Problems during the installation of IRanges
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Entering edit mode
wuliang2 • 0
@wuliang2-9016
Last seen 7.1 years ago

Dear all.

When i install the IRanges package on the off-line linux system, i get the following error:

Error : 'quantile.default' is not an exported object from 'namespace:stats'
Error : unable to load R code in package 'IRanges'

* removing '/home/R/x86_64-unknown-linux-gnu-library/3.1/IRanges'
* restoring previous '/home/R/x86_64-unknown-linux-gnu-library/3.1/IRanges'
Warning message:
In install.packages("IRanges_1.18.4.tar.gz", repos = NULL) :
installation of package 'IRanges_1.18.4.tar.gz' had non-zero exit status

any help?

bests

IRange • 1.5k views
3
Entering edit mode
@herve-pages-1542
Last seen 20 hours ago
Seattle, WA, United States

Hi,

99% of BioC installation problems are caused by version mismatches. When installing BioC on an on-line machine, you should always use biocLite() and it will take care of grabbing the package versions that match your version of BioC. When you install BioC on an off-line machine, you can't use biocLite() so you need to be very careful about grabbing the correct package versions. In your case, you are trying to install IRanges 1.18.4 which belongs to BioC 2.12 which is 2.5 year old. The current version of BioC is 3.2 (was released last week). Any older version is not supported. Also your version of R is 3.1 which is not current either. BioC 3.2 was designed/tested to work with R 3.2 only.

See the list of all packages in the current BioC release:

If you want to fetch these lists programmatically, it might be easier to go for these files:

The PACKAGES files are in DCF format.

Cheers,

H.