error in GenomicRanges package

[meghavarshney]

hii everyone,

i was working with this package so i got some error

> library("GenomicFeatures")
> testFile <- system.file("bam", "accepted_hits.bam", package = "leeBamViews")
> aligns <- readBamGappedAlignments(testFile)
Error: could not find function "readBamGappedAlignments"

after that i tried to install this package to overcome this problem. but i was not able to do so

> source("http://bioconductor.org/biocLite.R")
Bioconductor version 3.2 (BiocInstaller 1.19.6), ?biocLite for help
> biocLite("GenomicRanges")
BioC_mirror: http://bioconductor.org
Using Bioconductor 3.2 (BiocInstaller 1.19.6), R 3.2.0 (2015-04-16).
Installing package(s) ‘GenomicRanges’
trying URL 'http://bioconductor.org/packages/3.2/bioc/src/contrib/GenomicRanges_1.21.16.tar.gz'
Content type 'application/x-gzip' length 906397 bytes (885 KB)
==================================================
downloaded 885 KB

* installing *source* package ‘GenomicRanges’ ...
** libs
gcc -std=gnu99 -I/usr/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/usr/local/lib64/R/library/S4Vectors/include" -I"/usr/local/lib64/R/library/IRanges/include"   -fpic  -g -O2  -c IRanges_stubs.c -o IRanges_stubs.o
gcc -std=gnu99 -I/usr/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/usr/local/lib64/R/library/S4Vectors/include" -I"/usr/local/lib64/R/library/IRanges/include"   -fpic  -g -O2  -c R_init_GenomicRanges.c -o R_init_GenomicRanges.o
gcc -std=gnu99 -I/usr/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/usr/local/lib64/R/library/S4Vectors/include" -I"/usr/local/lib64/R/library/IRanges/include"   -fpic  -g -O2  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -std=gnu99 -I/usr/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/usr/local/lib64/R/library/S4Vectors/include" -I"/usr/local/lib64/R/library/IRanges/include"   -fpic  -g -O2  -c transcript_utils.c -o transcript_utils.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o GenomicRanges.so IRanges_stubs.o R_init_GenomicRanges.o S4Vectors_stubs.o transcript_utils.o
installing to /usr/local/lib64/R/library/GenomicRanges/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GenomicRanges)

The downloaded source packages are in
	‘/tmp/RtmpbPM2YS/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Old packages: 'survival'
Update all/some/none? [a/s/n]: a
trying URL 'http://cran.fhcrc.org/src/contrib/survival_2.38-3.tar.gz'
Error in download.file(url, destfile, method, mode = "wb", ...) : 
  cannot open URL 'http://cran.fhcrc.org/src/contrib/survival_2.38-3.tar.gz'
In addition: Warning message:
In download.file(url, destfile, method, mode = "wb", ...) :
  cannot open: HTTP status was '0 (null)'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package ‘survival’ failed
> install.package("GenomicRanges")
Error: could not find function "install.package"
> install.packages("GenomicRanges")
--- Please select a CRAN mirror for use in this session ---
Warning message:
package ‘GenomicRanges’ is not available (for R version 3.2.0)

so will you please give me some suggestion in this.


thanks

[meghavarshney]

get resolved

this problem is also get resolved after i replace the older version of survival package wid the latest one

Old packages: 'survival'
Update all/some/none? [a/s/n]: a
trying URL 'http://cran.fhcrc.org/src/contrib/survival_2.38-3.tar.gz'
Error in download.file(url, destfile, method, mode = "wb", ...) : 
  cannot open URL 'http://cran.fhcrc.org/src/contrib/survival_2.38-3.tar.gz'

[maxsalm]

Hi there,

I believe that function has been deprecated, and been replaced with readGAlignmentsFromBam() - see here for more details: https://support.bioconductor.org/p/61854/