[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 11:12:08 CET 2011
Dear Vincent,
I have the most upgraded Mac OS with most upgraded Xcode in my mac
book pro, when I reported the error at the first email.
I am not good at computer. Please help me.
Also, the same problem occurred for Linux server, as I showed in my
first email. Not only it is in Mac OS. I have not test it in Windows.
May I do it hours later.
Looking forwards to your reply.
Jian-Feng,
2011/2/7 Vincent Carey <stvjc at channing.harvard.edu>:
> 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,
>>
>
--
Jian-Feng, Mao
the Institute of Botany,
Chinese Academy of Botany,
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