problem while loading affycoretools
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@mayte-suarez-farinas-2068
Last seen 9.6 years ago
United States
I updated to the most recent R version. After this brand new installation, I get the following error while loading library affycoretools: library(affycoretools) Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : there is no package called ‘ff’ Error: package or namespace load failed for ‘affycoretools’ After checking mailing list, I followed James advice (https://stat.eth z.ch/pipermail/bioconductor/2012-December/049895.html) and updated all packages library(BiocInstaller) biocLite(character(0)) Additionally, I updated all R packages as well Still, the same problem arise. My R session info is bellow R version 3.0.1 (2013-05-16) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] KEGG.db_2.9.1 GO.db_2.9.0 RSQLite_0.11.4 DBI_0.2-7 [5] AnnotationDbi_1.22.6 affy_1.38.1 Biobase_2.20.1 BiocGenerics_0.6.0 [9] BiocInstaller_1.10.3 loaded via a namespace (and not attached): [1] affyio_1.28.0 annaffy_1.32.0 annotate_1.38.0 [4] AnnotationForge_1.2.2 biomaRt_2.16.0 Biostrings_2.28.0 [7] Category_2.26.0 gcrma_2.32.0 gdata_2.13.2 [10] genefilter_1.42.0 GenomicRanges_1.12.5 GOstats_2.26.0 [13] gplots_2.11.3 graph_1.38.3 grid_3.0.1 [16] GSEABase_1.22.0 gtools_3.0.0 IRanges_1.18.3 [19] lattice_0.20-23 limma_3.16.7 preprocessCore_1.22.0 [22] R2HTML_2.2.1 RBGL_1.36.2 RCurl_1.95-4.1 [25] splines_3.0.1 stats4_3.0.1 survival_2.37-4 [28] tools_3.0.1 XML_3.95-0.2 xtable_1.7-1 [31] zlibbioc_1.6.0 [[alternative HTML version deleted]]
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@steve-lianoglou-2771
Last seen 22 months ago
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Hi, On Sun, Sep 15, 2013 at 1:57 PM, Mayte Suarez-Farinas <farinam at="" mail.rockefeller.edu=""> wrote: > I updated to the most recent R version. After this brand new installation, I get the following error while loading library affycoretools: > > library(affycoretools) > Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : > there is no package called ?ff? > Error: package or namespace load failed for ?affycoretools? This is strange -- for some reason R is trying to load the ff package, but as far as I am aware, affycoretools does not depend on this package. You can try to install ff first and see if affycoretools will load: http://cran.r-project.org/web/packages/ff/index.html I'm curious if you have trouble loading any other package? Perhaps you can try something completely out of bioconductor land like ggplot2 or plyr. Do those work? You might want to start R via `R --vanilla` in your terminal. Perhaps there's some weirdness in an ~/.Rdata file that is being loaded and is tripping you up (I'd try this first, actually). HTH, -steve -- Steve Lianoglou Computational Biologist Bioinformatics and Computational Biology Genentech
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On Sun, Sep 15, 2013 at 2:51 PM, Steve Lianoglou <lianoglou.steve at="" gene.com=""> wrote: > Hi, > > On Sun, Sep 15, 2013 at 1:57 PM, Mayte Suarez-Farinas > <farinam at="" mail.rockefeller.edu=""> wrote: >> I updated to the most recent R version. After this brand new installation, I get the following error while loading library affycoretools: >> >> library(affycoretools) >> Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : >> there is no package called ?ff? >> Error: package or namespace load failed for ?affycoretools? > > This is strange -- for some reason R is trying to load the ff package, > but as far as I am aware, affycoretools does not depend on this > package. FYI, 'affycoretools' imports 'oligoClasses' which in turn imports 'ff'. Maybe there are other paths to 'ff' as well. /Henrik > > You can try to install ff first and see if affycoretools will load: > > http://cran.r-project.org/web/packages/ff/index.html > > I'm curious if you have trouble loading any other package? Perhaps you > can try something completely out of bioconductor land like ggplot2 or > plyr. > > Do those work? > > You might want to start R via `R --vanilla` in your terminal. Perhaps > there's some weirdness in an ~/.Rdata file that is being loaded and is > tripping you up (I'd try this first, actually). > > HTH, > -steve > > -- > Steve Lianoglou > Computational Biologist > Bioinformatics and Computational Biology > Genentech > > _______________________________________________ > 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
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@james-w-macdonald-5106
Last seen 2 days ago
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Hi Mayte, I have not seen this error in the past. Have you tried simply installing ff first? biocLite("ff") biocLite("affycoretools") Best, Jim On 9/15/2013 4:57 PM, Mayte Suarez-Farinas wrote: > I updated to the most recent R version. After this brand new installation, I get the following error while loading library affycoretools: > > library(affycoretools) > Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : > there is no package called ?ff? > Error: package or namespace load failed for ?affycoretools? > > After checking mailing list, I followed James advice (https://stat.e thz.ch/pipermail/bioconductor/2012-December/049895.html) and updated all packages > library(BiocInstaller) > biocLite(character(0)) > > Additionally, I updated all R packages as well > > Still, the same problem arise. My R session info is bellow > > > R version 3.0.1 (2013-05-16) > Platform: x86_64-apple-darwin10.8.0 (64-bit) > > locale: > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] parallel stats graphics grDevices utils datasets methods base > > other attached packages: > [1] KEGG.db_2.9.1 GO.db_2.9.0 RSQLite_0.11.4 DBI_0.2-7 > [5] AnnotationDbi_1.22.6 affy_1.38.1 Biobase_2.20.1 BiocGenerics_0.6.0 > [9] BiocInstaller_1.10.3 > > loaded via a namespace (and not attached): > [1] affyio_1.28.0 annaffy_1.32.0 annotate_1.38.0 > [4] AnnotationForge_1.2.2 biomaRt_2.16.0 Biostrings_2.28.0 > [7] Category_2.26.0 gcrma_2.32.0 gdata_2.13.2 > [10] genefilter_1.42.0 GenomicRanges_1.12.5 GOstats_2.26.0 > [13] gplots_2.11.3 graph_1.38.3 grid_3.0.1 > [16] GSEABase_1.22.0 gtools_3.0.0 IRanges_1.18.3 > [19] lattice_0.20-23 limma_3.16.7 preprocessCore_1.22.0 > [22] R2HTML_2.2.1 RBGL_1.36.2 RCurl_1.95-4.1 > [25] splines_3.0.1 stats4_3.0.1 survival_2.37-4 > [28] tools_3.0.1 XML_3.95-0.2 xtable_1.7-1 > [31] zlibbioc_1.6.0 > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
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Dear James, Henrik and Steve I tried biocLite("ff") and got the msg: package ?ff? is not available (for R version 3.0.1) (see below). Then I went ahead and download the tar package form (http://cran.r-project.org/web/packages/ff/index.html) and used R CMD install to install it. However, while loading ff (library(ff)) it complains that the package bit was missing, biocLite gave me same error (package ?bit? is not available (for R version 3.0.1) ) and I could not instll via CMD install gave me the following error dhcp-129-85-243-253:Desktop mayte$ R CMD INSTALL bit_1.1-10.tar * installing to library ?/Users/mayte/Library/R/3.0/library? * installing *source* package ?bit? ... ** package ?bit? successfully unpacked and MD5 sums checked ** libs sh: make: command not found ERROR: compilation failed for package ?bit? * removing ?/Users/mayte/Library/R/3.0/library/bit? dhcp-129-85-243-253:Desktop mayte$ Please help out, life without affycoretools is very difficult ;-) From: James W. MacDonald [jmacdon@uw.edu] Sent: Monday, September 16, 2013 11:03 AM To: Mayte Suarez-Farinas Cc: bioconductor at r-project.org Subject: Re: [BioC] problem while loading affycoretools Hi Mayte, I have not seen this error in the past. Have you tried simply installing ff first? biocLite("ff") biocLite("affycoretools") Best, Jim On 9/15/2013 4:57 PM, Mayte Suarez-Farinas wrote: > I updated to the most recent R version. After this brand new installation, I get the following error while loading library affycoretools: > > library(affycoretools) > Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : > there is no package called ?ff? > Error: package or namespace load failed for ?affycoretools? > > After checking mailing list, I followed James advice (https://stat.e thz.ch/pipermail/bioconductor/2012-December/049895.html) and updated all packages > library(BiocInstaller) > biocLite(character(0)) > > Additionally, I updated all R packages as well > > Still, the same problem arise. My R session info is bellow > > > R version 3.0.1 (2013-05-16) > Platform: x86_64-apple-darwin10.8.0 (64-bit) > > locale: > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] parallel stats graphics grDevices utils datasets methods base > > other attached packages: > [1] KEGG.db_2.9.1 GO.db_2.9.0 RSQLite_0.11.4 DBI_0.2-7 > [5] AnnotationDbi_1.22.6 affy_1.38.1 Biobase_2.20.1 BiocGenerics_0.6.0 > [9] BiocInstaller_1.10.3 > > loaded via a namespace (and not attached): > [1] affyio_1.28.0 annaffy_1.32.0 annotate_1.38.0 > [4] AnnotationForge_1.2.2 biomaRt_2.16.0 Biostrings_2.28.0 > [7] Category_2.26.0 gcrma_2.32.0 gdata_2.13.2 > [10] genefilter_1.42.0 GenomicRanges_1.12.5 GOstats_2.26.0 > [13] gplots_2.11.3 graph_1.38.3 grid_3.0.1 > [16] GSEABase_1.22.0 gtools_3.0.0 IRanges_1.18.3 > [19] lattice_0.20-23 limma_3.16.7 preprocessCore_1.22.0 > [22] R2HTML_2.2.1 RBGL_1.36.2 RCurl_1.95-4.1 > [25] splines_3.0.1 stats4_3.0.1 survival_2.37-4 > [28] tools_3.0.1 XML_3.95-0.2 xtable_1.7-1 > [31] zlibbioc_1.6.0 > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
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----- Original Message ----- > From: "Mayte Suarez-Farinas" <farinam at="" mail.rockefeller.edu=""> > To: "James W. MacDonald" <jmacdon at="" uw.edu=""> > Cc: "Steve Lianoglou" <lianoglou.steve at="" gene.com="">, bioconductor at r-project.org > Sent: Monday, September 16, 2013 9:14:00 AM > Subject: Re: [BioC] problem while loading affycoretools > > > Dear James, Henrik and Steve > > I tried biocLite("ff") and got the msg: package ?ff? is not available > (for R version 3.0.1) > (see below). Then I went ahead and download the tar package form > (http://cran.r-project.org/web/packages/ff/index.html) and used R > CMD install to install it. However, > while loading ff (library(ff)) it complains that the package bit was > missing, biocLite gave me > same error (package ?bit? is not available (for R version 3.0.1) ) > and I could not instll via CMD install > gave me the following error > > dhcp-129-85-243-253:Desktop mayte$ R CMD INSTALL bit_1.1-10.tar > * installing to library ?/Users/mayte/Library/R/3.0/library? > * installing *source* package ?bit? ... > ** package ?bit? successfully unpacked and MD5 sums checked > ** libs > sh: make: command not found You downloaded the source tarball for bit (.tar.gz); you wanted the Mac binary (.tgz). As for the problem with biocLite("bit") I'm not sure--are you behind a proxy or firewall? What is the output of the following: library(BiocInstaller) biocinstallRepos() ? Dan > ERROR: compilation failed for package ?bit? > * removing ?/Users/mayte/Library/R/3.0/library/bit? > dhcp-129-85-243-253:Desktop mayte$ > > Please help out, life without affycoretools is very difficult ;-) > > > From: James W. MacDonald [jmacdon at uw.edu] > Sent: Monday, September 16, 2013 11:03 AM > To: Mayte Suarez-Farinas > Cc: bioconductor at r-project.org > Subject: Re: [BioC] problem while loading affycoretools > > Hi Mayte, > > I have not seen this error in the past. Have you tried simply > installing > ff first? > > biocLite("ff") > biocLite("affycoretools") > > Best, > > Jim > > > On 9/15/2013 4:57 PM, Mayte Suarez-Farinas wrote: > > I updated to the most recent R version. After this brand new > > installation, I get the following error while loading library > > affycoretools: > > > > library(affycoretools) > > Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), > > versionCheck = vI[[j]]) : > > there is no package called ?ff? > > Error: package or namespace load failed for ?affycoretools? > > > > After checking mailing list, I followed James advice > > (https://stat.ethz.ch/pipermail/bioconductor/2012-December/049895. html) > > and updated all packages > > library(BiocInstaller) > > biocLite(character(0)) > > > > Additionally, I updated all R packages as well > > > > Still, the same problem arise. My R session info is bellow > > > > > > R version 3.0.1 (2013-05-16) > > Platform: x86_64-apple-darwin10.8.0 (64-bit) > > > > locale: > > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > > > attached base packages: > > [1] parallel stats graphics grDevices utils datasets > > methods base > > > > other attached packages: > > [1] KEGG.db_2.9.1 GO.db_2.9.0 RSQLite_0.11.4 > > DBI_0.2-7 > > [5] AnnotationDbi_1.22.6 affy_1.38.1 Biobase_2.20.1 > > BiocGenerics_0.6.0 > > [9] BiocInstaller_1.10.3 > > > > loaded via a namespace (and not attached): > > [1] affyio_1.28.0 annaffy_1.32.0 annotate_1.38.0 > > [4] AnnotationForge_1.2.2 biomaRt_2.16.0 Biostrings_2.28.0 > > [7] Category_2.26.0 gcrma_2.32.0 gdata_2.13.2 > > [10] genefilter_1.42.0 GenomicRanges_1.12.5 GOstats_2.26.0 > > [13] gplots_2.11.3 graph_1.38.3 grid_3.0.1 > > [16] GSEABase_1.22.0 gtools_3.0.0 IRanges_1.18.3 > > [19] lattice_0.20-23 limma_3.16.7 > > preprocessCore_1.22.0 > > [22] R2HTML_2.2.1 RBGL_1.36.2 RCurl_1.95-4.1 > > [25] splines_3.0.1 stats4_3.0.1 survival_2.37-4 > > [28] tools_3.0.1 XML_3.95-0.2 xtable_1.7-1 > > [31] zlibbioc_1.6.0 > > > > > > [[alternative HTML version deleted]] > > > > > > > > _______________________________________________ > > 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 > > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > > > _______________________________________________ > 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 >
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Hi James and Dan I installed R from scratch and then run the following two lines: biocLite() (success) biocLite("affycoretools") which, after installing several packages gave me the "error: package ‘AnnotationDbi’ could not be loaded" (see ALL outputs below)' Dan, here is the output of biocinstallRepos. librarybiocInstall() biocinstallRepos() BioCsoft "http://bioconductor.org/packages/2.12/bioc" BioCann "http://bioconductor.org/packages/2.12/data/annotation" BioCexp "http://bioconductor.org/packages/2.12/data/experiment" BioCextra "http://bioconductor.org/packages/2.12/extra" CRAN "http://cran.opensourceresources.org<http: cran.ope="" nsourceresources.org=""/>" ALL OUTPUTS: source("http://bioconductor.org/biocLite.R") Installing package into ‘/Users/mayte/Library/R/3.0/library’ (as ‘lib’ is unspecified) trying URL 'http://www.bioconductor.org/packages/2.12/bioc/bin/macosx/ contrib/3.0/BiocInstaller_1.10.3.tgz' Content type 'application/x-gzip' length 46533 bytes (45 Kb) opened URL ================================================== downloaded 45 Kb The downloaded binary packages are in /var/folders/r3/tlsb98mn33b3tl1wjd87hwch0000gn/T//RtmpARSLz6/downloade d_packages Bioconductor version 2.12 (BiocInstaller 1.10.3), ?biocLite for help > biocLite() BioC_mirror: http://bioconductor.org<http: bioconductor.org=""/> Using Bioconductor version 2.12 (BiocInstaller 1.10.3), R version 3.0.1. Installing package(s) 'Biobase' 'IRanges' 'AnnotationDbi' Warning: unable to access index for repository http://cran.opensourceresources.org/bin/macosx/contrib/3.0 Warning: dependencies ‘DBI’, ‘RSQLite’ are not available also installing the dependency ‘BiocGenerics’ trying URL 'http://bioconductor.org/packages/2.12/bioc/bin/macosx/cont rib/3.0/BiocGenerics_0.6.0.tgz' Content type 'application/x-gzip' length 333465 bytes (325 Kb) opened URL ================================================== downloaded 325 Kb trying URL 'http://bioconductor.org/packages/2.12/bioc/bin/macosx/cont rib/3.0/Biobase_2.20.1.tgz' Content type 'application/x-gzip' length 2354463 bytes (2.2 Mb) opened URL ================================================== downloaded 2.2 Mb trying URL 'http://bioconductor.org/packages/2.12/bioc/bin/macosx/cont rib/3.0/IRanges_1.18.3.tgz' Content type 'application/x-gzip' length 1978262 bytes (1.9 Mb) opened URL ================================================== downloaded 1.9 Mb trying URL 'http://bioconductor.org/packages/2.12/bioc/bin/macosx/cont rib/3.0/AnnotationDbi_1.22.6.tgz' Content type 'application/x-gzip' length 4066815 bytes (3.9 Mb) opened URL ================================================== downloaded 3.9 Mb The downloaded binary packages are in /var/folders/r3/tlsb98mn33b3tl1wjd87hwch0000gn/T//RtmpARSLz6/downloade d_packages Warning: unable to access index for repository http://cran.opensourceresources.org/bin/macosx/contrib/3.0 > biocLite("affycoretools") BioC_mirror: http://bioconductor.org<http: bioconductor.org=""/> Using Bioconductor version 2.12 (BiocInstaller 1.10.3), R version 3.0.1. Installing package(s) 'affycoretools' Warning: unable to access index for repository http://cran.opensourceresources.org/bin/macosx/contrib/3.0 Warning: dependencies ‘xtable’, ‘gplots’, ‘R2HTML’, ‘hwriter’, ‘XML’, ‘RCurl’, ‘DBI’, ‘foreach’, ‘R.utils’, ‘RSQLite’, ‘reshape2’, ‘gtable’, ‘gridExtra’, ‘scales’, ‘Hmisc’, ‘RColorBrewer’, ‘dichromat’, ‘bitops’ are not available also installing the dependencies ‘org.Hs.eg.db’, ‘biovizBase’, ‘GenomicFeatures’, ‘Rsamtools’, ‘BSgenome’, ‘VariantAnnotation’, ‘rtracklayer’, ‘affyio’, ‘preprocessCore’, ‘zlibbioc’, ‘Category’, ‘graph’, ‘RBGL’, ‘AnnotationForge’, ‘Biostrings’, ‘GenomicRanges’, ‘edgeR’, ‘PFAM.db’, ‘GSEABase’, ‘ggbio’, ‘affy’, ‘GO.db’, ‘KEGG.db’, ‘biomaRt’, ‘limma’, ‘GOstats’, ‘annotate’, ‘annaffy’, ‘gcrma’, ‘oligoClasses’, ‘ReportingTools’ trying URL 'http://bioconductor.org/packages/2.12/data/annotation/bin/ macosx/contrib/3.0/org.Hs.eg.db_2.9.0.tgz' Content type 'application/x-gzip' length 53095874 bytes (50.6 Mb) opened URL ================================================== downloaded 50.6 Mb trying URL 'http://bioconductor.org/packages/2.12/bioc/bin/macosx/cont rib/3.0/biovizBase_1.8.1.tgz' Content type 'application/x-gzip' length 1136533 bytes (1.1 Mb) opened URL ================================================== downloaded 1.1 Mb trying URL 'http://bioconductor.org/packages/2.12/bioc/bin/macosx/cont rib/3.0/GenomicFeatures_1.12.3.tgz' Content type 'application/x-gzip' length 971035 bytes (948 Kb) opened URL ================================================== downloaded 948 Kb trying URL 'http://bioconductor.org/packages/2.12/bioc/bin/macosx/cont rib/3.0/Rsamtools_1.12.4.tgz' Content type 'application/x-gzip' length 3768247 bytes (3.6 Mb) opened URL ================================================== downloaded 3.6 Mb trying URL 'http://bioconductor.org/packages/2.12/bioc/bin/macosx/cont rib/3.0/BSgenome_1.28.0.tgz' Content type 'application/x-gzip' length 746888 bytes (729 Kb) opened URL ================================================== downloaded 729 Kb trying URL 'http://bioconductor.org/packages/2.12/bioc/bin/macosx/cont rib/3.0/VariantAnnotation_1.6.7.tgz' Content type 'application/x-gzip' length 1689203 bytes (1.6 Mb) opened URL ================================================== downloaded 1.6 Mb trying URL 'http://bioconductor.org/packages/2.12/bioc/bin/macosx/cont rib/3.0/rtracklayer_1.20.4.tgz' Content type 'application/x-gzip' length 1861493 bytes (1.8 Mb) opened URL ================================================== downloaded 1.8 Mb trying URL 'http://bioconductor.org/packages/2.12/bioc/bin/macosx/cont rib/3.0/affyio_1.28.0.tgz' Content type 'application/x-gzip' length 94024 bytes (91 Kb) opened URL ================================================== downloaded 91 Kb trying URL 'http://bioconductor.org/packages/2.12/bioc/bin/macosx/cont rib/3.0/preprocessCore_1.22.0.tgz' Content type 'application/x-gzip' length 128027 bytes (125 Kb) opened URL ================================================== downloaded 125 Kb trying URL 'http://bioconductor.org/packages/2.12/bioc/bin/macosx/cont rib/3.0/zlibbioc_1.6.0.tgz' Content type 'application/x-gzip' length 124184 bytes (121 Kb) opened URL ================================================== downloaded 121 Kb trying URL 'http://bioconductor.org/packages/2.12/bioc/bin/macosx/cont rib/3.0/Category_2.26.0.tgz' Content type 'application/x-gzip' length 933299 bytes (911 Kb) opened URL ================================================== downloaded 911 Kb trying URL 'http://bioconductor.org/packages/2.12/bioc/bin/macosx/cont rib/3.0/graph_1.38.3.tgz' Content type 'application/x-gzip' length 1327243 bytes (1.3 Mb) opened URL ================================================== downloaded 1.3 Mb trying URL 'http://bioconductor.org/packages/2.12/bioc/bin/macosx/cont rib/3.0/RBGL_1.36.2.tgz' Content type 'application/x-gzip' length 911905 bytes (890 Kb) opened URL ================================================== downloaded 890 Kb trying URL 'http://bioconductor.org/packages/2.12/bioc/bin/macosx/cont rib/3.0/AnnotationForge_1.2.2.tgz' Content type 'application/x-gzip' length 4149568 bytes (4.0 Mb) opened URL ================================================== downloaded 4.0 Mb trying URL 'http://bioconductor.org/packages/2.12/bioc/bin/macosx/cont rib/3.0/Biostrings_2.28.0.tgz' Content type 'application/x-gzip' length 2215378 bytes (2.1 Mb) opened URL ================================================== downloaded 2.1 Mb trying URL 'http://bioconductor.org/packages/2.12/bioc/bin/macosx/cont rib/3.0/GenomicRanges_1.12.5.tgz' Content type 'application/x-gzip' length 3293184 bytes (3.1 Mb) opened URL ================================================== downloaded 3.1 Mb trying URL 'http://bioconductor.org/packages/2.12/bioc/bin/macosx/cont rib/3.0/edgeR_3.2.4.tgz' Content type 'application/x-gzip' length 1470863 bytes (1.4 Mb) opened URL ================================================== downloaded 1.4 Mb trying URL 'http://bioconductor.org/packages/2.12/data/annotation/bin/ macosx/contrib/3.0/PFAM.db_2.9.0.tgz' Content type 'application/x-gzip' length 2325707 bytes (2.2 Mb) opened URL ================================================== downloaded 2.2 Mb trying URL 'http://bioconductor.org/packages/2.12/bioc/bin/macosx/cont rib/3.0/GSEABase_1.22.0.tgz' Content type 'application/x-gzip' length 606089 bytes (591 Kb) opened URL ================================================== downloaded 591 Kb trying URL 'http://bioconductor.org/packages/2.12/bioc/bin/macosx/cont rib/3.0/ggbio_1.8.5.tgz' Content type 'application/x-gzip' length 2272353 bytes (2.2 Mb) opened URL ================================================== downloaded 2.2 Mb trying URL 'http://bioconductor.org/packages/2.12/bioc/bin/macosx/cont rib/3.0/affy_1.38.1.tgz' Content type 'application/x-gzip' length 1458286 bytes (1.4 Mb) opened URL ================================================== downloaded 1.4 Mb trying URL 'http://bioconductor.org/packages/2.12/data/annotation/bin/ macosx/contrib/3.0/GO.db_2.9.0.tgz' Content type 'application/x-gzip' length 25061115 bytes (23.9 Mb) opened URL ================================================== downloaded 23.9 Mb trying URL 'http://bioconductor.org/packages/2.12/data/annotation/bin/ macosx/contrib/3.0/KEGG.db_2.9.1.tgz' Content type 'application/x-gzip' length 2032486 bytes (1.9 Mb) opened URL ================================================== downloaded 1.9 Mb trying URL 'http://bioconductor.org/packages/2.12/bioc/bin/macosx/cont rib/3.0/biomaRt_2.16.0.tgz' Content type 'application/x-gzip' length 365452 bytes (356 Kb) opened URL ================================================== downloaded 356 Kb trying URL 'http://bioconductor.org/packages/2.12/bioc/bin/macosx/cont rib/3.0/limma_3.16.7.tgz' Content type 'application/x-gzip' length 1568068 bytes (1.5 Mb) opened URL ================================================== downloaded 1.5 Mb trying URL 'http://bioconductor.org/packages/2.12/bioc/bin/macosx/cont rib/3.0/GOstats_2.26.0.tgz' Content type 'application/x-gzip' length 1725303 bytes (1.6 Mb) opened URL ================================================== downloaded 1.6 Mb trying URL 'http://bioconductor.org/packages/2.12/bioc/bin/macosx/cont rib/3.0/annotate_1.38.0.tgz' Content type 'application/x-gzip' length 1971349 bytes (1.9 Mb) opened URL ================================================== downloaded 1.9 Mb trying URL 'http://bioconductor.org/packages/2.12/bioc/bin/macosx/cont rib/3.0/annaffy_1.32.0.tgz' Content type 'application/x-gzip' length 380113 bytes (371 Kb) opened URL ================================================== downloaded 371 Kb trying URL 'http://bioconductor.org/packages/2.12/bioc/bin/macosx/cont rib/3.0/gcrma_2.32.0.tgz' Content type 'application/x-gzip' length 240351 bytes (234 Kb) opened URL ================================================== downloaded 234 Kb trying URL 'http://bioconductor.org/packages/2.12/bioc/bin/macosx/cont rib/3.0/oligoClasses_1.22.0.tgz' Content type 'application/x-gzip' length 872393 bytes (851 Kb) opened URL ================================================== downloaded 851 Kb trying URL 'http://bioconductor.org/packages/2.12/bioc/bin/macosx/cont rib/3.0/ReportingTools_2.0.1.tgz' Content type 'application/x-gzip' length 2063622 bytes (2.0 Mb) opened URL ================================================== downloaded 2.0 Mb trying URL 'http://bioconductor.org/packages/2.12/bioc/bin/macosx/cont rib/3.0/affycoretools_1.32.1.tgz' Content type 'application/x-gzip' length 7077475 bytes (6.7 Mb) opened URL ================================================== downloaded 6.7 Mb The downloaded binary packages are in /var/folders/r3/tlsb98mn33b3tl1wjd87hwch0000gn/T//RtmpARSLz6/downloade d_packages Warning: unable to access index for repository http://cran.opensourceresources.org/bin/macosx/contrib/3.0 Mayte Suarez-Farinas Research Assistant Professor Laboratory of Investigative Dermatology Biostatistician, Center for Clinical and Translational Science The Rockefeller University 1230 York Ave, Box 178 New York, NY 10065 Phone: +1(212) 327-8213 Fax: +1(212) 327-8232 On Sep 16, 2013, at 1:36 PM, Dan Tenenbaum wrote: ----- Original Message ----- From: "Mayte Suarez-Farinas" <farinam@mail.rockefeller.edu<mailto:farinam@mail.rockefeller.edu>> To: "James W. MacDonald" <jmacdon@uw.edu<mailto:jmacdon@uw.edu>> Cc: "Steve Lianoglou" <lianoglou.steve@gene.com<mailto:lianoglou.steve@gene.com>>, bioconductor@r-project.org<mailto:bioconductor@r-project.org> Sent: Monday, September 16, 2013 9:14:00 AM Subject: Re: [BioC] problem while loading affycoretools Dear James, Henrik and Steve I tried biocLite("ff") and got the msg: package ‘ff’ is not available (for R version 3.0.1) (see below). Then I went ahead and download the tar package form (http://cran.r-project.org/web/packages/ff/index.html) and used R CMD install to install it. However, while loading ff (library(ff)) it complains that the package bit was missing, biocLite gave me same error (package ‘bit’ is not available (for R version 3.0.1) ) and I could not instll via CMD install gave me the following error dhcp-129-85-243-253:Desktop mayte$ R CMD INSTALL bit_1.1-10.tar * installing to library ‘/Users/mayte/Library/R/3.0/library’ * installing *source* package ‘bit’ ... ** package ‘bit’ successfully unpacked and MD5 sums checked ** libs sh: make: command not found You downloaded the source tarball for bit (.tar.gz); you wanted the Mac binary (.tgz). As for the problem with biocLite("bit") I'm not sure--are you behind a proxy or firewall? What is the output of the following: library(BiocInstaller) biocinstallRepos() ? Dan ERROR: compilation failed for package ‘bit’ * removing ‘/Users/mayte/Library/R/3.0/library/bit’ dhcp-129-85-243-253:Desktop mayte$ Please help out, life without affycoretools is very difficult ;-) From: James W. MacDonald [jmacdon@uw.edu<mailto:jmacdon@uw.edu>] Sent: Monday, September 16, 2013 11:03 AM To: Mayte Suarez-Farinas Cc: bioconductor@r-project.org<mailto:bioconductor@r-project.org> Subject: Re: [BioC] problem while loading affycoretools Hi Mayte, I have not seen this error in the past. Have you tried simply installing ff first? biocLite("ff") biocLite("affycoretools") Best, Jim On 9/15/2013 4:57 PM, Mayte Suarez-Farinas wrote: I updated to the most recent R version. After this brand new installation, I get the following error while loading library affycoretools: library(affycoretools) Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : there is no package called ‘ff’ Error: package or namespace load failed for ‘affycoretools’ After checking mailing list, I followed James advice (https://stat.ethz.ch/pipermail/bioconductor/2012-December/049895.html ) and updated all packages library(BiocInstaller) biocLite(character(0)) Additionally, I updated all R packages as well Still, the same problem arise. My R session info is bellow R version 3.0.1 (2013-05-16) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] KEGG.db_2.9.1 GO.db_2.9.0 RSQLite_0.11.4 DBI_0.2-7 [5] AnnotationDbi_1.22.6 affy_1.38.1 Biobase_2.20.1 BiocGenerics_0.6.0 [9] BiocInstaller_1.10.3 loaded via a namespace (and not attached): [1] affyio_1.28.0 annaffy_1.32.0 annotate_1.38.0 [4] AnnotationForge_1.2.2 biomaRt_2.16.0 Biostrings_2.28.0 [7] Category_2.26.0 gcrma_2.32.0 gdata_2.13.2 [10] genefilter_1.42.0 GenomicRanges_1.12.5 GOstats_2.26.0 [13] gplots_2.11.3 graph_1.38.3 grid_3.0.1 [16] GSEABase_1.22.0 gtools_3.0.0 IRanges_1.18.3 [19] lattice_0.20-23 limma_3.16.7 preprocessCore_1.22.0 [22] R2HTML_2.2.1 RBGL_1.36.2 RCurl_1.95-4.1 [25] splines_3.0.1 stats4_3.0.1 survival_2.37-4 [28] tools_3.0.1 XML_3.95-0.2 xtable_1.7-1 [31] zlibbioc_1.6.0 [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor@r-project.org<mailto:bioconductor@r-project.org> https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099 _______________________________________________ Bioconductor mailing list Bioconductor@r-project.org<mailto:bioconductor@r-project.org> https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]
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----- Original Message ----- > From: "Mayte Suarez-Farinas" <farinam at="" mail.rockefeller.edu=""> > To: "Dan Tenenbaum" <dtenenba at="" fhcrc.org=""> > Cc: "Mayte Suarez-Farinas" <farinam at="" mail.rockefeller.edu="">, "Steve Lianoglou" <lianoglou.steve at="" gene.com="">, > "<bioconductor at="" r-project.org="">" <bioconductor at="" r-project.org="">, "James W. MacDonald" <jmacdon at="" uw.edu=""> > Sent: Monday, September 16, 2013 10:50:08 AM > Subject: Re: [BioC] problem while loading affycoretools > > > > Hi James and Dan > > > I installed R from scratch and then run the following two lines: > > > biocLite() (success) > biocLite("affycoretools") > > which, after installing several packages gave me the "error: package > ?AnnotationDbi? could not be loaded" (see ALL outputs below)' > > > Dan, here is the output of biocinstallRepos. > librarybiocInstall() > biocinstallRepos() > > BioCsoft > " http://bioconductor.org/packages/2.12/bioc " > BioCann > " http://bioconductor.org/packages/2.12/data/annotation " > BioCexp > " http://bioconductor.org/packages/2.12/data/experiment " > BioCextra > " http://bioconductor.org/packages/2.12/extra " > CRAN > " http://cran.opensourceresources.org " > It appears that the CRAN mirror you are using is not working properly. Try picking a mirror from this list: http://cran.r-project.org/mirrors.html You can change mirrors with the chooseCRANmirror() function. Dan > > > > ALL OUTPUTS: > > > > > source(" http://bioconductor.org/biocLite.R ") > Installing package into ?/Users/mayte/Library/R/3.0/library? > (as ?lib? is unspecified) > trying URL ' > http://www.bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3. 0/BiocInstaller_1.10.3.tgz' > Content type 'application/x-gzip' length 46533 bytes (45 Kb) > opened URL > ================================================== > downloaded 45 Kb > > > > > The downloaded binary packages are in > /var/folders/r3/tlsb98mn33b3tl1wjd87hwch0000gn/T//RtmpARSLz6/downloa ded_packages > Bioconductor version 2.12 (BiocInstaller 1.10.3), ?biocLite for help > > biocLite() > BioC_mirror: http://bioconductor.org > Using Bioconductor version 2.12 (BiocInstaller 1.10.3), R version > 3.0.1. > Installing package(s) 'Biobase' 'IRanges' 'AnnotationDbi' > Warning: unable to access index for repository > http://cran.opensourceresources.org/bin/macosx/contrib/3.0 > Warning: dependencies ?DBI?, ?RSQLite? are not available > also installing the dependency ?BiocGenerics? > > > trying URL ' > http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/Bi ocGenerics_0.6.0.tgz' > Content type 'application/x-gzip' length 333465 bytes (325 Kb) > opened URL > ================================================== > downloaded 325 Kb > > > trying URL ' > http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/Bi obase_2.20.1.tgz' > Content type 'application/x-gzip' length 2354463 bytes (2.2 Mb) > opened URL > ================================================== > downloaded 2.2 Mb > > > trying URL ' > http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/IR anges_1.18.3.tgz' > Content type 'application/x-gzip' length 1978262 bytes (1.9 Mb) > opened URL > ================================================== > downloaded 1.9 Mb > > > trying URL ' > http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/An notationDbi_1.22.6.tgz' > Content type 'application/x-gzip' length 4066815 bytes (3.9 Mb) > opened URL > ================================================== > downloaded 3.9 Mb > > > > > The downloaded binary packages are in > /var/folders/r3/tlsb98mn33b3tl1wjd87hwch0000gn/T//RtmpARSLz6/downloa ded_packages > Warning: unable to access index for repository > http://cran.opensourceresources.org/bin/macosx/contrib/3.0 > > biocLite("affycoretools") > BioC_mirror: http://bioconductor.org > Using Bioconductor version 2.12 (BiocInstaller 1.10.3), R version > 3.0.1. > Installing package(s) 'affycoretools' > Warning: unable to access index for repository > http://cran.opensourceresources.org/bin/macosx/contrib/3.0 > Warning: dependencies ?xtable?, ?gplots?, ?R2HTML?, ?hwriter?, ?XML?, > ?RCurl?, ?DBI?, ?foreach?, ?R.utils?, ?RSQLite?, ?reshape2?, > ?gtable?, ?gridExtra?, ?scales?, ?Hmisc?, ?RColorBrewer?, > ?dichromat?, ?bitops? are not available > also installing the dependencies ?org.Hs.eg.db?, ?biovizBase?, > ?GenomicFeatures?, ?Rsamtools?, ?BSgenome?, ?VariantAnnotation?, > ?rtracklayer?, ?affyio?, ?preprocessCore?, ?zlibbioc?, ?Category?, > ?graph?, ?RBGL?, ?AnnotationForge?, ?Biostrings?, ?GenomicRanges?, > ?edgeR?, ?PFAM.db?, ?GSEABase?, ?ggbio?, ?affy?, ?GO.db?, ?KEGG.db?, > ?biomaRt?, ?limma?, ?GOstats?, ?annotate?, ?annaffy?, ?gcrma?, > ?oligoClasses?, ?ReportingTools? > > > trying URL ' > http://bioconductor.org/packages/2.12/data/annotation/bin/macosx/con trib/3.0/org.Hs.eg.db_2.9.0.tgz' > Content type 'application/x-gzip' length 53095874 bytes (50.6 Mb) > opened URL > ================================================== > downloaded 50.6 Mb > > > trying URL ' > http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/bi ovizBase_1.8.1.tgz' > Content type 'application/x-gzip' length 1136533 bytes (1.1 Mb) > opened URL > ================================================== > downloaded 1.1 Mb > > > trying URL ' > http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/Ge nomicFeatures_1.12.3.tgz' > Content type 'application/x-gzip' length 971035 bytes (948 Kb) > opened URL > ================================================== > downloaded 948 Kb > > > trying URL ' > http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/Rs amtools_1.12.4.tgz' > Content type 'application/x-gzip' length 3768247 bytes (3.6 Mb) > opened URL > ================================================== > downloaded 3.6 Mb > > > trying URL ' > http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/BS genome_1.28.0.tgz' > Content type 'application/x-gzip' length 746888 bytes (729 Kb) > opened URL > ================================================== > downloaded 729 Kb > > > trying URL ' > http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/Va riantAnnotation_1.6.7.tgz' > Content type 'application/x-gzip' length 1689203 bytes (1.6 Mb) > opened URL > ================================================== > downloaded 1.6 Mb > > > trying URL ' > http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/rt racklayer_1.20.4.tgz' > Content type 'application/x-gzip' length 1861493 bytes (1.8 Mb) > opened URL > ================================================== > downloaded 1.8 Mb > > > trying URL ' > http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/af fyio_1.28.0.tgz' > Content type 'application/x-gzip' length 94024 bytes (91 Kb) > opened URL > ================================================== > downloaded 91 Kb > > > trying URL ' > http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/pr eprocessCore_1.22.0.tgz' > Content type 'application/x-gzip' length 128027 bytes (125 Kb) > opened URL > ================================================== > downloaded 125 Kb > > > trying URL ' > http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/zl ibbioc_1.6.0.tgz' > Content type 'application/x-gzip' length 124184 bytes (121 Kb) > opened URL > ================================================== > downloaded 121 Kb > > > trying URL ' > http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/Ca tegory_2.26.0.tgz' > Content type 'application/x-gzip' length 933299 bytes (911 Kb) > opened URL > ================================================== > downloaded 911 Kb > > > trying URL ' > http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/gr aph_1.38.3.tgz' > Content type 'application/x-gzip' length 1327243 bytes (1.3 Mb) > opened URL > ================================================== > downloaded 1.3 Mb > > > trying URL ' > http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/RB GL_1.36.2.tgz' > Content type 'application/x-gzip' length 911905 bytes (890 Kb) > opened URL > ================================================== > downloaded 890 Kb > > > trying URL ' > http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/An notationForge_1.2.2.tgz' > Content type 'application/x-gzip' length 4149568 bytes (4.0 Mb) > opened URL > ================================================== > downloaded 4.0 Mb > > > trying URL ' > http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/Bi ostrings_2.28.0.tgz' > Content type 'application/x-gzip' length 2215378 bytes (2.1 Mb) > opened URL > ================================================== > downloaded 2.1 Mb > > > trying URL ' > http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/Ge nomicRanges_1.12.5.tgz' > Content type 'application/x-gzip' length 3293184 bytes (3.1 Mb) > opened URL > ================================================== > downloaded 3.1 Mb > > > trying URL ' > http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/ed geR_3.2.4.tgz' > Content type 'application/x-gzip' length 1470863 bytes (1.4 Mb) > opened URL > ================================================== > downloaded 1.4 Mb > > > trying URL ' > http://bioconductor.org/packages/2.12/data/annotation/bin/macosx/con trib/3.0/PFAM.db_2.9.0.tgz' > Content type 'application/x-gzip' length 2325707 bytes (2.2 Mb) > opened URL > ================================================== > downloaded 2.2 Mb > > > trying URL ' > http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/GS EABase_1.22.0.tgz' > Content type 'application/x-gzip' length 606089 bytes (591 Kb) > opened URL > ================================================== > downloaded 591 Kb > > > trying URL ' > http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/gg bio_1.8.5.tgz' > Content type 'application/x-gzip' length 2272353 bytes (2.2 Mb) > opened URL > ================================================== > downloaded 2.2 Mb > > > trying URL ' > http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/af fy_1.38.1.tgz' > Content type 'application/x-gzip' length 1458286 bytes (1.4 Mb) > opened URL > ================================================== > downloaded 1.4 Mb > > > trying URL ' > http://bioconductor.org/packages/2.12/data/annotation/bin/macosx/con trib/3.0/GO.db_2.9.0.tgz' > Content type 'application/x-gzip' length 25061115 bytes (23.9 Mb) > opened URL > ================================================== > downloaded 23.9 Mb > > > trying URL ' > http://bioconductor.org/packages/2.12/data/annotation/bin/macosx/con trib/3.0/KEGG.db_2.9.1.tgz' > Content type 'application/x-gzip' length 2032486 bytes (1.9 Mb) > opened URL > ================================================== > downloaded 1.9 Mb > > > trying URL ' > http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/bi omaRt_2.16.0.tgz' > Content type 'application/x-gzip' length 365452 bytes (356 Kb) > opened URL > ================================================== > downloaded 356 Kb > > > trying URL ' > http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/li mma_3.16.7.tgz' > Content type 'application/x-gzip' length 1568068 bytes (1.5 Mb) > opened URL > ================================================== > downloaded 1.5 Mb > > > trying URL ' > http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/GO stats_2.26.0.tgz' > Content type 'application/x-gzip' length 1725303 bytes (1.6 Mb) > opened URL > ================================================== > downloaded 1.6 Mb > > > trying URL ' > http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/an notate_1.38.0.tgz' > Content type 'application/x-gzip' length 1971349 bytes (1.9 Mb) > opened URL > ================================================== > downloaded 1.9 Mb > > > trying URL ' > http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/an naffy_1.32.0.tgz' > Content type 'application/x-gzip' length 380113 bytes (371 Kb) > opened URL > ================================================== > downloaded 371 Kb > > > trying URL ' > http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/gc rma_2.32.0.tgz' > Content type 'application/x-gzip' length 240351 bytes (234 Kb) > opened URL > ================================================== > downloaded 234 Kb > > > trying URL ' > http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/ol igoClasses_1.22.0.tgz' > Content type 'application/x-gzip' length 872393 bytes (851 Kb) > opened URL > ================================================== > downloaded 851 Kb > > > trying URL ' > http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/Re portingTools_2.0.1.tgz' > Content type 'application/x-gzip' length 2063622 bytes (2.0 Mb) > opened URL > ================================================== > downloaded 2.0 Mb > > > trying URL ' > http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/af fycoretools_1.32.1.tgz' > Content type 'application/x-gzip' length 7077475 bytes (6.7 Mb) > opened URL > ================================================== > downloaded 6.7 Mb > > > > > The downloaded binary packages are in > /var/folders/r3/tlsb98mn33b3tl1wjd87hwch0000gn/T//RtmpARSLz6/downloa ded_packages > Warning: unable to access index for repository > http://cran.opensourceresources.org/bin/macosx/contrib/3.0 > > > > > > > > > > > > Mayte Suarez-Farinas > Research Assistant Professor > Laboratory of Investigative Dermatology > Biostatistician, Center for Clinical and Translational Science > The Rockefeller University > 1230 York Ave, Box 178 > New York, NY 10065 > Phone: +1(212) 327-8213 > Fax: +1(212) 327-8232 > > > > > > On Sep 16, 2013, at 1:36 PM, Dan Tenenbaum wrote: > > > > > > ----- Original Message ----- > > > From: "Mayte Suarez-Farinas" < farinam at mail.rockefeller.edu > > > > To: "James W. MacDonald" < jmacdon at uw.edu > > > > Cc: "Steve Lianoglou" < lianoglou.steve at gene.com >, > bioconductor at r-project.org > > > Sent: Monday, September 16, 2013 9:14:00 AM > > > Subject: Re: [BioC] problem while loading affycoretools > > > > > > > > > Dear James, Henrik and Steve > > > > > > I tried biocLite("ff") and got the msg: package ?ff? is not available > > > (for R version 3.0.1) > > > (see below). Then I went ahead and download the tar package form > > > ( http://cran.r-project.org/web/packages/ff/index.html ) and used R > > > CMD install to install it. However, > > > while loading ff (library(ff)) it complains that the package bit was > > > missing, biocLite gave me > > > same error (package ?bit? is not available (for R version 3.0.1) ) > > > and I could not instll via CMD install > > > gave me the following error > > > > > > dhcp-129-85-243-253:Desktop mayte$ R CMD INSTALL bit_1.1-10.tar > > > * installing to library ?/Users/mayte/Library/R/3.0/library? > > > * installing *source* package ?bit? ... > > > ** package ?bit? successfully unpacked and MD5 sums checked > > > ** libs > > > sh: make: command not found > > > You downloaded the source tarball for bit (.tar.gz); you wanted the > Mac binary (.tgz). > > As for the problem with biocLite("bit") I'm not sure--are you behind > a proxy or firewall? > What is the output of the following: > > library(BiocInstaller) > biocinstallRepos() > > ? > > Dan > > > > > ERROR: compilation failed for package ?bit? > > > * removing ?/Users/mayte/Library/R/3.0/library/bit? > > > dhcp-129-85-243-253:Desktop mayte$ > > > > > > Please help out, life without affycoretools is very difficult ;-) > > > > > > > > > From: James W. MacDonald [ jmacdon at uw.edu ] > > > Sent: Monday, September 16, 2013 11:03 AM > > > To: Mayte Suarez-Farinas > > > Cc: bioconductor at r-project.org > > > Subject: Re: [BioC] problem while loading affycoretools > > > > > > Hi Mayte, > > > > > > I have not seen this error in the past. Have you tried simply > > > installing > > > ff first? > > > > > > biocLite("ff") > > > biocLite("affycoretools") > > > > > > Best, > > > > > > Jim > > > > > > > > > On 9/15/2013 4:57 PM, Mayte Suarez-Farinas wrote: > > > > > I updated to the most recent R version. After this brand new > > > > > installation, I get the following error while loading library > > > > > affycoretools: > > > > > > > > > > library(affycoretools) > > > > > Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), > > > > > versionCheck = vI[[j]]) : > > > > > there is no package called ?ff? > > > > > Error: package or namespace load failed for ?affycoretools? > > > > > > > > > > After checking mailing list, I followed James advice > > > > > ( > https://stat.ethz.ch/pipermail/bioconductor/2012-December/049895.html > ) > > > > > and updated all packages > > > > > library(BiocInstaller) > > > > > biocLite(character(0)) > > > > > > > > > > Additionally, I updated all R packages as well > > > > > > > > > > Still, the same problem arise. My R session info is bellow > > > > > > > > > > > > > > > R version 3.0.1 (2013-05-16) > > > > > Platform: x86_64-apple-darwin10.8.0 (64-bit) > > > > > > > > > > locale: > > > > > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > > > > > > > > > attached base packages: > > > > > [1] parallel stats graphics grDevices utils datasets > > > > > methods base > > > > > > > > > > other attached packages: > > > > > [1] KEGG.db_2.9.1 GO.db_2.9.0 RSQLite_0.11.4 > > > > > DBI_0.2-7 > > > > > [5] AnnotationDbi_1.22.6 affy_1.38.1 Biobase_2.20.1 > > > > > BiocGenerics_0.6.0 > > > > > [9] BiocInstaller_1.10.3 > > > > > > > > > > loaded via a namespace (and not attached): > > > > > [1] affyio_1.28.0 annaffy_1.32.0 annotate_1.38.0 > > > > > [4] AnnotationForge_1.2.2 biomaRt_2.16.0 Biostrings_2.28.0 > > > > > [7] Category_2.26.0 gcrma_2.32.0 gdata_2.13.2 > > > > > [10] genefilter_1.42.0 GenomicRanges_1.12.5 GOstats_2.26.0 > > > > > [13] gplots_2.11.3 graph_1.38.3 grid_3.0.1 > > > > > [16] GSEABase_1.22.0 gtools_3.0.0 IRanges_1.18.3 > > > > > [19] lattice_0.20-23 limma_3.16.7 > > > > > preprocessCore_1.22.0 > > > > > [22] R2HTML_2.2.1 RBGL_1.36.2 RCurl_1.95-4.1 > > > > > [25] splines_3.0.1 stats4_3.0.1 survival_2.37-4 > > > > > [28] tools_3.0.1 XML_3.95-0.2 xtable_1.7-1 > > > > > [31] zlibbioc_1.6.0 > > > > > > > > > > > > > > > [[alternative HTML version deleted]] > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > 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 > > > > > > -- > > > James W. MacDonald, M.S. > > > Biostatistician > > > University of Washington > > > Environmental and Occupational Health Sciences > > > 4225 Roosevelt Way NE, # 100 > > > Seattle WA 98105-6099 > > > > > > > > > _______________________________________________ > > > 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 > > > > >
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I tried all your advice: reinstall R, change mirror, still biocLite("affycoretools") does not install the package bit automatically and downloading the tgz from bit, the package bit does not compile Mayte Suarez-Farinas Research Assistant Professor Laboratory of Investigative Dermatology Biostatistician, Center for Clinical and Translational Science The Rockefeller University 1230 York Ave, Box 178 New York, NY 10065 Phone: +1(212) 327-8213 Fax: +1(212) 327-8232 On Sep 16, 2013, at 1:55 PM, Dan Tenenbaum wrote: ----- Original Message ----- From: "Mayte Suarez-Farinas" <farinam@mail.rockefeller.edu<mailto:farinam@mail.rockefeller.edu>> To: "Dan Tenenbaum" <dtenenba@fhcrc.org<mailto:dtenenba@fhcrc.org>> Cc: "Mayte Suarez-Farinas" <farinam@mail.rockefeller.edu<mailto:farinam@mail.rockefeller.edu>>, "Steve Lianoglou" <lianoglou.steve@gene.com<mailto:lianoglou.steve@gene.com>>, "<bioconductor@r-project.org<mailto:bioconductor@r-project.org>>" <bioconductor@r-project.org<mailto:bioconductor@r-project.org>>, "James W. MacDonald" <jmacdon@uw.edu<mailto:jmacdon@uw.edu>> Sent: Monday, September 16, 2013 10:50:08 AM Subject: Re: [BioC] problem while loading affycoretools Hi James and Dan I installed R from scratch and then run the following two lines: biocLite() (success) biocLite("affycoretools") which, after installing several packages gave me the "error: package ‘AnnotationDbi’ could not be loaded" (see ALL outputs below)' Dan, here is the output of biocinstallRepos. librarybiocInstall() biocinstallRepos() BioCsoft " http://bioconductor.org/packages/2.12/bioc " BioCann " http://bioconductor.org/packages/2.12/data/annotation " BioCexp " http://bioconductor.org/packages/2.12/data/experiment " BioCextra " http://bioconductor.org/packages/2.12/extra " CRAN " http://cran.opensourceresources.org " It appears that the CRAN mirror you are using is not working properly. Try picking a mirror from this list: http://cran.r-project.org/mirrors.html You can change mirrors with the chooseCRANmirror() function. Dan ALL OUTPUTS: source(" http://bioconductor.org/biocLite.R ") Installing package into ‘/Users/mayte/Library/R/3.0/library’ (as ‘lib’ is unspecified) trying URL ' http://www.bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/ BiocInstaller_1.10.3.tgz' Content type 'application/x-gzip' length 46533 bytes (45 Kb) opened URL ================================================== downloaded 45 Kb The downloaded binary packages are in /var/folders/r3/tlsb98mn33b3tl1wjd87hwch0000gn/T//RtmpARSLz6/downloade d_packages Bioconductor version 2.12 (BiocInstaller 1.10.3), ?biocLite for help biocLite() BioC_mirror: http://bioconductor.org Using Bioconductor version 2.12 (BiocInstaller 1.10.3), R version 3.0.1. Installing package(s) 'Biobase' 'IRanges' 'AnnotationDbi' Warning: unable to access index for repository http://cran.opensourceresources.org/bin/macosx/contrib/3.0 Warning: dependencies ‘DBI’, ‘RSQLite’ are not available also installing the dependency ‘BiocGenerics’ trying URL ' http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/Bioc Generics_0.6.0.tgz' Content type 'application/x-gzip' length 333465 bytes (325 Kb) opened URL ================================================== downloaded 325 Kb trying URL ' http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/Biob ase_2.20.1.tgz' Content type 'application/x-gzip' length 2354463 bytes (2.2 Mb) opened URL ================================================== downloaded 2.2 Mb trying URL ' http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/IRan ges_1.18.3.tgz' Content type 'application/x-gzip' length 1978262 bytes (1.9 Mb) opened URL ================================================== downloaded 1.9 Mb trying URL ' http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/Anno tationDbi_1.22.6.tgz' Content type 'application/x-gzip' length 4066815 bytes (3.9 Mb) opened URL ================================================== downloaded 3.9 Mb The downloaded binary packages are in /var/folders/r3/tlsb98mn33b3tl1wjd87hwch0000gn/T//RtmpARSLz6/downloade d_packages Warning: unable to access index for repository http://cran.opensourceresources.org/bin/macosx/contrib/3.0 biocLite("affycoretools") BioC_mirror: http://bioconductor.org Using Bioconductor version 2.12 (BiocInstaller 1.10.3), R version 3.0.1. Installing package(s) 'affycoretools' Warning: unable to access index for repository http://cran.opensourceresources.org/bin/macosx/contrib/3.0 Warning: dependencies ‘xtable’, ‘gplots’, ‘R2HTML’, ‘hwriter’, ‘XML’, ‘RCurl’, ‘DBI’, ‘foreach’, ‘R.utils’, ‘RSQLite’, ‘reshape2’, ‘gtable’, ‘gridExtra’, ‘scales’, ‘Hmisc’, ‘RColorBrewer’, ‘dichromat’, ‘bitops’ are not available also installing the dependencies ‘org.Hs.eg.db’, ‘biovizBase’, ‘GenomicFeatures’, ‘Rsamtools’, ‘BSgenome’, ‘VariantAnnotation’, ‘rtracklayer’, ‘affyio’, ‘preprocessCore’, ‘zlibbioc’, ‘Category’, ‘graph’, ‘RBGL’, ‘AnnotationForge’, ‘Biostrings’, ‘GenomicRanges’, ‘edgeR’, ‘PFAM.db’, ‘GSEABase’, ‘ggbio’, ‘affy’, ‘GO.db’, ‘KEGG.db’, ‘biomaRt’, ‘limma’, ‘GOstats’, ‘annotate’, ‘annaffy’, ‘gcrma’, ‘oligoClasses’, ‘ReportingTools’ trying URL ' http://bioconductor.org/packages/2.12/data/annotation/bin/macosx/contr ib/3.0/org.Hs.eg.db_2.9.0.tgz' Content type 'application/x-gzip' length 53095874 bytes (50.6 Mb) opened URL ================================================== downloaded 50.6 Mb trying URL ' http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/biov izBase_1.8.1.tgz' Content type 'application/x-gzip' length 1136533 bytes (1.1 Mb) opened URL ================================================== downloaded 1.1 Mb trying URL ' http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/Geno micFeatures_1.12.3.tgz' Content type 'application/x-gzip' length 971035 bytes (948 Kb) opened URL ================================================== downloaded 948 Kb trying URL ' http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/Rsam tools_1.12.4.tgz' Content type 'application/x-gzip' length 3768247 bytes (3.6 Mb) opened URL ================================================== downloaded 3.6 Mb trying URL ' http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/BSge nome_1.28.0.tgz' Content type 'application/x-gzip' length 746888 bytes (729 Kb) opened URL ================================================== downloaded 729 Kb trying URL ' http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/Vari antAnnotation_1.6.7.tgz' Content type 'application/x-gzip' length 1689203 bytes (1.6 Mb) opened URL ================================================== downloaded 1.6 Mb trying URL ' http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/rtra cklayer_1.20.4.tgz' Content type 'application/x-gzip' length 1861493 bytes (1.8 Mb) opened URL ================================================== downloaded 1.8 Mb trying URL ' http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/affy io_1.28.0.tgz' Content type 'application/x-gzip' length 94024 bytes (91 Kb) opened URL ================================================== downloaded 91 Kb trying URL ' http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/prep rocessCore_1.22.0.tgz' Content type 'application/x-gzip' length 128027 bytes (125 Kb) opened URL ================================================== downloaded 125 Kb trying URL ' http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/zlib bioc_1.6.0.tgz' Content type 'application/x-gzip' length 124184 bytes (121 Kb) opened URL ================================================== downloaded 121 Kb trying URL ' http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/Cate gory_2.26.0.tgz' Content type 'application/x-gzip' length 933299 bytes (911 Kb) opened URL ================================================== downloaded 911 Kb trying URL ' http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/grap h_1.38.3.tgz' Content type 'application/x-gzip' length 1327243 bytes (1.3 Mb) opened URL ================================================== downloaded 1.3 Mb trying URL ' http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/RBGL _1.36.2.tgz' Content type 'application/x-gzip' length 911905 bytes (890 Kb) opened URL ================================================== downloaded 890 Kb trying URL ' http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/Anno tationForge_1.2.2.tgz' Content type 'application/x-gzip' length 4149568 bytes (4.0 Mb) opened URL ================================================== downloaded 4.0 Mb trying URL ' http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/Bios trings_2.28.0.tgz' Content type 'application/x-gzip' length 2215378 bytes (2.1 Mb) opened URL ================================================== downloaded 2.1 Mb trying URL ' http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/Geno micRanges_1.12.5.tgz' Content type 'application/x-gzip' length 3293184 bytes (3.1 Mb) opened URL ================================================== downloaded 3.1 Mb trying URL ' http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/edge R_3.2.4.tgz' Content type 'application/x-gzip' length 1470863 bytes (1.4 Mb) opened URL ================================================== downloaded 1.4 Mb trying URL ' http://bioconductor.org/packages/2.12/data/annotation/bin/macosx/contr ib/3.0/PFAM.db_2.9.0.tgz' Content type 'application/x-gzip' length 2325707 bytes (2.2 Mb) opened URL ================================================== downloaded 2.2 Mb trying URL ' http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/GSEA Base_1.22.0.tgz' Content type 'application/x-gzip' length 606089 bytes (591 Kb) opened URL ================================================== downloaded 591 Kb trying URL ' http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/ggbi o_1.8.5.tgz' Content type 'application/x-gzip' length 2272353 bytes (2.2 Mb) opened URL ================================================== downloaded 2.2 Mb trying URL ' http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/affy _1.38.1.tgz' Content type 'application/x-gzip' length 1458286 bytes (1.4 Mb) opened URL ================================================== downloaded 1.4 Mb trying URL ' http://bioconductor.org/packages/2.12/data/annotation/bin/macosx/contr ib/3.0/GO.db_2.9.0.tgz' Content type 'application/x-gzip' length 25061115 bytes (23.9 Mb) opened URL ================================================== downloaded 23.9 Mb trying URL ' http://bioconductor.org/packages/2.12/data/annotation/bin/macosx/contr ib/3.0/KEGG.db_2.9.1.tgz' Content type 'application/x-gzip' length 2032486 bytes (1.9 Mb) opened URL ================================================== downloaded 1.9 Mb trying URL ' http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/biom aRt_2.16.0.tgz' Content type 'application/x-gzip' length 365452 bytes (356 Kb) opened URL ================================================== downloaded 356 Kb trying URL ' http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/limm a_3.16.7.tgz' Content type 'application/x-gzip' length 1568068 bytes (1.5 Mb) opened URL ================================================== downloaded 1.5 Mb trying URL ' http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/GOst ats_2.26.0.tgz' Content type 'application/x-gzip' length 1725303 bytes (1.6 Mb) opened URL ================================================== downloaded 1.6 Mb trying URL ' http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/anno tate_1.38.0.tgz' Content type 'application/x-gzip' length 1971349 bytes (1.9 Mb) opened URL ================================================== downloaded 1.9 Mb trying URL ' http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/anna ffy_1.32.0.tgz' Content type 'application/x-gzip' length 380113 bytes (371 Kb) opened URL ================================================== downloaded 371 Kb trying URL ' http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/gcrm a_2.32.0.tgz' Content type 'application/x-gzip' length 240351 bytes (234 Kb) opened URL ================================================== downloaded 234 Kb trying URL ' http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/olig oClasses_1.22.0.tgz' Content type 'application/x-gzip' length 872393 bytes (851 Kb) opened URL ================================================== downloaded 851 Kb trying URL ' http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/Repo rtingTools_2.0.1.tgz' Content type 'application/x-gzip' length 2063622 bytes (2.0 Mb) opened URL ================================================== downloaded 2.0 Mb trying URL ' http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/affy coretools_1.32.1.tgz' Content type 'application/x-gzip' length 7077475 bytes (6.7 Mb) opened URL ================================================== downloaded 6.7 Mb The downloaded binary packages are in /var/folders/r3/tlsb98mn33b3tl1wjd87hwch0000gn/T//RtmpARSLz6/downloade d_packages Warning: unable to access index for repository http://cran.opensourceresources.org/bin/macosx/contrib/3.0 Mayte Suarez-Farinas Research Assistant Professor Laboratory of Investigative Dermatology Biostatistician, Center for Clinical and Translational Science The Rockefeller University 1230 York Ave, Box 178 New York, NY 10065 Phone: +1(212) 327-8213 Fax: +1(212) 327-8232 On Sep 16, 2013, at 1:36 PM, Dan Tenenbaum wrote: ----- Original Message ----- From: "Mayte Suarez-Farinas" < farinam@mail.rockefeller.edu > To: "James W. MacDonald" < jmacdon@uw.edu > Cc: "Steve Lianoglou" < lianoglou.steve@gene.com >, bioconductor@r-project.org Sent: Monday, September 16, 2013 9:14:00 AM Subject: Re: [BioC] problem while loading affycoretools Dear James, Henrik and Steve I tried biocLite("ff") and got the msg: package ‘ff’ is not available (for R version 3.0.1) (see below). Then I went ahead and download the tar package form ( http://cran.r-project.org/web/packages/ff/index.html ) and used R CMD install to install it. However, while loading ff (library(ff)) it complains that the package bit was missing, biocLite gave me same error (package ‘bit’ is not available (for R version 3.0.1) ) and I could not instll via CMD install gave me the following error dhcp-129-85-243-253:Desktop mayte$ R CMD INSTALL bit_1.1-10.tar * installing to library ‘/Users/mayte/Library/R/3.0/library’ * installing *source* package ‘bit’ ... ** package ‘bit’ successfully unpacked and MD5 sums checked ** libs sh: make: command not found You downloaded the source tarball for bit (.tar.gz); you wanted the Mac binary (.tgz). As for the problem with biocLite("bit") I'm not sure--are you behind a proxy or firewall? What is the output of the following: library(BiocInstaller) biocinstallRepos() ? Dan ERROR: compilation failed for package ‘bit’ * removing ‘/Users/mayte/Library/R/3.0/library/bit’ dhcp-129-85-243-253:Desktop mayte$ Please help out, life without affycoretools is very difficult ;-) From: James W. MacDonald [ jmacdon@uw.edu ] Sent: Monday, September 16, 2013 11:03 AM To: Mayte Suarez-Farinas Cc: bioconductor@r-project.org Subject: Re: [BioC] problem while loading affycoretools Hi Mayte, I have not seen this error in the past. Have you tried simply installing ff first? biocLite("ff") biocLite("affycoretools") Best, Jim On 9/15/2013 4:57 PM, Mayte Suarez-Farinas wrote: I updated to the most recent R version. After this brand new installation, I get the following error while loading library affycoretools: library(affycoretools) Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : there is no package called ‘ff’ Error: package or namespace load failed for ‘affycoretools’ After checking mailing list, I followed James advice ( https://stat.ethz.ch/pipermail/bioconductor/2012-December/049895.html ) and updated all packages library(BiocInstaller) biocLite(character(0)) Additionally, I updated all R packages as well Still, the same problem arise. My R session info is bellow R version 3.0.1 (2013-05-16) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] KEGG.db_2.9.1 GO.db_2.9.0 RSQLite_0.11.4 DBI_0.2-7 [5] AnnotationDbi_1.22.6 affy_1.38.1 Biobase_2.20.1 BiocGenerics_0.6.0 [9] BiocInstaller_1.10.3 loaded via a namespace (and not attached): [1] affyio_1.28.0 annaffy_1.32.0 annotate_1.38.0 [4] AnnotationForge_1.2.2 biomaRt_2.16.0 Biostrings_2.28.0 [7] Category_2.26.0 gcrma_2.32.0 gdata_2.13.2 [10] genefilter_1.42.0 GenomicRanges_1.12.5 GOstats_2.26.0 [13] gplots_2.11.3 graph_1.38.3 grid_3.0.1 [16] GSEABase_1.22.0 gtools_3.0.0 IRanges_1.18.3 [19] lattice_0.20-23 limma_3.16.7 preprocessCore_1.22.0 [22] R2HTML_2.2.1 RBGL_1.36.2 RCurl_1.95-4.1 [25] splines_3.0.1 stats4_3.0.1 survival_2.37-4 [28] tools_3.0.1 XML_3.95-0.2 xtable_1.7-1 [31] zlibbioc_1.6.0 [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor@r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099 _______________________________________________ Bioconductor mailing list Bioconductor@r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]
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----- Original Message ----- > From: "Mayte Suarez-Farinas" <farinam at="" mail.rockefeller.edu=""> > To: "Dan Tenenbaum" <dtenenba at="" fhcrc.org=""> > Cc: "Mayte Suarez-Farinas" <farinam at="" mail.rockefeller.edu="">, "Steve Lianoglou" <lianoglou.steve at="" gene.com="">, > "bioconductor" <bioconductor at="" r-project.org="">, "James W. MacDonald" <jmacdon at="" uw.edu=""> > Sent: Monday, September 16, 2013 11:50:04 AM > Subject: Re: [BioC] problem while loading affycoretools > > I tried all your advice: reinstall R, change mirror, still > biocLite("affycoretools") does not install the package bit > automatically > and downloading the tgz from bit, the package bit does not compile > > The call to chooseCRANmirror() is not persistent; you need to change mirrors every time you start R, or do it in your ~/.Rprofile so it happens automatically every time you start R. I don't recommend downloading files from the web and trying to install them with R CMD INSTALL. I would suggest trying to get biocLite() working first. But for the record, a .tgz is a binary package which should already be compiled (if it contains compiled code) so I'd need to see the exact error message you are getting. Dan > > > > > Mayte Suarez-Farinas > Research Assistant Professor > Laboratory of Investigative Dermatology > Biostatistician, Center for Clinical and Translational Science > The Rockefeller University > 1230 York Ave, Box 178 > New York, NY 10065 > Phone: +1(212) 327-8213 > Fax: +1(212) 327-8232 > > > > > > On Sep 16, 2013, at 1:55 PM, Dan Tenenbaum wrote: > > > > > > ----- Original Message ----- > > > From: "Mayte Suarez-Farinas" < farinam at mail.rockefeller.edu > > > > To: "Dan Tenenbaum" < dtenenba at fhcrc.org > > > > Cc: "Mayte Suarez-Farinas" < farinam at mail.rockefeller.edu >, "Steve > Lianoglou" < lianoglou.steve at gene.com >, > > > "< bioconductor at r-project.org >" < bioconductor at r-project.org >, > "James W. MacDonald" < jmacdon at uw.edu > > > > Sent: Monday, September 16, 2013 10:50:08 AM > > > Subject: Re: [BioC] problem while loading affycoretools > > > > > > > > > > > > Hi James and Dan > > > > > > > > > I installed R from scratch and then run the following two lines: > > > > > > > > > biocLite() (success) > > > biocLite("affycoretools") > > > > > > which, after installing several packages gave me the "error: package > > > ?AnnotationDbi? could not be loaded" (see ALL outputs below)' > > > > > > > > > Dan, here is the output of biocinstallRepos. > > > librarybiocInstall() > > > biocinstallRepos() > > > > > > BioCsoft > > > " http://bioconductor.org/packages/2.12/bioc " > > > BioCann > > > " http://bioconductor.org/packages/2.12/data/annotation " > > > BioCexp > > > " http://bioconductor.org/packages/2.12/data/experiment " > > > BioCextra > > > " http://bioconductor.org/packages/2.12/extra " > > > CRAN > > > " http://cran.opensourceresources.org " > > > > > It appears that the CRAN mirror you are using is not working > properly. > Try picking a mirror from this list: > http://cran.r-project.org/mirrors.html > > You can change mirrors with the chooseCRANmirror() function. > Dan > > > > > > > > > > > > > > > > ALL OUTPUTS: > > > > > > > > > > > > > > > source(" http://bioconductor.org/biocLite.R ") > > > Installing package into ?/Users/mayte/Library/R/3.0/library? > > > (as ?lib? is unspecified) > > > trying URL ' > > > http://www.bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3. 0/BiocInstaller_1.10.3.tgz' > > > Content type 'application/x-gzip' length 46533 bytes (45 Kb) > > > opened URL > > > ================================================== > > > downloaded 45 Kb > > > > > > > > > > > > > > > The downloaded binary packages are in > > > /var/folders/r3/tlsb98mn33b3tl1wjd87hwch0000gn/T//RtmpARSLz6/downloa ded_packages > > > Bioconductor version 2.12 (BiocInstaller 1.10.3), ?biocLite for help > > > > > biocLite() > > > BioC_mirror: http://bioconductor.org > > > Using Bioconductor version 2.12 (BiocInstaller 1.10.3), R version > > > 3.0.1. > > > Installing package(s) 'Biobase' 'IRanges' 'AnnotationDbi' > > > Warning: unable to access index for repository > > > http://cran.opensourceresources.org/bin/macosx/contrib/3.0 > > > Warning: dependencies ?DBI?, ?RSQLite? are not available > > > also installing the dependency ?BiocGenerics? > > > > > > > > > trying URL ' > > > http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/Bi ocGenerics_0.6.0.tgz' > > > Content type 'application/x-gzip' length 333465 bytes (325 Kb) > > > opened URL > > > ================================================== > > > downloaded 325 Kb > > > > > > > > > trying URL ' > > > http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/Bi obase_2.20.1.tgz' > > > Content type 'application/x-gzip' length 2354463 bytes (2.2 Mb) > > > opened URL > > > ================================================== > > > downloaded 2.2 Mb > > > > > > > > > trying URL ' > > > http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/IR anges_1.18.3.tgz' > > > Content type 'application/x-gzip' length 1978262 bytes (1.9 Mb) > > > opened URL > > > ================================================== > > > downloaded 1.9 Mb > > > > > > > > > trying URL ' > > > http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/An notationDbi_1.22.6.tgz' > > > Content type 'application/x-gzip' length 4066815 bytes (3.9 Mb) > > > opened URL > > > ================================================== > > > downloaded 3.9 Mb > > > > > > > > > > > > > > > The downloaded binary packages are in > > > /var/folders/r3/tlsb98mn33b3tl1wjd87hwch0000gn/T//RtmpARSLz6/downloa ded_packages > > > Warning: unable to access index for repository > > > http://cran.opensourceresources.org/bin/macosx/contrib/3.0 > > > > > biocLite("affycoretools") > > > BioC_mirror: http://bioconductor.org > > > Using Bioconductor version 2.12 (BiocInstaller 1.10.3), R version > > > 3.0.1. > > > Installing package(s) 'affycoretools' > > > Warning: unable to access index for repository > > > http://cran.opensourceresources.org/bin/macosx/contrib/3.0 > > > Warning: dependencies ?xtable?, ?gplots?, ?R2HTML?, ?hwriter?, ?XML?, > > > ?RCurl?, ?DBI?, ?foreach?, ?R.utils?, ?RSQLite?, ?reshape2?, > > > ?gtable?, ?gridExtra?, ?scales?, ?Hmisc?, ?RColorBrewer?, > > > ?dichromat?, ?bitops? are not available > > > also installing the dependencies ?org.Hs.eg.db?, ?biovizBase?, > > > ?GenomicFeatures?, ?Rsamtools?, ?BSgenome?, ?VariantAnnotation?, > > > ?rtracklayer?, ?affyio?, ?preprocessCore?, ?zlibbioc?, ?Category?, > > > ?graph?, ?RBGL?, ?AnnotationForge?, ?Biostrings?, ?GenomicRanges?, > > > ?edgeR?, ?PFAM.db?, ?GSEABase?, ?ggbio?, ?affy?, ?GO.db?, ?KEGG.db?, > > > ?biomaRt?, ?limma?, ?GOstats?, ?annotate?, ?annaffy?, ?gcrma?, > > > ?oligoClasses?, ?ReportingTools? > > > > > > > > > trying URL ' > > > http://bioconductor.org/packages/2.12/data/annotation/bin/macosx/con trib/3.0/org.Hs.eg.db_2.9.0.tgz' > > > Content type 'application/x-gzip' length 53095874 bytes (50.6 Mb) > > > opened URL > > > ================================================== > > > downloaded 50.6 Mb > > > > > > > > > trying URL ' > > > http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/bi ovizBase_1.8.1.tgz' > > > Content type 'application/x-gzip' length 1136533 bytes (1.1 Mb) > > > opened URL > > > ================================================== > > > downloaded 1.1 Mb > > > > > > > > > trying URL ' > > > http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/Ge nomicFeatures_1.12.3.tgz' > > > Content type 'application/x-gzip' length 971035 bytes (948 Kb) > > > opened URL > > > ================================================== > > > downloaded 948 Kb > > > > > > > > > trying URL ' > > > http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/Rs amtools_1.12.4.tgz' > > > Content type 'application/x-gzip' length 3768247 bytes (3.6 Mb) > > > opened URL > > > ================================================== > > > downloaded 3.6 Mb > > > > > > > > > trying URL ' > > > http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/BS genome_1.28.0.tgz' > > > Content type 'application/x-gzip' length 746888 bytes (729 Kb) > > > opened URL > > > ================================================== > > > downloaded 729 Kb > > > > > > > > > trying URL ' > > > http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/Va riantAnnotation_1.6.7.tgz' > > > Content type 'application/x-gzip' length 1689203 bytes (1.6 Mb) > > > opened URL > > > ================================================== > > > downloaded 1.6 Mb > > > > > > > > > trying URL ' > > > http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/rt racklayer_1.20.4.tgz' > > > Content type 'application/x-gzip' length 1861493 bytes (1.8 Mb) > > > opened URL > > > ================================================== > > > downloaded 1.8 Mb > > > > > > > > > trying URL ' > > > http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/af fyio_1.28.0.tgz' > > > Content type 'application/x-gzip' length 94024 bytes (91 Kb) > > > opened URL > > > ================================================== > > > downloaded 91 Kb > > > > > > > > > trying URL ' > > > http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/pr eprocessCore_1.22.0.tgz' > > > Content type 'application/x-gzip' length 128027 bytes (125 Kb) > > > opened URL > > > ================================================== > > > downloaded 125 Kb > > > > > > > > > trying URL ' > > > http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/zl ibbioc_1.6.0.tgz' > > > Content type 'application/x-gzip' length 124184 bytes (121 Kb) > > > opened URL > > > ================================================== > > > downloaded 121 Kb > > > > > > > > > trying URL ' > > > http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/Ca tegory_2.26.0.tgz' > > > Content type 'application/x-gzip' length 933299 bytes (911 Kb) > > > opened URL > > > ================================================== > > > downloaded 911 Kb > > > > > > > > > trying URL ' > > > http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/gr aph_1.38.3.tgz' > > > Content type 'application/x-gzip' length 1327243 bytes (1.3 Mb) > > > opened URL > > > ================================================== > > > downloaded 1.3 Mb > > > > > > > > > trying URL ' > > > http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/RB GL_1.36.2.tgz' > > > Content type 'application/x-gzip' length 911905 bytes (890 Kb) > > > opened URL > > > ================================================== > > > downloaded 890 Kb > > > > > > > > > trying URL ' > > > http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/An notationForge_1.2.2.tgz' > > > Content type 'application/x-gzip' length 4149568 bytes (4.0 Mb) > > > opened URL > > > ================================================== > > > downloaded 4.0 Mb > > > > > > > > > trying URL ' > > > http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/Bi ostrings_2.28.0.tgz' > > > Content type 'application/x-gzip' length 2215378 bytes (2.1 Mb) > > > opened URL > > > ================================================== > > > downloaded 2.1 Mb > > > > > > > > > trying URL ' > > > http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/Ge nomicRanges_1.12.5.tgz' > > > Content type 'application/x-gzip' length 3293184 bytes (3.1 Mb) > > > opened URL > > > ================================================== > > > downloaded 3.1 Mb > > > > > > > > > trying URL ' > > > http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/ed geR_3.2.4.tgz' > > > Content type 'application/x-gzip' length 1470863 bytes (1.4 Mb) > > > opened URL > > > ================================================== > > > downloaded 1.4 Mb > > > > > > > > > trying URL ' > > > http://bioconductor.org/packages/2.12/data/annotation/bin/macosx/con trib/3.0/PFAM.db_2.9.0.tgz' > > > Content type 'application/x-gzip' length 2325707 bytes (2.2 Mb) > > > opened URL > > > ================================================== > > > downloaded 2.2 Mb > > > > > > > > > trying URL ' > > > http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/GS EABase_1.22.0.tgz' > > > Content type 'application/x-gzip' length 606089 bytes (591 Kb) > > > opened URL > > > ================================================== > > > downloaded 591 Kb > > > > > > > > > trying URL ' > > > http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/gg bio_1.8.5.tgz' > > > Content type 'application/x-gzip' length 2272353 bytes (2.2 Mb) > > > opened URL > > > ================================================== > > > downloaded 2.2 Mb > > > > > > > > > trying URL ' > > > http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/af fy_1.38.1.tgz' > > > Content type 'application/x-gzip' length 1458286 bytes (1.4 Mb) > > > opened URL > > > ================================================== > > > downloaded 1.4 Mb > > > > > > > > > trying URL ' > > > http://bioconductor.org/packages/2.12/data/annotation/bin/macosx/con trib/3.0/GO.db_2.9.0.tgz' > > > Content type 'application/x-gzip' length 25061115 bytes (23.9 Mb) > > > opened URL > > > ================================================== > > > downloaded 23.9 Mb > > > > > > > > > trying URL ' > > > http://bioconductor.org/packages/2.12/data/annotation/bin/macosx/con trib/3.0/KEGG.db_2.9.1.tgz' > > > Content type 'application/x-gzip' length 2032486 bytes (1.9 Mb) > > > opened URL > > > ================================================== > > > downloaded 1.9 Mb > > > > > > > > > trying URL ' > > > http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/bi omaRt_2.16.0.tgz' > > > Content type 'application/x-gzip' length 365452 bytes (356 Kb) > > > opened URL > > > ================================================== > > > downloaded 356 Kb > > > > > > > > > trying URL ' > > > http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/li mma_3.16.7.tgz' > > > Content type 'application/x-gzip' length 1568068 bytes (1.5 Mb) > > > opened URL > > > ================================================== > > > downloaded 1.5 Mb > > > > > > > > > trying URL ' > > > http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/GO stats_2.26.0.tgz' > > > Content type 'application/x-gzip' length 1725303 bytes (1.6 Mb) > > > opened URL > > > ================================================== > > > downloaded 1.6 Mb > > > > > > > > > trying URL ' > > > http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/an notate_1.38.0.tgz' > > > Content type 'application/x-gzip' length 1971349 bytes (1.9 Mb) > > > opened URL > > > ================================================== > > > downloaded 1.9 Mb > > > > > > > > > trying URL ' > > > http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/an naffy_1.32.0.tgz' > > > Content type 'application/x-gzip' length 380113 bytes (371 Kb) > > > opened URL > > > ================================================== > > > downloaded 371 Kb > > > > > > > > > trying URL ' > > > http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/gc rma_2.32.0.tgz' > > > Content type 'application/x-gzip' length 240351 bytes (234 Kb) > > > opened URL > > > ================================================== > > > downloaded 234 Kb > > > > > > > > > trying URL ' > > > http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/ol igoClasses_1.22.0.tgz' > > > Content type 'application/x-gzip' length 872393 bytes (851 Kb) > > > opened URL > > > ================================================== > > > downloaded 851 Kb > > > > > > > > > trying URL ' > > > http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/Re portingTools_2.0.1.tgz' > > > Content type 'application/x-gzip' length 2063622 bytes (2.0 Mb) > > > opened URL > > > ================================================== > > > downloaded 2.0 Mb > > > > > > > > > trying URL ' > > > http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/af fycoretools_1.32.1.tgz' > > > Content type 'application/x-gzip' length 7077475 bytes (6.7 Mb) > > > opened URL > > > ================================================== > > > downloaded 6.7 Mb > > > > > > > > > > > > > > > The downloaded binary packages are in > > > /var/folders/r3/tlsb98mn33b3tl1wjd87hwch0000gn/T//RtmpARSLz6/downloa ded_packages > > > Warning: unable to access index for repository > > > http://cran.opensourceresources.org/bin/macosx/contrib/3.0 > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > Mayte Suarez-Farinas > > > Research Assistant Professor > > > Laboratory of Investigative Dermatology > > > Biostatistician, Center for Clinical and Translational Science > > > The Rockefeller University > > > 1230 York Ave, Box 178 > > > New York, NY 10065 > > > Phone: +1(212) 327-8213 > > > Fax: +1(212) 327-8232 > > > > > > > > > > > > > > > > > > On Sep 16, 2013, at 1:36 PM, Dan Tenenbaum wrote: > > > > > > > > > > > > > > > > > > ----- Original Message ----- > > > > > > > > > From: "Mayte Suarez-Farinas" < farinam at mail.rockefeller.edu > > > > > > > > > > To: "James W. MacDonald" < jmacdon at uw.edu > > > > > > > > > > Cc: "Steve Lianoglou" < lianoglou.steve at gene.com >, > > > bioconductor at r-project.org > > > > > > > > > Sent: Monday, September 16, 2013 9:14:00 AM > > > > > > > > > Subject: Re: [BioC] problem while loading affycoretools > > > > > > > > > > > > > > > > > > > > > > > > > > > Dear James, Henrik and Steve > > > > > > > > > > > > > > > > > > I tried biocLite("ff") and got the msg: package ?ff? is not available > > > > > > > > > (for R version 3.0.1) > > > > > > > > > (see below). Then I went ahead and download the tar package form > > > > > > > > > ( http://cran.r-project.org/web/packages/ff/index.html ) and used R > > > > > > > > > CMD install to install it. However, > > > > > > > > > while loading ff (library(ff)) it complains that the package bit was > > > > > > > > > missing, biocLite gave me > > > > > > > > > same error (package ?bit? is not available (for R version 3.0.1) ) > > > > > > > > > and I could not instll via CMD install > > > > > > > > > gave me the following error > > > > > > > > > > > > > > > > > > dhcp-129-85-243-253:Desktop mayte$ R CMD INSTALL bit_1.1-10.tar > > > > > > > > > * installing to library ?/Users/mayte/Library/R/3.0/library? > > > > > > > > > * installing *source* package ?bit? ... > > > > > > > > > ** package ?bit? successfully unpacked and MD5 sums checked > > > > > > > > > ** libs > > > > > > > > > sh: make: command not found > > > > > > > > > You downloaded the source tarball for bit (.tar.gz); you wanted the > > > Mac binary (.tgz). > > > > > > As for the problem with biocLite("bit") I'm not sure--are you behind > > > a proxy or firewall? > > > What is the output of the following: > > > > > > library(BiocInstaller) > > > biocinstallRepos() > > > > > > ? > > > > > > Dan > > > > > > > > > > > > > > > ERROR: compilation failed for package ?bit? > > > > > > > > > * removing ?/Users/mayte/Library/R/3.0/library/bit? > > > > > > > > > dhcp-129-85-243-253:Desktop mayte$ > > > > > > > > > > > > > > > > > > Please help out, life without affycoretools is very difficult ;-) > > > > > > > > > > > > > > > > > > > > > > > > > > > From: James W. MacDonald [ jmacdon at uw.edu ] > > > > > > > > > Sent: Monday, September 16, 2013 11:03 AM > > > > > > > > > To: Mayte Suarez-Farinas > > > > > > > > > Cc: bioconductor at r-project.org > > > > > > > > > Subject: Re: [BioC] problem while loading affycoretools > > > > > > > > > > > > > > > > > > Hi Mayte, > > > > > > > > > > > > > > > > > > I have not seen this error in the past. Have you tried simply > > > > > > > > > installing > > > > > > > > > ff first? > > > > > > > > > > > > > > > > > > biocLite("ff") > > > > > > > > > biocLite("affycoretools") > > > > > > > > > > > > > > > > > > Best, > > > > > > > > > > > > > > > > > > Jim > > > > > > > > > > > > > > > > > > > > > > > > > > > On 9/15/2013 4:57 PM, Mayte Suarez-Farinas wrote: > > > > > > > > > > > > > > > I updated to the most recent R version. After this brand new > > > > > > > > > > > > > > > installation, I get the following error while loading library > > > > > > > > > > > > > > > affycoretools: > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > library(affycoretools) > > > > > > > > > > > > > > > Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), > > > > > > > > > > > > > > > versionCheck = vI[[j]]) : > > > > > > > > > > > > > > > there is no package called ?ff? > > > > > > > > > > > > > > > Error: package or namespace load failed for ?affycoretools? > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > After checking mailing list, I followed James advice > > > > > > > > > > > > > > > ( > > > https://stat.ethz.ch/pipermail/bioconductor/2012-December/049895.html > > > ) > > > > > > > > > > > > > > > and updated all packages > > > > > > > > > > > > > > > library(BiocInstaller) > > > > > > > > > > > > > > > biocLite(character(0)) > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > Additionally, I updated all R packages as well > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > Still, the same problem arise. My R session info is bellow > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > R version 3.0.1 (2013-05-16) > > > > > > > > > > > > > > > Platform: x86_64-apple-darwin10.8.0 (64-bit) > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > locale: > > > > > > > > > > > > > > > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > attached base packages: > > > > > > > > > > > > > > > [1] parallel stats graphics grDevices utils datasets > > > > > > > > > > > > > > > methods base > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > other attached packages: > > > > > > > > > > > > > > > [1] KEGG.db_2.9.1 GO.db_2.9.0 RSQLite_0.11.4 > > > > > > > > > > > > > > > DBI_0.2-7 > > > > > > > > > > > > > > > [5] AnnotationDbi_1.22.6 affy_1.38.1 Biobase_2.20.1 > > > > > > > > > > > > > > > BiocGenerics_0.6.0 > > > > > > > > > > > > > > > [9] BiocInstaller_1.10.3 > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > loaded via a namespace (and not attached): > > > > > > > > > > > > > > > [1] affyio_1.28.0 annaffy_1.32.0 annotate_1.38.0 > > > > > > > > > > > > > > > [4] AnnotationForge_1.2.2 biomaRt_2.16.0 Biostrings_2.28.0 > > > > > > > > > > > > > > > [7] Category_2.26.0 gcrma_2.32.0 gdata_2.13.2 > > > > > > > > > > > > > > > [10] genefilter_1.42.0 GenomicRanges_1.12.5 GOstats_2.26.0 > > > > > > > > > > > > > > > [13] gplots_2.11.3 graph_1.38.3 grid_3.0.1 > > > > > > > > > > > > > > > [16] GSEABase_1.22.0 gtools_3.0.0 IRanges_1.18.3 > > > > > > > > > > > > > > > [19] lattice_0.20-23 limma_3.16.7 > > > > > > > > > > > > > > > preprocessCore_1.22.0 > > > > > > > > > > > > > > > [22] R2HTML_2.2.1 RBGL_1.36.2 RCurl_1.95-4.1 > > > > > > > > > > > > > > > [25] splines_3.0.1 stats4_3.0.1 survival_2.37-4 > > > > > > > > > > > > > > > [28] tools_3.0.1 XML_3.95-0.2 xtable_1.7-1 > > > > > > > > > > > > > > > [31] zlibbioc_1.6.0 > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > [[alternative HTML version deleted]] > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > > > > > > > > > > > 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 > > > > > > > > > > > > > > > > > > -- > > > > > > > > > James W. MacDonald, M.S. > > > > > > > > > Biostatistician > > > > > > > > > University of Washington > > > > > > > > > Environmental and Occupational Health Sciences > > > > > > > > > 4225 Roosevelt Way NE, # 100 > > > > > > > > > Seattle WA 98105-6099 > > > > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > > > > > 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 > > > > > > > > > > > > > > > > >
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Hi Mayte, I am unable to replicate your issue. I just installed R-3.0.1 on my MacOS X box, and then did the following: source("http://www.bioconductor.org/biocLite.R") biocLite() biocLite("affycoretools") library(affycoretools) sessionInfo() R version 3.0.1 (2013-05-16) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] C attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] affycoretools_1.32.1 KEGG.db_2.9.1 GO.db_2.9.0 [4] RSQLite_0.11.4 DBI_0.2-7 AnnotationDbi_1.22.6 [7] affy_1.38.1 Biobase_2.20.1 BiocGenerics_0.6.0 [10] BiocInstaller_1.10.3 loaded via a namespace (and not attached): [1] AnnotationForge_1.2.2 BSgenome_1.28.0 Biostrings_2.28.0 [4] Category_2.26.0 GOstats_2.26.0 GSEABase_1.22.0 [7] GenomicFeatures_1.12.3 GenomicRanges_1.12.5 Hmisc_3.12-2 [10] IRanges_1.18.3 MASS_7.3-29 PFAM.db_2.9.0 [13] R.methodsS3_1.5.0 R.oo_1.15.1 R.utils_1.26.2 [16] R2HTML_2.2.1 RBGL_1.36.2 RColorBrewer_1.0-5 [19] RCurl_1.95-4.1 ReportingTools_2.0.1 Rsamtools_1.12.4 [22] VariantAnnotation_1.6.7 XML_3.95-0.2 affyio_1.28.0 [25] annaffy_1.32.0 annotate_1.38.0 biomaRt_2.16.0 [28] biovizBase_1.8.1 bit_1.1-10 bitops_1.0-6 [31] cluster_1.14.4 codetools_0.2-8 colorspace_1.2-2 [34] dichromat_2.0-0 digest_0.6.3 edgeR_3.2.4 [37] ff_2.2-11 foreach_1.4.1 gcrma_2.32.0 [40] gdata_2.13.2 genefilter_1.42.0 ggbio_1.8.5 [43] ggplot2_0.9.3.1 gplots_2.11.3 graph_1.38.3 [46] grid_3.0.1 gridExtra_0.9.1 gtable_0.1.2 [49] gtools_3.0.0 hwriter_1.3 iterators_1.0.6 [52] labeling_0.2 lattice_0.20-23 limma_3.16.7 [55] munsell_0.4.2 oligoClasses_1.22.0 plyr_1.8 [58] preprocessCore_1.22.0 proto_0.3-10 reshape2_1.2.2 [61] rpart_4.1-3 rtracklayer_1.20.4 scales_0.2.3 [64] splines_3.0.1 stats4_3.0.1 stringr_0.6.2 [67] survival_2.37-4 tools_3.0.1 xtable_1.7-1 [70] zlibbioc_1.6.0 As you can see, both bit and ff installed correctly. Are you installing source or binary packages? Best, Jim On 9/16/13 12:14 PM, Mayte Suarez-Farinas wrote: > Dear James, Henrik and Steve > > I tried biocLite("ff") and got the msg: package ?ff? is not available (for R version 3.0.1) > (see below). Then I went ahead and download the tar package form (http://cran.r-project.org/web/packages/ff/index.html) and used R CMD install to install it. However, > while loading ff (library(ff)) it complains that the package bit was missing, biocLite gave me > same error (package ?bit? is not available (for R version 3.0.1) ) and I could not instll via CMD install > gave me the following error > > dhcp-129-85-243-253:Desktop mayte$ R CMD INSTALL bit_1.1-10.tar > * installing to library ?/Users/mayte/Library/R/3.0/library? > * installing *source* package ?bit? ... > ** package ?bit? successfully unpacked and MD5 sums checked > ** libs > sh: make: command not found > ERROR: compilation failed for package ?bit? > * removing ?/Users/mayte/Library/R/3.0/library/bit? > dhcp-129-85-243-253:Desktop mayte$ > > Please help out, life without affycoretools is very difficult ;-) > > > From: James W. MacDonald [jmacdon at uw.edu] > Sent: Monday, September 16, 2013 11:03 AM > To: Mayte Suarez-Farinas > Cc: bioconductor at r-project.org > Subject: Re: [BioC] problem while loading affycoretools > > Hi Mayte, > > I have not seen this error in the past. Have you tried simply installing > ff first? > > biocLite("ff") > biocLite("affycoretools") > > Best, > > Jim > > > On 9/15/2013 4:57 PM, Mayte Suarez-Farinas wrote: >> I updated to the most recent R version. After this brand new installation, I get the following error while loading library affycoretools: >> >> library(affycoretools) >> Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : >> there is no package called ?ff? >> Error: package or namespace load failed for ?affycoretools? >> >> After checking mailing list, I followed James advice (https://stat. ethz.ch/pipermail/bioconductor/2012-December/049895.html) and updated all packages >> library(BiocInstaller) >> biocLite(character(0)) >> >> Additionally, I updated all R packages as well >> >> Still, the same problem arise. My R session info is bellow >> >> >> R version 3.0.1 (2013-05-16) >> Platform: x86_64-apple-darwin10.8.0 (64-bit) >> >> locale: >> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >> >> attached base packages: >> [1] parallel stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] KEGG.db_2.9.1 GO.db_2.9.0 RSQLite_0.11.4 DBI_0.2-7 >> [5] AnnotationDbi_1.22.6 affy_1.38.1 Biobase_2.20.1 BiocGenerics_0.6.0 >> [9] BiocInstaller_1.10.3 >> >> loaded via a namespace (and not attached): >> [1] affyio_1.28.0 annaffy_1.32.0 annotate_1.38.0 >> [4] AnnotationForge_1.2.2 biomaRt_2.16.0 Biostrings_2.28.0 >> [7] Category_2.26.0 gcrma_2.32.0 gdata_2.13.2 >> [10] genefilter_1.42.0 GenomicRanges_1.12.5 GOstats_2.26.0 >> [13] gplots_2.11.3 graph_1.38.3 grid_3.0.1 >> [16] GSEABase_1.22.0 gtools_3.0.0 IRanges_1.18.3 >> [19] lattice_0.20-23 limma_3.16.7 preprocessCore_1.22.0 >> [22] R2HTML_2.2.1 RBGL_1.36.2 RCurl_1.95-4.1 >> [25] splines_3.0.1 stats4_3.0.1 survival_2.37-4 >> [28] tools_3.0.1 XML_3.95-0.2 xtable_1.7-1 >> [31] zlibbioc_1.6.0 >> >> >> [[alternative HTML version deleted]] >> >> >> >> _______________________________________________ >> 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 > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 >
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