[BioC] need helps on Error when package GGtools loading in Mac OSX and Linux server

Martin Morgan mtmorgan at fhcrc.org
Sun Feb 6 15:17:41 CET 2011


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



More information about the Bioconductor mailing list