Question

installation of "airway" had non-zero exit status

0

Entering edit mode

liyi983923 • 0

@liyi983923-12249

Last seen 7.8 years ago

Hello,

I am a new guy in bioconductor and I fail to install package "airway":

Here is my command:

source("http://www.bioconductor.org/biocLite.R")
biocLite("airway")

My problem is:

Error in untar2(tarfile, files, list, exdir, restore_times) : incomplete block on file

Can anyone help me?

Thank you very much in advance,

airway • 4.0k views

ADD COMMENT • link updated 7.8 years ago by Martin Morgan 25k • written 7.8 years ago by liyi983923 • 0

0

Entering edit mode

Could you add your sessionInfo()? Especially the version of Bioconductor and R are relevant.

ADD REPLY • link 7.8 years ago WouterDeCoster ▴ 130

0

Entering edit mode

Hi WouterDeCoster,

Thank you very much for your reply. the following is the information.

Jimmy

> biocLite("airway")

BioC_mirror: https://bioconductor.org
Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.2 (2016-10-31).
Installing package(s) ‘airway’
installing the source package ‘airway’

trying URL 'https://bioconductor.org/packages/3.4/data/experiment/src/contrib/airway_0.108.0.tar.gz'
Content type 'application/x-gzip' length 11755934 bytes (11.2 MB)
downloaded 11.2 MB

Error in untar2(tarfile, files, list, exdir, restore_times) :
incomplete block on file

The downloaded source packages are in
‘C:\Users\Yi Li\AppData\Local\Temp\RtmpasmgTS\downloaded_packages’
Warning messages:
1: running command '"C:/R/R-33~1.2/bin/x64/R" CMD INSTALL -l "C:\Users\Yi Li\Documents\R\win-library\3.3" C:\Users\Yi Li\AppData\Local\Temp\RtmpasmgTS/downloaded_packages/airway_0.108.0.tar.gz' had status 1
2: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘airway’ had non-zero exit status

ADD REPLY • link 7.8 years ago liyi983923 • 0

score 1 · Answer 1 · 2017-01-29

1

Entering edit mode

Martin Morgan 25k

@martin-morgan-1513

Last seen 3 months ago

United States

R can sometimes have problems when directory names have spaces ("Yi Li"). You could try creating a temporary directory that does not have a space in the path and then

biocLite("airway", destdir="c:/Path/Without/Spaces")

(Note the direction of the slash in the path name, /)But if this works it is likely to require repeated application of the same solution; it would be better to have a user directory without a space in it.

ADD COMMENT • link 7.8 years ago Martin Morgan 25k

0

Entering edit mode

Hi Martin,

I reset the directory without a space and it works.

Thank you very much.

ADD REPLY • link 7.8 years ago liyi983923 • 0

0

Entering edit mode

I got the same error while installing "GenomeInfoDbData" . Got it solved by creating a directory and installing in it.

ADD REPLY • link 6.9 years ago fawazfebin ▴ 60