Error occured while installing bioconductor in R



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


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

serenity:/tmp -> curl -I
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 (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?


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.



Hi Josh,

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

Thank You,