[BioC] need helps on Error when package GGtools loading in Mac OSX and Linux server
Mao Jianfeng
jianfeng.mao at gmail.com
Sun Feb 6 13:35:31 CET 2011
Dear listers,
This the second time for me to post this same question in the list.
I am now asking your helps on fix Error when GGtools loading in Mac
OSX and Linux server. I listed the command I used and the error I got,
and also the sessionInfo()s for each platform I used. It looks that
GGtools has been installed, the problem may come from package 'GGBase'
which can not be installed.
Thanks in advance.
#######################################################################
# (1) Mac OS X
# I have the most upgraded OS X, though it was showed "darwin9.8.0" in
the result of "version"
# command. I do not know why.
> source("http://bioconductor.org/biocLite.R")
BioC_mirror = http://www.bioconductor.org
Change using chooseBioCmirror().
> biocLite("GGtools")
Using R version 2.12.1, biocinstall version 2.7.4.
Installing Bioconductor version 2.7 packages:
[1] "GGtools"
Please wait...
trying URL 'http://www.bioconductor.org/packages/2.7/bioc/bin/macosx/leopard/contrib/2.12/GGtools_3.8.4.tgz'
Content type 'application/x-gzip' length 63768931 bytes (60.8 Mb)
opened URL
=================================================
downloaded 60.8 Mb
The downloaded packages are in
/var/folders/Ic/IcbLL0ELH9uqwZPaFP9Nz++++TQ/-Tmp-//RtmpyvXcQ8/downloaded_packages
> library(GGtools)
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()'. To cite Bioconductor, see
'citation("Biobase")' and for packages 'citation(pkgname)'.
Loading required package: GGBase
Loading required package: snpMatrix
Loading required package: survival
Loading required package: splines
Loading required package: RSQLite
Loading required package: DBI
Error in as.environment(pos) :
no item called "newtable" on the search list
In addition: Warning message:
In objects(newtable, all.names = TRUE) :
‘newtable’ converted to character string
Error: package 'GGBase' could not be loaded
> sessionInfo()
R version 2.12.1 (2010-12-16)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
locale:
[1] C/UTF-8/C/C/C/C
attached base packages:
[1] splines stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] biomaRt_2.6.0 BSgenome_1.18.3 Biostrings_2.18.2
[4] GenomicRanges_1.2.3 IRanges_1.8.8 RSQLite_0.9-4
[7] DBI_0.2-5 snpMatrix_1.14.6 survival_2.36-2
[10] Biobase_2.10.0
loaded via a namespace (and not attached):
[1] AnnotationDbi_1.12.0 GSEABase_1.12.2 RCurl_1.4-3
[4] XML_3.2-0 annotate_1.28.0 graph_1.28.0
[7] tools_2.12.1 xtable_1.5-6
> version
_
platform x86_64-apple-darwin9.8.0
arch x86_64
os darwin9.8.0
system x86_64, darwin9.8.0
status
major 2
minor 12.1
year 2010
month 12
day 16
svn rev 53855
language R
version.string R version 2.12.1 (2010-12-16)
#######################################################################
# (1) Linux server
> source("http://bioconductor.org/biocLite.R")
BioC_mirror = http://www.bioconductor.org
Change using chooseBioCmirror().
> library(GGtools)
Error in library(GGtools) : there is no package called 'GGtools'
> biocLite("GGtools")
Using R version 2.12.0, biocinstall version 2.7.4.
Installing Bioconductor version 2.7 packages:
[1] "GGtools"
Please wait...
Installing package(s) into ‘/ebio/abt6/jmao/rpacks’
(as ‘lib’ is unspecified)
also installing the dependencies ‘RCurl’, ‘XML’, ‘GGBase’,
‘rtracklayer’, ‘GSEABase’
trying URL 'http://cran.fhcrc.org/src/contrib/RCurl_1.5-0.tar.gz'
Content type 'application/x-gzip' length 744626 bytes (727 Kb)
opened URL
==================================================
downloaded 727 Kb
trying URL 'http://cran.fhcrc.org/src/contrib/XML_3.2-0.tar.gz'
Content type 'application/x-gzip' length 779406 bytes (761 Kb)
opened URL
==================================================
downloaded 761 Kb
trying URL 'http://www.bioconductor.org/packages/2.7/bioc/src/contrib/GGBase_3.10.0.tar.gz'
Content type 'application/x-gzip' length 50398547 bytes (48.1 Mb)
opened URL
=================================================
downloaded 48.1 Mb
trying URL 'http://www.bioconductor.org/packages/2.7/bioc/src/contrib/rtracklayer_1.10.6.tar.gz'
Content type 'application/x-gzip' length 1611074 bytes (1.5 Mb)
opened URL
==================================================
downloaded 1.5 Mb
trying URL 'http://www.bioconductor.org/packages/2.7/bioc/src/contrib/GSEABase_1.12.2.tar.gz'
Content type 'application/x-gzip' length 170133 bytes (166 Kb)
opened URL
==================================================
downloaded 166 Kb
trying URL 'http://www.bioconductor.org/packages/2.7/bioc/src/contrib/GGtools_3.8.4.tar.gz'
Content type 'application/x-gzip' length 63730571 bytes (60.8 Mb)
opened URL
=================================================
downloaded 60.8 Mb
* installing *source* package ‘RCurl’ ...
checking for curl-config... no
Cannot find curl-config
ERROR: configuration failed for package ‘RCurl’
* removing ‘/ebio/abt6/jmao/rpacks/RCurl’
* installing *source* package ‘XML’ ...
checking for gcc... gcc
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 accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for sed... /bin/sed
checking for pkg-config... /usr/bin/pkg-config
checking for xml2-config... no
Cannot find xml2-config
ERROR: configuration failed for package ‘XML’
* removing ‘/ebio/abt6/jmao/rpacks/XML’
ERROR: dependencies ‘RCurl’, ‘XML’ are not available for package ‘rtracklayer’
* removing ‘/ebio/abt6/jmao/rpacks/rtracklayer’
ERROR: dependency ‘XML’ is not available for package ‘GSEABase’
* removing ‘/ebio/abt6/jmao/rpacks/GSEABase’
ERROR: dependency ‘GSEABase’ is not available for package ‘GGBase’
* removing ‘/ebio/abt6/jmao/rpacks/GGBase’
ERROR: dependencies ‘GGBase’, ‘rtracklayer’, ‘GSEABase’ are not
available for package ‘GGtools’
* removing ‘/ebio/abt6/jmao/rpacks/GGtools’
The downloaded packages are in
‘/tmp/RtmpMtMIp6/downloaded_packages’
Warning messages:
1: In install.packages(pkgs = pkgs, repos = repos, ...) :
installation of package 'RCurl' had non-zero exit status
2: In install.packages(pkgs = pkgs, repos = repos, ...) :
installation of package 'XML' had non-zero exit status
3: In install.packages(pkgs = pkgs, repos = repos, ...) :
installation of package 'rtracklayer' had non-zero exit status
4: In install.packages(pkgs = pkgs, repos = repos, ...) :
installation of package 'GSEABase' had non-zero exit status
5: In install.packages(pkgs = pkgs, repos = repos, ...) :
installation of package 'GGBase' had non-zero exit status
6: In install.packages(pkgs = pkgs, repos = repos, ...) :
installation of package 'GGtools' had non-zero exit status
> sessionInfo()
R version 2.12.0 (2010-10-15)
Platform: x86_64-unknown-linux-gnu (64-bit)
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=C 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
loaded via a namespace (and not attached):
[1] tools_2.12.0
> version
_
platform x86_64-unknown-linux-gnu
arch x86_64
os linux-gnu
system x86_64, linux-gnu
status
major 2
minor 12.0
year 2010
month 10
day 15
svn rev 53317
language R
version.string R version 2.12.0 (2010-10-15)
--
Jian-Feng, Mao
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