[BioC] compilation error for rtracklayer

[Martin Morgan]

I'd try to remove that -Dinline flag, or to set the optimization level 
to -O0. For the latter, download and unpack rtracklayer

   tar xzf rtracklayer_x.y.z.tar.gz

then create or edit a plain text file ~/.R/Makevars with

   CFLAGS=-O0

(that's 'Oh-zero') then

   R CMD INSTALL --preclean rtracklayer

Alternatively, to avoid -Dinline="' I think you need to edit 
rtracklayer/src/Makevars.common.

Martin

On 11/13/2011 11:38 AM, Michael Lawrence wrote:
> Well, no real idea here. My guess is that IRanges is bringing in one copy,
> and the UCSC stuff another.
>
> Michael
>
> On Sun, Nov 13, 2011 at 10:50 AM, rcaloger<raffaele.calogero at gmail.com>wrote:
>
>> 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<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<http://www.bioinformatica.unito.it>
>>
>> ______________________________**_________________
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