Entering edit mode
Hey all,
i am in window seven 64 bit and R 3.2.0, when i typed:
> source("http://bioconductor.org/biocLite.R")
Bioconductor version 3.1 (BiocInstaller 1.18.2), ?biocLite for help
> biocLite("qpgraph")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.1 (BiocInstaller 1.18.2), R version 3.2.0.
Installing package(s) ‘qpgraph’
also installing the dependencies ‘lambda.r’, ‘futile.options’, ‘zlibbioc’, ‘Rsamtools’, ‘GenomicAlignments’, ‘xtable’, ‘futile.logger’, ‘snow’, ‘XVector’, ‘Biostrings’, ‘rtracklayer’, ‘biomaRt’, ‘annotate’, ‘graph’, ‘BiocParallel’, ‘GenomicRanges’, ‘GenomicFeatures’, ‘mvtnorm’, ‘qtl’, ‘Rgraphviz’
Content type 'application/zip' length 72811 bytes (71 KB)
downloaded 71 KB
Content type 'application/zip' length 16699 bytes (16 KB)
downloaded 16 KB
Content type 'application/zip' length 693703 bytes (677 KB)
downloaded 677 KB
Content type 'application/zip' length 8138016 bytes (7.8 MB)
downloaded 5.7 MB
trying URL 'http://bioconductor.org/packages/3.1/bioc/bin/windows/contrib/3.2/GenomicAlignments_1.4.1.zip'
Content type 'application/zip' length 2679746 bytes (2.6 MB)
downloaded 2.6 MB
Content type 'application/zip' length 382566 bytes (373 KB)
downloaded 373 KB
Content type 'application/zip' length 83484 bytes (81 KB)
downloaded 81 KB
Content type 'application/zip' length 67187 bytes (65 KB)
downloaded 65 KB
Content type 'application/zip' length 725766 bytes (708 KB)
downloaded 708 KB
trying URL 'http://bioconductor.org/packages/3.1/bioc/bin/windows/contrib/3.2/Biostrings_2.36.1.zip'
Content type 'application/zip' length 27187933 bytes (25.9 MB)
downloaded 2.7 MB
trying URL 'http://bioconductor.org/packages/3.1/bioc/bin/windows/contrib/3.2/rtracklayer_1.28.4.zip'
Content type 'application/zip' length 3704149 bytes (3.5 MB)
downloaded 3.5 MB
Content type 'application/zip' length 766131 bytes (748 KB)
downloaded 748 KB
Content type 'application/zip' length 3852771 bytes (3.7 MB)
downloaded 2.0 MB
Content type 'application/zip' length 2706689 bytes (2.6 MB)
downloaded 2.6 MB
trying URL 'http://bioconductor.org/packages/3.1/bioc/bin/windows/contrib/3.2/BiocParallel_1.2.2.zip'
Content type 'application/zip' length 940833 bytes (918 KB)
downloaded 918 KB
trying URL 'http://bioconductor.org/packages/3.1/bioc/bin/windows/contrib/3.2/GenomicRanges_1.20.3.zip'
Content type 'application/zip' length 2970715 bytes (2.8 MB)
downloaded 2.8 MB
trying URL 'http://bioconductor.org/packages/3.1/bioc/bin/windows/contrib/3.2/GenomicFeatures_1.20.1.zip'
Error in download.file(url, destfile, method, mode = "wb", ...) :
cannot open URL 'http://bioconductor.org/packages/3.1/bioc/bin/windows/contrib/3.2/GenomicFeatures_1.20.1.zip'
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
downloaded length 5975350 != reported length 8138016
2: In download.file(url, destfile, method, mode = "wb", ...) :
downloaded length 2833747 != reported length 27187933
3: In download.file(url, destfile, method, mode = "wb", ...) :
downloaded length 2098578 != reported length 3852771
4: In download.file(url, destfile, method, mode = "wb", ...) :
unable to resolve 'bioconductor.org'
Warning in download.packages(pkgs, destdir = tmpd, available = available, :
download of package ‘GenomicFeatures’ failed
Content type 'application/zip' length 222974 bytes (217 KB)
downloaded 217 KB
Content type 'application/zip' length 5477132 bytes (5.2 MB)
downloaded 5.2 MB
Content type 'application/zip' length 3663538 bytes (3.5 MB)
downloaded 3.5 MB
Content type 'application/zip' length 7011360 bytes (6.7 MB)
downloaded 4.8 MB
package ‘lambda.r’ successfully unpacked and MD5 sums checked
package ‘futile.options’ successfully unpacked and MD5 sums checked
package ‘zlibbioc’ successfully unpacked and MD5 sums checked
Error in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) :
cannot open the connection
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
downloaded length 5040433 != reported length 7011360
2: In unzip(zipname, exdir = dest) : error 1 in extracting from zip file
3: In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) :
cannot open compressed file 'Rsamtools/DESCRIPTION', probable reason 'No such file or directory'
>
to any packages im facing with the same warning even in Rstudio...
what is your suggestion please?
You could also try
setInternet2(TRUE)And then try again and see if that works.
thank you i tried chooseBioCmirror()
and chose japan