Question: Can not install Bioconductor 3.5's GenomicRanges package via biocLite.
2
gravatar for Charles Plessy
2.0 years ago by
Japan
Charles Plessy90 wrote:

On a fresh system, I can not install GenomicRanges, because biocLite tries do download 1.28.1 while 1.28.2 is the one available.

> BiocInstaller::biocLite("GenomicRanges")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.5 (BiocInstaller 1.26.0), R 3.4.0 (2017-04-21).
Installing package(s) ‘GenomicRanges’
trying URL 'https://bioconductor.org/packages/3.5/bioc/src/contrib/GenomicRanges_1.28.1.tar.gz'
Error in download.file(url, destfile, method, mode = "wb", ...) :
  cannot open URL 'https://bioconductor.org/packages/3.5/bioc/src/contrib/GenomicRanges_1.28.1.tar.gz'
In addition: Warning message:
In download.file(url, destfile, method, mode = "wb", ...) :
  cannot open URL 'https://bioconductor.org/packages/3.5/bioc/src/contrib/GenomicRanges_1.28.1.tar.gz': HTTP status was '404 Not Found'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package ‘GenomicRanges’ failed

 

$ wget https://bioconductor.org/packages/3.5/bioc/src/contrib/GenomicRanges_1.28.1.tar.gz
--2017-05-17 10:33:45--  https://bioconductor.org/packages/3.5/bioc/src/contrib/GenomicRanges_1.28.1.tar.gz
Resolving bioconductor.org (bioconductor.org)... 52.222.205.48, 52.222.205.68, 52.222.205.109, ...
Connecting to bioconductor.org (bioconductor.org)|52.222.205.48|:443... connected.
HTTP request sent, awaiting response... 404 Not Found
2017-05-17 10:33:45 ERROR 404: Not Found.

$ wget https://bioconductor.org/packages/3.5/bioc/src/contrib/GenomicRanges_1.28.2.tar.gz
--2017-05-17 10:33:50--  https://bioconductor.org/packages/3.5/bioc/src/contrib/GenomicRanges_1.28.2.tar.gz
Resolving bioconductor.org (bioconductor.org)... 52.222.205.162, 52.222.205.41, 52.222.205.52, ...
Connecting to bioconductor.org (bioconductor.org)|52.222.205.162|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 1010076 (986K) [application/x-gzip]
Saving to: ‘GenomicRanges_1.28.2.tar.gz’

GenomicRanges_1.28.2.tar.gz     100%[=====================================================>] 986.40K   883KB/s    in 1.1s    

2017-05-17 10:33:52 (883 KB/s) - ‘GenomicRanges_1.28.2.tar.gz’ saved [1010076/1010076]
package installation • 925 views
ADD COMMENTlink modified 2.0 years ago by Martin Morgan ♦♦ 23k • written 2.0 years ago by Charles Plessy90
Answer: Can not install Bioconductor 3.5's GenomicRanges package via biocLite.
2
gravatar for Martin Morgan
2.0 years ago by
Martin Morgan ♦♦ 23k
United States
Martin Morgan ♦♦ 23k wrote:

The problem is that R uses a 'cache' to remember packages that are available for installation, and your cache is stale -- try installing the package from a new session (start R, preferably from the command line and with the --vanilla option), rather than from a long-running session.

But you say 'fresh system', and maybe you are already doing that?

ADD COMMENTlink modified 2.0 years ago • written 2.0 years ago by Martin Morgan ♦♦ 23k

Thanks for the answer. Yes, I was running BiocInstaller::biocLite("GenomicRanges") from a command line session (though not with --vanilla), and the same problem was also observed on a different machine operated by a colleague. This morning, running the same commands in the same context succeeded (and downloaded version 1.28.2) on both machines.

ADD REPLYlink written 2.0 years ago by Charles Plessy90

Was the installation that failed a long-running session, or a session that you started to install the package?

ADD REPLYlink written 2.0 years ago by Martin Morgan ♦♦ 23k

The sessions were started and re-started to install the package (we tried a couple of times).

ADD REPLYlink written 2.0 years ago by Charles Plessy90

Thanks, that helps to isolate the problem.

ADD REPLYlink written 2.0 years ago by Martin Morgan ♦♦ 23k
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