[BioC] need helps on Error when package GGtools loading in Mac OSX and Linux server
Vincent Carey
stvjc at channing.harvard.edu
Mon Feb 7 03:41:24 CET 2011
http://developer.apple.com/technologies/tools/xcode.html
without Xcode (which is distributed with the MacOSX install disk as an
additional package) you cannot build R packages from source, and in
particular Ruuid is unlikely to be usable. You should be able to get
a copy of Xcode tools for free from apple.com, but it is if I recall
correctly a download of several GB. it will be easier for you if you
have the installer disk around.
On Sun, Feb 6, 2011 at 6:08 PM, Mao Jianfeng <jianfeng.mao at gmail.com> wrote:
> 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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