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Question: need helps on Error when package GGtools loading in Mac OSX and Linux server
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gravatar for Mao Jianfeng
7.8 years ago by
Mao Jianfeng290
Mao Jianfeng290 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/l eopard/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 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) -- Jian-Feng, Mao
ADD COMMENTlink modified 7.8 years ago by Martin Morgan ♦♦ 22k • written 7.8 years ago by Mao Jianfeng290
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gravatar for Martin Morgan
7.8 years ago by
Martin Morgan ♦♦ 22k
United States
Martin Morgan ♦♦ 22k wrote:
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/contri b/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/contri b/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/contri b/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/contri b/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
ADD COMMENTlink written 7.8 years ago by Martin Morgan ♦♦ 22k
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/l eopard/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/l eopard/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/macos x/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/contr ib/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/contr ib/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/contr ib/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/contr ib/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,
ADD REPLYlink written 7.8 years ago by Mao Jianfeng290
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/maco sx/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-//RtmpyvXcQ 8/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/cont rib/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/cont rib/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/cont rib/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/cont rib/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 >
ADD REPLYlink written 7.8 years ago by Vincent J. Carey, Jr.6.2k
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/li brary/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-/Rtm pReHOOb/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/macos x/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-//RtmpReHOO b/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/macos x/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-//RtmpReHOO b/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/mac osx/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-//RtmpyvXc Q8/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/con trib/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/con trib/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/con trib/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/con trib/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,
ADD REPLYlink written 7.8 years ago by Mao Jianfeng290
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/contri b/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/Ruu id? > > The downloaded packages are in > ? ? ? ??/private/var/folders/Ic/IcbLL0ELH9uqwZPaFP9Nz++++TQ/-Tmp-/Rt mpReHOOb/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/maco sx/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-//RtmpReHO Ob/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/maco sx/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-//RtmpReHO Ob/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/ma cosx/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-//RtmpyvX cQ8/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/co ntrib/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/co ntrib/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/co ntrib/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/co ntrib/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, >
ADD REPLYlink written 7.8 years ago by Vincent J. Carey, Jr.6.2k
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/contr ib/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/Ru uid? >> >> The downloaded packages are in >> ? ? ? ??/private/var/folders/Ic/IcbLL0ELH9uqwZPaFP9Nz++++TQ/-Tmp-/R tmpReHOOb/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/mac osx/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-//RtmpReH OOb/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/mac osx/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-//RtmpReH OOb/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/m acosx/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-//Rtmpyv XcQ8/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/c ontrib/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/c ontrib/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/c ontrib/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/c ontrib/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,
ADD REPLYlink written 7.8 years ago by Mao Jianfeng290
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/cont rib/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/Resource s/library/Ruuid? >>> * restoring previous >>> ?/Library/Frameworks/R.framework/Versions/2.12/Resources/library/R uuid? >>> >>> 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/ma cosx/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-//RtmpRe HOOb/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/ma cosx/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-//RtmpRe HOOb/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-//Rtmpy vXcQ8/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, >
ADD REPLYlink written 7.8 years ago by Vincent J. Carey, Jr.6.2k
Dear Vincent, Thanks a lot. I have got GGtools installed in my Mac book pro (with updated Mac OS and Xcode). What I have done: (1). install fink in order to let all unix program run in Mac, following the manual in fink website (http://www.finkproject.org/). (2). then, run "sudo fink install glib glib2-dev". (3). next, log in R, and source("http://bioconductor.org/biocLite.R") biocLite("Ruuid", type="source") # you must install Ruuid from source. biocLite("GGtools") (4). invoke GGtools library(GGtools) I need to mention that all my progresses were got under helps of Mr. Vincent and Martin, especially Vincent has given me much. Thanks a lot. Best, Jian-Feng, 2011/2/7 Vincent Carey <stvjc at="" channing.harvard.edu="">: > 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/con trib/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/Resourc es/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/m acosx/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-//RtmpR eHOOb/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/m acosx/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-//RtmpR eHOOb/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-//Rtmp yvXcQ8/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 >>>>>>> >>>>>> >>>>>> >>>>>> >>>>
ADD REPLYlink written 7.8 years ago by Mao Jianfeng290
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