./config.cache
creating ./config.status
creating src/Makevars
** libs
gcc -I/opt/math/R/lib/R/include -DHAVE_ZLIB=1 -I/usr/local/include
-D__NO_MATH_INLINES -mieee-fp -fPIC -g -O2 -c chipbackground.c -o
chipbackground.o
gcc -I/opt/math/R/lib/R/include -DHAVE_ZLIB=1 -I/usr/local/include
-D__NO_MATH_INLINES -mieee-fp -fPIC -g -O2 -c getall_locations.c -o
getall_locations.o
In file included from /usr/include/bits/posix1_lim.h:126,
from /usr/include/limits.h:144,
from
/usr/lib/gcc-lib/i386-redhat-linux/2.96/include/limits.h:130,
from
/usr/lib/gcc-lib/i386-redhat-linux/2.96/include/syslimits.h:7,
from
/usr/lib/gcc-lib/i386-redhat-linux/2.96/include/limits.h:11,
from /opt/math/R/lib/R/include/R.h:34,
from getall_locations.c:8:
/usr/include/bits/local_lim.h:36:26: linux/limits.h: No such file or
directory
In file included from /usr/include/errno.h:36,
from /opt/math/R/lib/R/include/Rinternals.h:32,
from /opt/math/R/lib/R/include/Rdefines.h:42,
from getall_locations.c:9:
/usr/include/bits/errno.h:25:26: linux/errno.h: No such file or
directory
make: *** [getall_locations.o] Error 1
ERROR: compilation failed for package 'affy'
[1] "Attempting to download genefilter from
http://www.bioconductor.org/repository/release1.2/package/Source"
[1] "Download complete."
[1] "Installing genefilter"
* Installing *source* package 'genefilter' ...
** libs
gcc -I/opt/math/R/lib/R/include -I/usr/local/include
-D__NO_MATH_INLINES -mieee-fp -fPIC -g -O2 -c genedist.c -o genedist.o
In file included from /usr/include/bits/posix1_lim.h:126,
from /usr/include/limits.h:144,
from
/usr/lib/gcc-lib/i386-redhat-linux/2.96/include/limits.h:130,
from
/usr/lib/gcc-lib/i386-redhat-linux/2.96/include/syslimits.h:7,
from
/usr/lib/gcc-lib/i386-redhat-linux/2.96/include/limits.h:11,
from /opt/math/R/lib/R/include/R.h:34,
from genedist.c:27:
/usr/include/bits/local_lim.h:36:26: linux/limits.h: No such file or
directory
In file included from /usr/include/errno.h:36,
from /opt/math/R/lib/R/include/Rinternals.h:32,
from genedist.c:28:
/usr/include/bits/errno.h:25:26: linux/errno.h: No such file or
directory
make: *** [genedist.o] Error 1
ERROR: compilation failed for package 'genefilter'
[1] "Attempting to download multtest from
http://www.bioconductor.org/repository/release1.2/package/Source"
[1] "Download complete."
[1] "Installing multtest"
* Installing *source* package 'multtest' ...
** libs
gcc -I/opt/math/R/lib/R/include -I/usr/local/include
-D__NO_MATH_INLINES -mieee-fp -O -Wall -DUSEDOUBLE -fPIC -g -O2 -c
block_sampling_fixed.c -o block_sampling_fixed.o
In file included from /usr/include/bits/posix1_lim.h:126,
from /usr/include/limits.h:144,
from
/usr/lib/gcc-lib/i386-redhat-linux/2.96/include/limits.h:130,
from
/usr/lib/gcc-lib/i386-redhat-linux/2.96/include/syslimits.h:7,
from
/usr/lib/gcc-lib/i386-redhat-linux/2.96/include/limits.h:11,
from /opt/math/R/lib/R/include/R.h:34,
from mt.h:8,
from block_sampling_fixed.c:7:
/usr/include/bits/local_lim.h:36:26: linux/limits.h: No such file or
directory
make: *** [block_sampling_fixed.o] Error 1
ERROR: compilation failed for package 'multtest'
[1] "Attempting to download rhdf5 from
http://www.bioconductor.org/repository/release1.2/package/Source"
[1] "Download complete."
[1] "Installing rhdf5"
* Installing *source* package 'rhdf5' ...
checking for gcc... gcc
checking for C compiler default output... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for executable suffix...
checking for object suffix... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking how to run the C preprocessor... gcc -E
checking for hdf5... yes
checking for H5Fopen in -lhdf5... no
checking for hdf5.h... no
checking hdf5 in /sw... failed
configure: error: please specify a valid hdf5 installation with
--with-hdf5=DIR
ERROR: configuration failed for package 'rhdf5'
>From URL:
http://www.bioconductor.org/repository/release1.2/package/Source
Rgraphviz version 1.0
RBGL version 1.0-0
Ruuid version 1.0
affy version 1.2.30
genefilter version 1.0.5
multtest version 1.0.2
rhdf5 version 1.0.1
Packages that were not updated:
AnnBuilder
Biobase
DynDoc
ROC
SAGElyzer
affycomp
affydata
annotate
edd
geneplotter
graph
hexbin
limma
makecdfenv
marrayClasses
marrayInput
marrayNorm
marrayPlots
marrayTools
reposTools
tkWidgets
vsn
widgetTools
Packages Rgraphviz and rhdf5 require special libraries to be installed.
Please see the URL http://www.bioconductor.org/faq.html#Other Notes for
more details on installing these packages if they fail
to install properly
Warning messages:
1: Installation of package Rgraphviz had non-zero exit status in:
installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce)
2: Installation of package RBGL had non-zero exit status in:
installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce)
3: Installation of package Ruuid had non-zero exit status in:
installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce)
4: Installation of package affy had non-zero exit status in:
installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce)
5: Installation of package genefilter had non-zero exit status in:
installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce)
6: Installation of package multtest had non-zero exit status in:
installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce)
7: Installation of package rhdf5 had non-zero exit status in:
installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce)
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