Benilton, absolutely no problem at all, I have the release version
available, I was just doing a little testing and hoped my feedback would be
helpful. Thanks for your efforts on this valuable package!

Mark

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


On Sat, Dec 5, 2009 at 12:08 AM, Benilton Carvalho <bcarvalh@jhsph.edu>wrote:

> 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
> >
> >        [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > Bioc-devel@stat.math.ethz.ch mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>

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