[BioC] need helps on Error when package GGtools loading in Mac OSX and Linux server
Vincent Carey
stvjc at channing.harvard.edu
Sun Feb 6 22:08:47 CET 2011
I am sorry that you are running into this problem. I encounter it
with a small fraction of mac users when teaching courses. If you have
enough infrastructure to build the Ruuid package from source you will
probably get around this. Please ensure that you have a current Xcode
tools image on your mac, and then try
biocLite("Ruuid", type="source")
report any error messages you encounter as you go through the same
steps with GGBase and GGtools. Thank you for your patience.
On Sun, Feb 6, 2011 at 4:04 PM, Mao Jianfeng <jianfeng.mao at gmail.com> wrote:
> 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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