[BioC] need helps on Error when package GGtools loading in Mac OSX and Linux server
Mao Jianfeng
jianfeng.mao at gmail.com
Mon Feb 7 00:08:48 CET 2011
Hi Vincent and Martin,
Sorry. I am not good at computer. And, I do not understand "Please
ensure that you have a current Xcode
tools image on your mac". I do not know how to do that.
So, could you please show any lines of unix command to do that?
And, I want to mention that the error I reported forward also occurred
in linux server as I showed you in my first email.
I do not know if I have a current Xcode tools image on your mac. In
fact, I failed to install Ruuid package in my Mac OS X.
> biocLite("Ruuid", type="source")
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/src/contrib/Ruuid_1.28.0.tar.gz'
Content type 'application/x-gzip' length 71906 bytes (70 Kb)
opened URL
==================================================
downloaded 70 Kb
* installing *source* package ‘Ruuid’ ...
checking for pkg-config... no
checking for glib-config... no
configure: error: No glib package information found
ERROR: configuration failed for package ‘Ruuid’
* removing ‘/Library/Frameworks/R.framework/Versions/2.12/Resources/library/Ruuid’
* restoring previous
‘/Library/Frameworks/R.framework/Versions/2.12/Resources/library/Ruuid’
The downloaded packages are in
‘/private/var/folders/Ic/IcbLL0ELH9uqwZPaFP9Nz++++TQ/-Tmp-/RtmpReHOOb/downloaded_packages’
Updating HTML index of packages in '.Library'
Warning message:
In install.packages(pkgs = pkgs, repos = repos, ...) :
installation of package 'Ruuid' had non-zero exit status
2011/2/6 Vincent Carey <stvjc at channing.harvard.edu>:
> 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,
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
>
--
Jian-Feng, Mao
the Institute of Botany,
Chinese Academy of Botany,
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