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Question: Warning in R
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gravatar for Angel
3.3 years ago by
Angel40
Berlin
Angel40 wrote:

hey guys,

i am in windows seven 64 bit...i installed R 3.1.1, 3.1.2. 3.2.0 and etc but always and for any package i face with errors like below:

 

> source("http://bioconductor.org/biocLite.R")

trying URL 'http://www.bioconductor.org/packages/3.0/bioc/bin/windows/contrib/3.1/BiocInstaller_1.16.5.zip'

Content type 'application/zip' length 54033 bytes (52 Kb)

opened URL

downloaded 52 Kb

 

 

The downloaded binary packages are in

        C:\Users\yang\AppData\Local\Temp\RtmpakCQlc\downloaded_packages

Bioconductor version 3.0 (BiocInstaller 1.16.5), ?biocLite for help

A new version of Bioconductor is available after installing the most recent

  version of R; see http://bioconductor.org/install

> biocLite("pd.aragene.1.0.st")

BioC_mirror: http://bioconductor.org

Using Bioconductor version 3.0 (BiocInstaller 1.16.5), R version 3.1.2.

Installing package(s) 'pd.aragene.1.0.st'

also installing the dependencies ‘GenomeInfoDb’, ‘bit’, ‘iterators’, ‘BiocGenerics’, ‘XVector’, ‘zlibbioc’, ‘Biobase’, ‘GenomicRanges’, ‘affyio’, ‘ff’, ‘foreach’, ‘affxparser’, ‘preprocessCore’, ‘Biostrings’, ‘RSQLite’, ‘oligoClasses’, ‘oligo’, ‘DBI’, ‘IRanges’, ‘S4Vectors’

 

trying URL 'http://bioconductor.org/packages/3.0/bioc/bin/windows/contrib/3.1/GenomeInfoDb_1.2.5.zip'

Content type 'application/zip' length 828291 bytes (808 Kb)

opened URL

downloaded 808 Kb

 

trying URL 'http://cran.fhcrc.org/bin/windows/contrib/3.1/bit_1.1-12.zip'

Content type 'application/zip' length 217260 bytes (212 Kb)

opened URL

downloaded 212 Kb

 

trying URL 'http://cran.fhcrc.org/bin/windows/contrib/3.1/iterators_1.0.7.zip'

Content type 'application/zip' length 315647 bytes (308 Kb)

opened URL

downloaded 308 Kb

 

trying URL 'http://bioconductor.org/packages/3.0/bioc/bin/windows/contrib/3.1/BiocGenerics_0.12.1.zip'

Content type 'application/zip' length 855784 bytes (835 Kb)

opened URL

downloaded 835 Kb

 

trying URL 'http://bioconductor.org/packages/3.0/bioc/bin/windows/contrib/3.1/XVector_0.6.0.zip'

Content type 'application/zip' length 753111 bytes (735 Kb)

opened URL

downloaded 735 Kb

 

trying URL 'http://bioconductor.org/packages/3.0/bioc/bin/windows/contrib/3.1/zlibbioc_1.12.0.zip'

Content type 'application/zip' length 494105 bytes (482 Kb)

opened URL

downloaded 482 Kb

 

trying URL 'http://bioconductor.org/packages/3.0/bioc/bin/windows/contrib/3.1/Biobase_2.26.0.zip'

Content type 'application/zip' length 4268946 bytes (4.1 Mb)

opened URL

downloaded 4.1 Mb

 

trying URL 'http://bioconductor.org/packages/3.0/bioc/bin/windows/contrib/3.1/GenomicRanges_1.18.4.zip'

Content type 'application/zip' length 2450653 bytes (2.3 Mb)

opened URL

downloaded 2.3 Mb

 

trying URL 'http://bioconductor.org/packages/3.0/bioc/bin/windows/contrib/3.1/affyio_1.34.0.zip'

Content type 'application/zip' length 306453 bytes (299 Kb)

opened URL

downloaded 299 Kb

 

trying URL 'http://cran.fhcrc.org/bin/windows/contrib/3.1/ff_2.2-13.zip'

Content type 'application/zip' length 1459380 bytes (1.4 Mb)

opened URL

downloaded 1.4 Mb

 

trying URL 'http://cran.fhcrc.org/bin/windows/contrib/3.1/foreach_1.4.2.zip'

Content type 'application/zip' length 388715 bytes (379 Kb)

opened URL

downloaded 379 Kb

 

trying URL 'http://bioconductor.org/packages/3.0/bioc/bin/windows/contrib/3.1/affxparser_1.38.0.zip'

Content type 'application/zip' length 3849239 bytes (3.7 Mb)

opened URL

downloaded 1.5 Mb

 

trying URL 'http://bioconductor.org/packages/3.0/bioc/bin/windows/contrib/3.1/preprocessCore_1.28.0.zip'

Content type 'application/zip' length 413181 bytes (403 Kb)

opened URL

downloaded 403 Kb

 

trying URL 'http://bioconductor.org/packages/3.0/bioc/bin/windows/contrib/3.1/Biostrings_2.34.1.zip'

Content type 'application/zip' length 27219263 bytes (26.0 Mb)

opened URL

downloaded 26.0 Mb

 

trying URL 'http://cran.fhcrc.org/bin/windows/contrib/3.1/RSQLite_1.0.0.zip'

Content type 'application/zip' length 1211185 bytes (1.2 Mb)

opened URL

downloaded 1.2 Mb

 

trying URL 'http://bioconductor.org/packages/3.0/bioc/bin/windows/contrib/3.1/oligoClasses_1.28.0.zip'

Content type 'application/zip' length 1758046 bytes (1.7 Mb)

opened URL

downloaded 1.7 Mb

 

trying URL 'http://bioconductor.org/packages/3.0/bioc/bin/windows/contrib/3.1/oligo_1.30.0.zip'

Content type 'application/zip' length 6241114 bytes (6.0 Mb)

opened URL

downloaded 6.0 Mb

 

trying URL 'http://cran.fhcrc.org/bin/windows/contrib/3.1/DBI_0.3.1.zip'

Content type 'application/zip' length 153972 bytes (150 Kb)

opened URL

downloaded 150 Kb

 

trying URL 'http://bioconductor.org/packages/3.0/bioc/bin/windows/contrib/3.1/IRanges_2.0.1.zip'

Content type 'application/zip' length 3273003 bytes (3.1 Mb)

opened URL

downloaded 3.1 Mb

 

trying URL 'http://bioconductor.org/packages/3.0/bioc/bin/windows/contrib/3.1/S4Vectors_0.4.0.zip'

Content type 'application/zip' length 1411503 bytes (1.3 Mb)

opened URL

downloaded 1.3 Mb

 

trying URL 'http://bioconductor.org/packages/3.0/data/annotation/bin/windows/contrib/3.1/pd.aragene.1.0.st_3.10.0.zip'

Content type 'application/zip' length 41807845 bytes (39.9 Mb)

opened URL

downloaded 39.9 Mb

 

package ‘GenomeInfoDb’ successfully unpacked and MD5 sums checked

package ‘bit’ successfully unpacked and MD5 sums checked

package ‘iterators’ successfully unpacked and MD5 sums checked

package ‘BiocGenerics’ successfully unpacked and MD5 sums checked

package ‘XVector’ successfully unpacked and MD5 sums checked

package ‘zlibbioc’ successfully unpacked and MD5 sums checked

package ‘Biobase’ successfully unpacked and MD5 sums checked

package ‘GenomicRanges’ successfully unpacked and MD5 sums checked

package ‘affyio’ successfully unpacked and MD5 sums checked

package ‘ff’ successfully unpacked and MD5 sums checked

package ‘foreach’ 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 1541240 != reported length 3849239

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 'affxparser/DESCRIPTION', probable reason 'No such file or directory'

i tried options such as chooseBioCmirror() and setInternet2(TRUE), but the problem is stay with me

please help me

ADD COMMENTlink modified 3.3 years ago • written 3.3 years ago by Angel40
1

See A: warning in R to your previous nearly identical question.  Try to download just the package that you had trouble with

source("http://bioconductor.org/biocLite.R")
biocLite("affxparser")

If that succeeds try again to install pd.aragene.1.0.st

biocLite("pd.aragene.1.0.st")

...it will not have to download the previous packages, so should get further along.

ADD REPLYlink written 3.3 years ago by Martin Morgan ♦♦ 22k

thank you i did so but the warning yet,

what does mean selecting a proxy by chance? 

when i tried your tip, i saw like this:

 

 

Content type 'application/zip' length 54033 bytes (52 Kb)
opened URL
downloaded 52 Kb

 

 
The downloaded binary packages are in
        C:\Users\yang\AppData\Local\Temp\RtmpCSs349\downloaded_packages
Bioconductor version 3.0 (BiocInstaller 1.16.5), ?biocLite for help
A new version of Bioconductor is available after installing the most recent
  version of R; see http://bioconductor.org/install
> biocLite("affxparser")
Using Bioconductor version 3.0 (BiocInstaller 1.16.5), R version 3.1.1.
Installing package(s) 'affxparser'
Content type 'application/zip' length 3849239 bytes (3.7 Mb)
opened URL
downloaded 3.7 Mb

package ‘affxparser’ successfully unpacked and MD5 sums checked

 

The downloaded binary packages are in
        C:\Users\yang\AppData\Local\Temp\RtmpCSs349\downloaded_packages
Old packages: 'boot', 'class', 'cluster', 'codetools', 'foreign', 'KernSmooth',
  'lattice', 'MASS', 'Matrix', 'mgcv', 'nlme', 'nnet', 'rpart', 'spatial',
  'survival'
Update all/some/none? [a/s/n]: 

 

ADD REPLYlink modified 3.3 years ago • written 3.3 years ago by Angel40
1

OK, you updated your reply. This time you were able to download and install affxparser, whereas last time you were not able to do that. Good!

The warnings that you now see can be ignored for the moment.

Please now try to install pd.aragene.1.0.st

biocLite("pd.aragene.1.0.st")

...it will not have to download the previous packages, so should get further along.

ADD REPLYlink modified 3.3 years ago • written 3.3 years ago by Martin Morgan ♦♦ 22k

ok i will do so thank you

ADD REPLYlink written 3.3 years ago by Angel40

thank you very much your tips worked

ADD REPLYlink modified 3.3 years ago • written 3.3 years ago by Angel40
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