[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 22:04:01 CET 2011
Dear Martin,
I followed your advice. But, the error is still there. Please help me.
Jian-Feng,
> source("http://bioconductor.org/biocLite.R")
BioC_mirror = http://www.bioconductor.org
Change using chooseBioCmirror().
> biocLite('Ruuid')
Using R version 2.12.1, biocinstall version 2.7.4.
Installing Bioconductor version 2.7 packages:
[1] "Ruuid"
Please wait...
trying URL 'http://www.bioconductor.org/packages/2.7/bioc/bin/macosx/leopard/contrib/2.12/Ruuid_1.28.0.tgz'
Content type 'application/x-gzip' length 84154 bytes (82 Kb)
opened URL
==================================================
downloaded 82 Kb
The downloaded packages are in
/var/folders/Ic/IcbLL0ELH9uqwZPaFP9Nz++++TQ/-Tmp-//RtmpReHOOb/downloaded_packages
> 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-//RtmpReHOOb/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] RSQLite_0.9-4 DBI_0.2-5 snpMatrix_1.14.6 survival_2.36-2
[5] Biobase_2.10.0
loaded via a namespace (and not attached):
[1] AnnotationDbi_1.12.0 GSEABase_1.12.2 XML_3.2-0
[4] annotate_1.28.0 graph_1.28.0 tools_2.12.1
[7] 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)
2011/2/6 Martin Morgan <mtmorgan at fhcrc.org>:
> On 02/06/2011 04:35 AM, Mao Jianfeng wrote:
>> 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
>
> THis is an obscure error. Try
>
> biocLite('Ruuid')
>
> first, and then biocLite("GGtools")
>
> Martin
>
>> 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)
>>
>
>
> --
> Computational Biology
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
>
> Location: M1-B861
> Telephone: 206 667-2793
>
--
Jian-Feng, Mao
the Institute of Botany,
Chinese Academy of Botany,
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