[BioC] compilation error for rtracklayer

rcaloger raffaele.calogero at gmail.com
Sun Nov 13 19:50:11 CET 2011


Dear all,
I am trying to install rtracklayer on my server running linux suse 
enterprise 10
any suggestion how to solve the problem?
cheers
raffaele

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

gcc -std=gnu99 -I/home/calogero/bin/R-2.14.0/lib64/R/include 
-D_FILE_OFFSET_BITS=64 -I/usr/local/include 
-I"/mnt/raidDisk/calogero/Documents/bin/R-2.14.0/lib64/R/library/IRanges/include" 
-g -Dinline="" -fpic -g -O2 -c ucsc/udc.c -o ucsc/udc.o
ucsc/udc.c: In function ‘udcInfoViaHttp’:
ucsc/udc.c:405: warning: implicit declaration of function ‘strptime’
ucsc/udc.c:405: warning: comparison between pointer and integer
......
/usr/local/lib/gcc/x86_64-unknown-linux-gnu/4.4.1/include-fixed/bits/string2.h:1235: 
multiple definition of `__strsep_1c'
IRanges_stubs.o:/usr/local/lib/gcc/x86_64-unknown-linux-gnu/4.4.1/include-fixed/bits/string2.h:1235: 
first defined here
collect2: ld returned 1 exit status
make: *** [rtracklayer.so] Error 1
ERROR: compilation failed for package ‘rtracklayer’
* removing 
‘/mnt/raidDisk/calogero/Documents/bin/R-2.14.0/lib64/R/library/rtracklayer’

The downloaded packages are in
‘/tmp/RtmpbcA6gw/downloaded_packages’
Warning message:
In install.packages(pkgs = pkgs, repos = repos, ...) :
installation of package ‘rtracklayer’ had non-zero exit status


The IRanges


 > sessionInfo()
R version 2.14.0 (2011-10-31)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] BiocInstaller_1.2.1

loaded via a namespace (and not attached):
[1] tools_2.14.0
 >

-- 

----------------------------------------
Prof. Raffaele A. Calogero
Bioinformatics and Genomics Unit
MBC Centro di Biotecnologie Molecolari
Via Nizza 52, Torino 10126
tel.   ++39 0116706457
Fax    ++39 0112366457
Mobile ++39 3333827080
email: raffaele.calogero at unito.it
        raffaele[dot]calogero[at]gmail[dot]com
www:   http://www.bioinformatica.unito.it



More information about the Bioconductor mailing list