Hi, I am using a command similar to R --vanilla < script.R 2> STDERR > STDOUT to run some scripts. When I include the convert library, some messages go in STDERR and they are not related to any error. [boiseb01 at lw125 ~]$ echo "library(convert)" | R --vanilla 2> STDERR > STDOUT [boiseb01 at lw125 ~]$ cat STDERR Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()' or start with 'help(Biobase)'. For details on reading vignettes, see the openVignette help page. So I was wondering if this could be changed. Thank you! [boiseb01 at lw125 ~]$ cat /usr/lib64/R/library/convert/DESCRIPTION | grep Version Version: 1.4.0 [boiseb01 at lw125 ~]$ R --version | grep -i Version R version 2.3.0 (2006-04-24) [boiseb01 at lw125 ~]$ uname -rvsmop Linux 2.6.16-1.2111_FC5 #1 SMP Thu May 4 21:16:04 EDT 2006 x86_64 x86_64 GNU/Linux Thanks! -- _ S?bastien Boisvert, bioinformatics student ?v? bioinformatician -- Quebec Genomic Center /(_)\ www: http://pages.usherbrooke.ca/sebhtml/ ^ ^ Phone : 1 (418) 525 4444 #46333 Email : s at member.fsf.org

Agree. You can catch stderr and stdout in R using sink() and capture.output() - I think the latter only works for stdout though. /Henrik On 8/7/06, S?bastien Boisvert wrote: > Hi, > > I am using a command similar to > > R --vanilla < script.R 2> STDERR > STDOUT > > to run some scripts. When I include the convert library, some messages go in > STDERR and they are not related to any error. > > > > [boiseb01 at lw125 ~]$ echo "library(convert)" | R --vanilla 2> STDERR > STDOUT > [boiseb01 at lw125 ~]$ cat STDERR > > Welcome to Bioconductor > > Vignettes contain introductory material. To view, type > 'openVignette()' or start with 'help(Biobase)'. For details > on reading vignettes, see the openVignette help page. > > > > So I was wondering if this could be changed. Thank you! > > [boiseb01 at lw125 ~]$ cat /usr/lib64/R/library/convert/DESCRIPTION | grep Version > Version: 1.4.0 > > [boiseb01 at lw125 ~]$ R --version | grep -i Version > R version 2.3.0 (2006-04-24) > > [boiseb01 at lw125 ~]$ uname -rvsmop > Linux 2.6.16-1.2111_FC5 #1 SMP Thu May 4 21:16:04 EDT 2006 x86_64 x86_64 > GNU/Linux > > Thanks! > > -- > _ S?bastien Boisvert, bioinformatics student > ?v? bioinformatician -- Quebec Genomic Center > /(_)\ www: http://pages.usherbrooke.ca/sebhtml/ > ^ ^ Phone : 1 (418) 525 4444 #46333 > Email : s at member.fsf.org > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >

S?bastien Boisvert writes: > Hi, > > I am using a command similar to > > R --vanilla < script.R 2> STDERR > STDOUT > > to run some scripts. When I include the convert library, some messages go in > STDERR and they are not related to any error. > > > > [boiseb01 at lw125 ~]$ echo "library(convert)" | R --vanilla 2> STDERR > STDOUT > [boiseb01 at lw125 ~]$ cat STDERR > > Welcome to Bioconductor > > Vignettes contain introductory material. To view, type > 'openVignette()' or start with 'help(Biobase)'. For details > on reading vignettes, see the openVignette help page. > > > > So I was wondering if this could be changed. Thank you! The code producing that startup message in Biobase uses the message() function from base. This function writes output to STDERR. I'm not sure whether I think it makes sense or not, but it really is an R-devel issue. + seth