Error occured while installing bioconductor in R

rstudio

#1

I was trying to install bioconductor in R version 3.5.1 and faced the following problem while running biocLite()

package ‘foreign’ 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 3059712 != reported length 4618652
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 'survival/DESCRIPTION', probable reason 'No such file or directory'

How can I solve this problem, I have already tried to run Rstudio as an administrator, still it didn't worked.

Thanks, Santosh


#2

It looks like you are attempting to install on Windows, as the expected byte count matches:

serenity:/tmp -> curl -I https://cran.rstudio.com/bin/windows/contrib/3.5/survival_2.42-6.zip
HTTP/2 200
content-type: application/zip
content-length: 4618652
date: Wed, 25 Jul 2018 03:09:36 GMT
server: Apache/2.2.22 (Ubuntu)
last-modified: Tue, 24 Jul 2018 17:33:22 GMT
etag: "186ec526-46799c-571c22894fc80"
accept-ranges: bytes
cache-control: max-age=1800
expires: Wed, 25 Jul 2018 03:39:36 GMT
age: 616
x-cache: Hit from cloudfront
via: 1.1 d1c6b0af1d2d0f3694496e7cbde73924.cloudfront.net (CloudFront)
x-amz-cf-id: 4ef11o85eVX2iZnkh6QKacRMrZ7pPCACTuibD_mGM-efkt79gX2WQA==

However, the full file was not able to be downloaded, and when it was unzip'd, it failed.

If you attempt to install.packages('survival') by itself does it succeed?


#3

Dear Josh

Sorry for delay in replying. yes, I am able to install the package "survival".

What else could be the issue and how to fix it.

Thanks,
Santosh


#4

Hi Josh,

After installing "survival" package I am able to install the other bioconductor packages.

Thank You,