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Question: Warning messages with biocLite()
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gravatar for Robert Baer
4.1 years ago by
Robert Baer70
United States
Robert Baer70 wrote:

R 3.1.2 from RStudio 0.98.1062 on Windows 8.1

I got the following warnings which are hard to understand since the file sizes seem to match despite the messages:

biocLite()

... snip

The downloaded binary packages are in
    C:\Users\rbaer.KCOM2K\AppData\Local\Temp\Rtmpq6tgf2\downloaded_packages
Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 4268946 != reported length 4268946
2: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 3275570 != reported length 3275570

Any insights about what this is telling me?  Can I trust the downloads?

Thanks, Rob

Details of output:

--------------------------------------------------------------------------------

> biocLite()
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.0 (BiocInstaller 1.16.1), R
  version 3.1.2.
Installing package(s) 'Biobase' 'IRanges' 'AnnotationDbi'
also installing the dependencies ‘BiocGenerics’, ‘S4Vectors’, ‘GenomeInfoDb’, ‘DBI’, ‘RSQLite’

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/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/bioc/bin/windows/contrib/3.1/GenomeInfoDb_1.2.3.zip'
Content type 'application/zip' length 828583 bytes (809 Kb)
opened URL
downloaded 809 Kb

trying URL 'http://cran.rstudio.com/bin/windows/contrib/3.1/DBI_0.3.1.zip'
Content type 'application/zip' length 153831 bytes (150 Kb)
opened URL
downloaded 150 Kb

trying URL 'http://cran.rstudio.com/bin/windows/contrib/3.1/RSQLite_1.0.0.zip'
Content type 'application/zip' length 1211130 bytes (1.2 Mb)
opened URL
downloaded 1.2 Mb

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/IRanges_2.0.0.zip'
Content type 'application/zip' length 3275570 bytes (3.1 Mb)
opened URL
downloaded 3.1 Mb

trying URL 'http://bioconductor.org/packages/3.0/bioc/bin/windows/contrib/3.1/AnnotationDbi_1.28.1.zip'
Content type 'application/zip' length 9485655 bytes (9.0 Mb)
opened URL
downloaded 9.0 Mb

package ‘BiocGenerics’ successfully unpacked and MD5 sums checked
package ‘S4Vectors’ successfully unpacked and MD5 sums checked
package ‘GenomeInfoDb’ successfully unpacked and MD5 sums checked
package ‘DBI’ successfully unpacked and MD5 sums checked
package ‘RSQLite’ successfully unpacked and MD5 sums checked
package ‘Biobase’ successfully unpacked and MD5 sums checked
package ‘IRanges’ successfully unpacked and MD5 sums checked
package ‘AnnotationDbi’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\rbaer.KCOM2K\AppData\Local\Temp\Rtmpq6tgf2\downloaded_packages
Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 4268946 != reported length 4268946
2: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 3275570 != reported length 3275570
>

------------------------------------------------

> R.Version()
$platform
[1] "x86_64-w64-mingw32"

$arch
[1] "x86_64"

$os
[1] "mingw32"

$system
[1] "x86_64, mingw32"

$status
[1] ""

$major
[1] "3"

$minor
[1] "1.2"

$year
[1] "2014"

$month
[1] "10"

$day
[1] "31"

$`svn rev`
[1] "66913"

$language
[1] "R"

$version.string
[1] "R version 3.1.2 (2014-10-31)"

$nickname
[1] "Pumpkin Helmet"

 

ADD COMMENTlink written 4.1 years ago by Robert Baer70

These warnings are coming from install.packages() and they are indeed odd. Are you using a proxy by any chance?

ADD REPLYlink written 4.1 years ago by Dan Tenenbaum ♦♦ 8.2k
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