[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 11:38:33 CET 2011
Here I will address both operating systems; I missed the linux in the
first email.
The failure on the linux server concerns lack of curl and XML
infrastructure -- these error messages are reasonably clear:
* 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
so you will have to work with a sysadmin to obtain curl development resources
http://curl.haxx.se/download.html
and libxml2 development resources from
http://xmlsoft.org/
Ideally the resources will be installed in "standard" locations and
the default source installation activities of biocLite() will lead to
successful installation of RCurl and XML packages. Otherwise you will
have to set PKG_CONFIG_PATH suitably.
For the MacOSX I have asked you to do
biocLite("Ruuid", type="source")
if that succeeds, please do
library(Ruuid)
and show all the results. I suspect the installation will fail and we
will discover what infrastructure elements are missing.
On Mon, Feb 7, 2011 at 5:12 AM, Mao Jianfeng <jianfeng.mao at gmail.com> wrote:
> 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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