[Bioc-devel] package "oligo" fails to build on R-devel using 64-bit Ubuntu 9.10 Karmic Koala

[Benilton Carvalho]

Hi Mark,

Apologies for the inconvenience this may cause. We've been working on oligo & friends, implementing changes that will simplify usage and improve user's experience.

Slowly things are falling back in place: earlier today I committed changes that address some of the problems below. And I believe that this particular version isn't yet visible for most of the users, although you will be able to get it straight from the svn server.

In the meantime, I hope that oligo on the release branch is sufficient for your tasks.

Cheers,

b

On Dec 5, 2009, at 2:40 AM, Mark Kimpel wrote:

> Today I installed the current R-devel for the first time and all packages
> build except "oligo" and a couple packages that depend on it. Below is my
> buid output followed by sessionInfo(). Please let me know if I can provide
> any other information that might be helpful. Thanks,
> D
> Mark
> 
> downloaded 696 Kb
> 
> Loading required package: utils
> * installing *source* package ‘oligo’ ...
> ** libs
> gcc -std=gnu99 -I/home/mkimpel/R_HOME/R-devel/R-build/lib64/R/include
> -I/usr/local/include
> -I"/home/mkimpel/R_HOME/site-library-2.11.0/preprocessCore/include"   -fpic
> -g -O2 -c ParserXYS.c -o ParserXYS.o
> ParserXYS.c: In function ‘xys_header_field’:
> ParserXYS.c:144: warning: ignoring return value of ‘fgets’, declared with
> attribute warn_unused_result
> ParserXYS.c: In function ‘R_read_xys_header’:
> ParserXYS.c:318: warning: ignoring return value of ‘fgets’, declared with
> attribute warn_unused_result
> gcc -std=gnu99 -I/home/mkimpel/R_HOME/R-devel/R-build/lib64/R/include
> -I/usr/local/include
> -I"/home/mkimpel/R_HOME/site-library-2.11.0/preprocessCore/include"   -fpic
> -g -O2 -c baseProfile.c -o baseProfile.o
> gcc -std=gnu99 -I/home/mkimpel/R_HOME/R-devel/R-build/lib64/R/include
> -I/usr/local/include
> -I"/home/mkimpel/R_HOME/site-library-2.11.0/preprocessCore/include"   -fpic
> -g -O2 -c basecontent.c -o basecontent.o
> gcc -std=gnu99 -I/home/mkimpel/R_HOME/R-devel/R-build/lib64/R/include
> -I/usr/local/include
> -I"/home/mkimpel/R_HOME/site-library-2.11.0/preprocessCore/include"   -fpic
> -g -O2 -c rma2.c -o rma2.o
> gcc -std=gnu99 -I/home/mkimpel/R_HOME/R-devel/R-build/lib64/R/include
> -I/usr/local/include
> -I"/home/mkimpel/R_HOME/site-library-2.11.0/preprocessCore/include"   -fpic
> -g -O2 -c rma_common.c -o rma_common.o
> gcc -std=gnu99 -I/home/mkimpel/R_HOME/R-devel/R-build/lib64/R/include
> -I/usr/local/include
> -I"/home/mkimpel/R_HOME/site-library-2.11.0/preprocessCore/include"   -fpic
> -g -O2 -c trimmed.c -o trimmed.o
> gcc -std=gnu99 -shared -L/usr/local/lib64 -o oligo.so ParserXYS.o
> baseProfile.o basecontent.o rma2.o rma_common.o trimmed.o
> ** R
> ** inst
> ** preparing package for lazy loading
> Loading required package: Biobase
> 
> Welcome to Bioconductor
> 
>  Vignettes contain introductory material. To view, type
>  'openVignette()'. To cite Bioconductor, see
>  'citation("Biobase")' and for packages 'citation(pkgname)'.
> 
> Error in setMethod("pmSequence", "FeatureSet", function(object)
> pmSequence(getPD(object))) :
>  no existing definition for function "pmSequence"
> Error : unable to load R code in package 'oligo'
> ERROR: lazy loading failed for package ‘oligo’
> * removing ‘/home/mkimpel/R_HOME/site-library-2.11.0/oligo’
> 
> The downloaded packages are in
> ‘/tmp/RtmpTF8R6F/downloaded_packages’
> Warning message:
> In install.packages(pkgs = pkgs, repos = repos, ...) :
>  installation of package 'oligo' had non-zero exit status
>> sessionInfo()
> R version 2.11.0 Under development (unstable) (2009-12-03 r50653)
> x86_64-unknown-linux-gnu
> 
> 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=C              LC_MESSAGES=en_US.UTF-8
> [7] LC_PAPER=en_US.UTF-8       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 datasets  utils     methods   base
> 
> other attached packages:
> [1] Biobase_2.7.0
> 
> loaded via a namespace (and not attached):
> [1] tools_2.11.0
> 
> Mark W. Kimpel MD  ** Neuroinformatics ** Dept. of Psychiatry
> Indiana University School of Medicine
> 
> 15032 Hunter Court, Westfield, IN  46074
> 
> (317) 490-5129 Work, & Mobile & VoiceMail
> (317) 399-1219 Skype No Voicemail please
> 
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