Dear all, Using Tinn-R 2.3.7.1. and R 2.12.1 and following the instructions on: http://www.bioconductor.org/install/ I got several error and warning messages and bioClite failed to install (see below). What is going wrong? Thanks for any help, Louis Peperzak > source("http://bioconductor.org/biocLite.R") BioC_mirror = http://www.bioconductor.org Change using chooseBioCmirror(). > biocLite() Using R version 2.12.1, biocinstall version 2.7.4. Installing Bioconductor version 2.7 packages: [1] "affy" "affydata" "affyPLM" "affyQCReport" "annaffy" "annotate" "Biobase" "biomaRt" "Biostrings" "DynDoc" "gcrma" "genefilter" "geneplotter" "GenomicRanges" [15] "hgu95av2.db" "limma" "marray" "multtest" "vsn" "xtable" Please wait... also installing the dependencies ‘GO.db’, ‘KEGG.db’, ‘AnnotationDbi’, ‘DBI’, ‘XML’, ‘RCurl’, ‘IRanges’, ‘org.Hs.eg.db’ trying URL 'http://www.bioconductor.org/packages/2.7/data/annotation/b in/windows/contrib/2.12/GO.db_2.4.5.zip' Content type 'application/zip' length 17075248 bytes (16.3 Mb) opened URL downloaded 143 Kb trying URL 'http://www.bioconductor.org/packages/2.7/data/annotation/b in/windows/contrib/2.12/KEGG.db_2.4.5.zip' Content type 'application/zip' length 1776351 bytes (1.7 Mb) opened URL downloaded 1.7 Mb trying URL 'http://www.bioconductor.org/packages/2.7/bioc/bin/windows/ contrib/2.12/AnnotationDbi_1.12.0.zip' Content type 'application/zip' length 5267008 bytes (5.0 Mb) opened URL downloaded 72 Kb trying URL 'http://cran.xl- mirror.nl/bin/windows/contrib/2.12/DBI_0.2-5.zip' Content type 'application/zip' length 387335 bytes (378 Kb) opened URL downloaded 378 Kb trying URL 'http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/2.1 2/XML_3.2-0.2.zip' Content type 'application/zip' length 3562676 bytes (3.4 Mb) opened URL downloaded 3.4 Mb trying URL 'http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/2.1 2/RCurl_1.5-0.1.zip' Content type 'application/zip' length 2745711 bytes (2.6 Mb) opened URL downloaded 2.6 Mb trying URL 'http://www.bioconductor.org/packages/2.7/bioc/bin/windows/ contrib/2.12/IRanges_1.8.9.zip' Content type 'application/zip' length 1625241 bytes (1.5 Mb) opened URL downloaded 100 Kb trying URL 'http://www.bioconductor.org/packages/2.7/data/annotation/b in/windows/contrib/2.12/org.Hs.eg.db_2.4.6.zip' Content type 'application/zip' length 42049960 bytes (40.1 Mb) opened URL downloaded 373 Kb trying URL 'http://www.bioconductor.org/packages/2.7/bioc/bin/windows/ contrib/2.12/affy_1.28.0.zip' Content type 'application/zip' length 2067173 bytes (2.0 Mb) opened URL downloaded 987 Kb trying URL 'http://www.bioconductor.org/packages/2.7/data/experiment/b in/windows/contrib/2.12/affydata_1.11.10.zip' Content type 'application/zip' length 12756122 bytes (12.2 Mb) opened URL downloaded 820 Kb trying URL 'http://www.bioconductor.org/packages/2.7/bioc/bin/windows/ contrib/2.12/affyPLM_1.26.1.zip' Content type 'application/zip' length 5327317 bytes (5.1 Mb) opened URL downloaded 256 Kb trying URL 'http://www.bioconductor.org/packages/2.7/bioc/bin/windows/ contrib/2.12/affyQCReport_1.28.1.zip' Content type 'application/zip' length 233364 bytes (227 Kb) opened URL downloaded 227 Kb trying URL 'http://www.bioconductor.org/packages/2.7/bioc/bin/windows/ contrib/2.12/annaffy_1.22.0.zip' Content type 'application/zip' length 376624 bytes (367 Kb) opened URL downloaded 367 Kb trying URL 'http://www.bioconductor.org/packages/2.7/bioc/bin/windows/ contrib/2.12/annotate_1.28.1.zip' Content type 'application/zip' length 2212806 bytes (2.1 Mb) opened URL downloaded 133 Kb trying URL 'http://www.bioconductor.org/packages/2.7/bioc/bin/windows/ contrib/2.12/Biobase_2.10.0.zip' Content type 'application/zip' length 2594549 bytes (2.5 Mb) opened URL downloaded 547 Kb trying URL 'http://www.bioconductor.org/packages/2.7/bioc/bin/windows/ contrib/2.12/biomaRt_2.6.0.zip' Content type 'application/zip' length 333329 bytes (325 Kb) opened URL downloaded 325 Kb trying URL 'http://www.bioconductor.org/packages/2.7/bioc/bin/windows/ contrib/2.12/Biostrings_2.18.4.zip' Content type 'application/zip' length 2347595 bytes (2.2 Mb) opened URL downloaded 35 Kb trying URL 'http://www.bioconductor.org/packages/2.7/bioc/bin/windows/ contrib/2.12/DynDoc_1.28.0.zip' Content type 'application/zip' length 97807 bytes (95 Kb) opened URL downloaded 95 Kb trying URL 'http://www.bioconductor.org/packages/2.7/bioc/bin/windows/ contrib/2.12/gcrma_2.22.0.zip' Content type 'application/zip' length 236187 bytes (230 Kb) opened URL downloaded 230 Kb trying URL 'http://www.bioconductor.org/packages/2.7/bioc/bin/windows/ contrib/2.12/genefilter_1.32.0.zip' Content type 'application/zip' length 965461 bytes (942 Kb) opened URL downloaded 96 Kb trying URL 'http://www.bioconductor.org/packages/2.7/bioc/bin/windows/ contrib/2.12/geneplotter_1.28.0.zip' Content type 'application/zip' length 1816638 bytes (1.7 Mb) opened URL downloaded 1.7 Mb trying URL 'http://www.bioconductor.org/packages/2.7/bioc/bin/windows/ contrib/2.12/GenomicRanges_1.2.3.zip' Content type 'application/zip' length 1719777 bytes (1.6 Mb) opened URL downloaded 819 Kb trying URL 'http://www.bioconductor.org/packages/2.7/data/annotation/b in/windows/contrib/2.12/hgu95av2.db_2.4.5.zip' Content type 'application/zip' length 552869 bytes (539 Kb) opened URL downloaded 539 Kb trying URL 'http://www.bioconductor.org/packages/2.7/bioc/bin/windows/ contrib/2.12/limma_3.6.9.zip' Content type 'application/zip' length 1278421 bytes (1.2 Mb) opened URL downloaded 458 Kb trying URL 'http://www.bioconductor.org/packages/2.7/bioc/bin/windows/ contrib/2.12/marray_1.28.0.zip' Content type 'application/zip' length 5257909 bytes (5.0 Mb) opened URL downloaded 52 Kb trying URL 'http://cran.xl- mirror.nl/bin/windows/contrib/2.12/multtest_2.7.1.zip' Content type 'application/zip' length 1636476 bytes (1.6 Mb) opened URL downloaded 1.6 Mb trying URL 'http://www.bioconductor.org/packages/2.7/bioc/bin/windows/ contrib/2.12/vsn_3.18.0.zip' Content type 'application/zip' length 1608921 bytes (1.5 Mb) opened URL downloaded 649 Kb trying URL 'http://cran.xl- mirror.nl/bin/windows/contrib/2.12/xtable_1.5-6.zip' Content type 'application/zip' length 178816 bytes (174 Kb) opened URL downloaded 174 Kb Error in gzfile(file, "r") : cannot open the connection In addition: There were 17 warnings (use warnings() to see them) > warnings() Warning messages: 1: In download.file(url, destfile, method, mode = "wb", ...) : downloaded length 147185 != reported length 17075248 2: In download.file(url, destfile, method, mode = "wb", ...) : downloaded length 74187 != reported length 5267008 3: In download.file(url, destfile, method, mode = "wb", ...) : downloaded length 103387 != reported length 1625241 4: In download.file(url, destfile, method, mode = "wb", ...) : downloaded length 382245 != reported length 42049960 5: In download.file(url, destfile, method, mode = "wb", ...) : downloaded length 1011507 != reported length 2067173 6: In download.file(url, destfile, method, mode = "wb", ...) : downloaded length 840686 != reported length 12756122 7: In download.file(url, destfile, method, mode = "wb", ...) : downloaded length 262527 != reported length 5327317 8: In download.file(url, destfile, method, mode = "wb", ...) : downloaded length 136967 != reported length 2212806 9: In download.file(url, destfile, method, mode = "wb", ...) : downloaded length 560367 != reported length 2594549 10: In download.file(url, destfile, method, mode = "wb", ...) : downloaded length 36227 != reported length 2347595 11: In download.file(url, destfile, method, mode = "wb", ...) : downloaded length 99009 != reported length 965461 12: In download.file(url, destfile, method, mode = "wb", ...) : downloaded length 839227 != reported length 1719777 13: In download.file(url, destfile, method, mode = "wb", ...) : downloaded length 469847 != reported length 1278421 14: In download.file(url, destfile, method, mode = "wb", ...) : downloaded length 53747 != reported length 5257909 15: In download.file(url, destfile, method, mode = "wb", ...) : downloaded length 665487 != reported length 1608921 16: In unzip(zipname, exdir = dest) : error 1 in extracting from zip file 17: In gzfile(file, "r") : cannot open compressed file 'GO.db/DESCRIPTION', probable reason 'No such file or directory' > 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Hi Louis -- On 03/05/2011 06:41 AM, Louis Peperzak wrote: > > Dear all, > > Using Tinn-R 2.3.7.1. and R 2.12.1 > and following the instructions on: http://www.bioconductor.org/install/ > > I got several error and warning messages and bioClite failed to install (see below). > What is going wrong? > > Thanks for any help, > > Louis Peperzak > >> source("http://bioconductor.org/biocLite.R") > BioC_mirror = http://www.bioconductor.org > Change using chooseBioCmirror(). >> biocLite() > Using R version 2.12.1, biocinstall version 2.7.4. > Installing Bioconductor version 2.7 packages: > [1] "affy" "affydata" "affyPLM" "affyQCReport" "annaffy" "annotate" "Biobase" "biomaRt" "Biostrings" "DynDoc" "gcrma" "genefilter" "geneplotter" "GenomicRanges" > [15] "hgu95av2.db" "limma" "marray" "multtest" "vsn" "xtable" > Please wait... > > also installing the dependencies ?GO.db?, ?KEGG.db?, ?AnnotationDbi?, ?DBI?, ?XML?, ?RCurl?, ?IRanges?, ?org.Hs.eg.db? > > trying URL 'http://www.bioconductor.org/packages/2.7/data/annotation /bin/windows/contrib/2.12/GO.db_2.4.5.zip' > Content type 'application/zip' length 17075248 bytes (16.3 Mb) > opened URL > downloaded 143 Kb This looks like a network issue of some kind. The reported file size (16.3Mb) is very different from the downloaded size (143kb). We did have some hardware issues on our end, and there may be some ongoing problems. Can you (a) try to download the above file (or one of the files below like IRanges_1.8.9.zip, it has a similar size mismatch, so it's easier for you to test) just via your web browser, (b) try using biocLite on just that file, biocLite("IRanges"), (c) try biocLite() again. If there are similar warnings / errors, it would help to see what was downloaded, by looking for the file (e.g., 'IRanges_1.8.9.zip") in the location returned by tempdir() and forwarding it to me. The file will be in a subdirectory of tempdir(). The mailing list software will strip the attachment, so please forward to me directly. Martin > > trying URL 'http://www.bioconductor.org/packages/2.7/data/annotation /bin/windows/contrib/2.12/KEGG.db_2.4.5.zip' > Content type 'application/zip' length 1776351 bytes (1.7 Mb) > opened URL > downloaded 1.7 Mb > > trying URL 'http://www.bioconductor.org/packages/2.7/bioc/bin/window s/contrib/2.12/AnnotationDbi_1.12.0.zip' > Content type 'application/zip' length 5267008 bytes (5.0 Mb) > opened URL > downloaded 72 Kb > > trying URL 'http://cran.xl- mirror.nl/bin/windows/contrib/2.12/DBI_0.2-5.zip' > Content type 'application/zip' length 387335 bytes (378 Kb) > opened URL > downloaded 378 Kb > > trying URL 'http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/2 .12/XML_3.2-0.2.zip' > Content type 'application/zip' length 3562676 bytes (3.4 Mb) > opened URL > downloaded 3.4 Mb > > trying URL 'http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/2 .12/RCurl_1.5-0.1.zip' > Content type 'application/zip' length 2745711 bytes (2.6 Mb) > opened URL > downloaded 2.6 Mb > > trying URL 'http://www.bioconductor.org/packages/2.7/bioc/bin/window s/contrib/2.12/IRanges_1.8.9.zip' > Content type 'application/zip' length 1625241 bytes (1.5 Mb) > opened URL > downloaded 100 Kb > > trying URL 'http://www.bioconductor.org/packages/2.7/data/annotation /bin/windows/contrib/2.12/org.Hs.eg.db_2.4.6.zip' > Content type 'application/zip' length 42049960 bytes (40.1 Mb) > opened URL > downloaded 373 Kb > > trying URL 'http://www.bioconductor.org/packages/2.7/bioc/bin/window s/contrib/2.12/affy_1.28.0.zip' > Content type 'application/zip' length 2067173 bytes (2.0 Mb) > opened URL > downloaded 987 Kb > > trying URL 'http://www.bioconductor.org/packages/2.7/data/experiment /bin/windows/contrib/2.12/affydata_1.11.10.zip' > Content type 'application/zip' length 12756122 bytes (12.2 Mb) > opened URL > downloaded 820 Kb > > trying URL 'http://www.bioconductor.org/packages/2.7/bioc/bin/window s/contrib/2.12/affyPLM_1.26.1.zip' > Content type 'application/zip' length 5327317 bytes (5.1 Mb) > opened URL > downloaded 256 Kb > > trying URL 'http://www.bioconductor.org/packages/2.7/bioc/bin/window s/contrib/2.12/affyQCReport_1.28.1.zip' > Content type 'application/zip' length 233364 bytes (227 Kb) > opened URL > downloaded 227 Kb > > trying URL 'http://www.bioconductor.org/packages/2.7/bioc/bin/window s/contrib/2.12/annaffy_1.22.0.zip' > Content type 'application/zip' length 376624 bytes (367 Kb) > opened URL > downloaded 367 Kb > > trying URL 'http://www.bioconductor.org/packages/2.7/bioc/bin/window s/contrib/2.12/annotate_1.28.1.zip' > Content type 'application/zip' length 2212806 bytes (2.1 Mb) > opened URL > downloaded 133 Kb > > trying URL 'http://www.bioconductor.org/packages/2.7/bioc/bin/window s/contrib/2.12/Biobase_2.10.0.zip' > Content type 'application/zip' length 2594549 bytes (2.5 Mb) > opened URL > downloaded 547 Kb > > trying URL 'http://www.bioconductor.org/packages/2.7/bioc/bin/window s/contrib/2.12/biomaRt_2.6.0.zip' > Content type 'application/zip' length 333329 bytes (325 Kb) > opened URL > downloaded 325 Kb > > trying URL 'http://www.bioconductor.org/packages/2.7/bioc/bin/window s/contrib/2.12/Biostrings_2.18.4.zip' > Content type 'application/zip' length 2347595 bytes (2.2 Mb) > opened URL > downloaded 35 Kb > > trying URL 'http://www.bioconductor.org/packages/2.7/bioc/bin/window s/contrib/2.12/DynDoc_1.28.0.zip' > Content type 'application/zip' length 97807 bytes (95 Kb) > opened URL > downloaded 95 Kb > > trying URL 'http://www.bioconductor.org/packages/2.7/bioc/bin/window s/contrib/2.12/gcrma_2.22.0.zip' > Content type 'application/zip' length 236187 bytes (230 Kb) > opened URL > downloaded 230 Kb > > trying URL 'http://www.bioconductor.org/packages/2.7/bioc/bin/window s/contrib/2.12/genefilter_1.32.0.zip' > Content type 'application/zip' length 965461 bytes (942 Kb) > opened URL > downloaded 96 Kb > > trying URL 'http://www.bioconductor.org/packages/2.7/bioc/bin/window s/contrib/2.12/geneplotter_1.28.0.zip' > Content type 'application/zip' length 1816638 bytes (1.7 Mb) > opened URL > downloaded 1.7 Mb > > trying URL 'http://www.bioconductor.org/packages/2.7/bioc/bin/window s/contrib/2.12/GenomicRanges_1.2.3.zip' > Content type 'application/zip' length 1719777 bytes (1.6 Mb) > opened URL > downloaded 819 Kb > > trying URL 'http://www.bioconductor.org/packages/2.7/data/annotation /bin/windows/contrib/2.12/hgu95av2.db_2.4.5.zip' > Content type 'application/zip' length 552869 bytes (539 Kb) > opened URL > downloaded 539 Kb > > trying URL 'http://www.bioconductor.org/packages/2.7/bioc/bin/window s/contrib/2.12/limma_3.6.9.zip' > Content type 'application/zip' length 1278421 bytes (1.2 Mb) > opened URL > downloaded 458 Kb > > trying URL 'http://www.bioconductor.org/packages/2.7/bioc/bin/window s/contrib/2.12/marray_1.28.0.zip' > Content type 'application/zip' length 5257909 bytes (5.0 Mb) > opened URL > downloaded 52 Kb > > trying URL 'http://cran.xl- mirror.nl/bin/windows/contrib/2.12/multtest_2.7.1.zip' > Content type 'application/zip' length 1636476 bytes (1.6 Mb) > opened URL > downloaded 1.6 Mb > > trying URL 'http://www.bioconductor.org/packages/2.7/bioc/bin/window s/contrib/2.12/vsn_3.18.0.zip' > Content type 'application/zip' length 1608921 bytes (1.5 Mb) > opened URL > downloaded 649 Kb > > trying URL 'http://cran.xl- mirror.nl/bin/windows/contrib/2.12/xtable_1.5-6.zip' > Content type 'application/zip' length 178816 bytes (174 Kb) > opened URL > downloaded 174 Kb > > Error in gzfile(file, "r") : cannot open the connection > In addition: There were 17 warnings (use warnings() to see them) >> warnings() > Warning messages: > 1: In download.file(url, destfile, method, mode = "wb", ...) : > downloaded length 147185 != reported length 17075248 > 2: In download.file(url, destfile, method, mode = "wb", ...) : > downloaded length 74187 != reported length 5267008 > 3: In download.file(url, destfile, method, mode = "wb", ...) : > downloaded length 103387 != reported length 1625241 > 4: In download.file(url, destfile, method, mode = "wb", ...) : > downloaded length 382245 != reported length 42049960 > 5: In download.file(url, destfile, method, mode = "wb", ...) : > downloaded length 1011507 != reported length 2067173 > 6: In download.file(url, destfile, method, mode = "wb", ...) : > downloaded length 840686 != reported length 12756122 > 7: In download.file(url, destfile, method, mode = "wb", ...) : > downloaded length 262527 != reported length 5327317 > 8: In download.file(url, destfile, method, mode = "wb", ...) : > downloaded length 136967 != reported length 2212806 > 9: In download.file(url, destfile, method, mode = "wb", ...) : > downloaded length 560367 != reported length 2594549 > 10: In download.file(url, destfile, method, mode = "wb", ...) : > downloaded length 36227 != reported length 2347595 > 11: In download.file(url, destfile, method, mode = "wb", ...) : > downloaded length 99009 != reported length 965461 > 12: In download.file(url, destfile, method, mode = "wb", ...) : > downloaded length 839227 != reported length 1719777 > 13: In download.file(url, destfile, method, mode = "wb", ...) : > downloaded length 469847 != reported length 1278421 > 14: In download.file(url, destfile, method, mode = "wb", ...) : > downloaded length 53747 != reported length 5257909 > 15: In download.file(url, destfile, method, mode = "wb", ...) : > downloaded length 665487 != reported length 1608921 > 16: In unzip(zipname, exdir = dest) : error 1 in extracting from zip file > 17: In gzfile(file, "r") : > cannot open compressed file 'GO.db/DESCRIPTION', probable reason 'No such file or directory' >> > > > [[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 -- Computational Biology Fred Hutchinson Cancer Research Center 1100 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