
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

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/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/2.12/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/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/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/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/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/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/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/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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