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Question: error in getBioC("exprs")
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gravatar for Robert Baertsch
13.0 years ago by
Robert Baertsch60 wrote:
I've gotten this error a few times. Each time I rerun getBioC("exprs") , it get past it and then it happens again. * DONE (multtest) [1] "Installation complete" Error in if ((is.null(deps)) || (length(deps) == 0) || (deps == "")) return(NULL) : missing value where TRUE/FALSE needed I'm running R 1.9.1 on linux compiled from source. -Robert
ADD COMMENTlink modified 13.0 years ago by michael watson IAH-C3.4k • written 13.0 years ago by Robert Baertsch60
0
gravatar for Jeff Gentry
13.0 years ago by
Jeff Gentry3.9k
Jeff Gentry3.9k wrote:
> I've gotten this error a few times. Each time I rerun getBioC("exprs") , > it get past it and then it happens again. Yes ... I've gotten a rash of these reports, have not been able to personally reproduce it. Originally the first couple of people were using Mac OS X, so thought it was a problem specific to that OS, but now have a few people using Win32 and Unix machines. I'm a bit baffled as everyone is using release side stuff, and nothing should have changed there, but clearly something is not right. Will let folks know ASAP when I figure something out. Thanks -J
ADD COMMENTlink written 13.0 years ago by Jeff Gentry3.9k
Hello ... For those of you experiencing errors with getBioC() using R-1.9.1 and release options, I believe that this problem has been solved. If you're still encountering any difficulties, just let me know. Thanks -Jeff
ADD REPLYlink written 13.0 years ago by Jeff Gentry3.9k
While you are at it, can you please allow people to install R without being root? Our sysadmin will install only RPMs and since bioconductor has no RPMS, all of the R users need to compile the source for R. It is a real pain and many long time R users are frustrated by it. What do you guys have to do something special? Every other unix app in the world has an RPM. RPM good. installation scripts bad. Get the picture. Jeff Gentry wrote: >>I've gotten this error a few times. Each time I rerun getBioC("exprs") , >>it get past it and then it happens again. >> >> > >Yes ... I've gotten a rash of these reports, have not been able to >personally reproduce it. Originally the first couple of people were using >Mac OS X, so thought it was a problem specific to that OS, but now have a >few people using Win32 and Unix machines. I'm a bit baffled as everyone >is using release side stuff, and nothing should have changed there, but >clearly something is not right. Will let folks know ASAP when I figure >something out. > >Thanks >-J > >
ADD REPLYlink written 13.0 years ago by Robert Baertsch60
> While you are at it, can you please allow people to install R without > being root? Our sysadmin will install only RPMs and since bioconductor Considering that I'm not a member of R-core, there's not a whole lot I can do to R "while I'm at it". You don't have to be root to install R. > has no RPMS, all of the R users need to compile the source for R. That's what I do. > It is a real pain and many long time R users are frustrated by it. What > do you guys have to do something special? Every other unix app in the > world has an RPM. Are you confusing R and Bioconductor? R is the application. You can install R without being root, obviously you can't install it as a RPM without being root. Bioconductor is just a set of packages for R. We happen to provide a script which is a wrapper around one of those packages (to provide bootstrapping), aka reposTools, which manages downloads and installations. Here's a hint: You can use a Root-installed R and still install these packages to any directory that you have permission to. The method of how to do this has been discussed on this list and the R-help list many times. Look at the .libPaths() function. > RPM good. > installation scripts bad. > Get the picture. We're an open development project. If you would like to provide and maintain an RPM of R with all of the Bioconductor packages built into it, and then keep it up to date - we'd welcome the contribution. Otherwise, there is absolutely *no* need to have R installed on your own just to install packages for R, Bioconductor or otherwise. -J
ADD REPLYlink written 13.0 years ago by Jeff Gentry3.9k
Robert Baertsch wrote: > While you are at it, can you please allow people to install R without > being root? Our sysadmin will install only RPMs and since > bioconductor has no RPMS, all of the R users need to compile the > source for R. > > It is a real pain and many long time R users are frustrated by it. > What do you guys have to do something special? Every other unix app in > the world has an RPM. There are RPMs for R. Please see http://cran.us.r-project.org/bin/linux In addition, this is the Bioconductor listserv. If you have requests for R-core, you might try the R-devel listserv: r-devel@stat.math.ethz.ch Jim > > RPM good. > installation scripts bad. > > Get the picture. > > Jeff Gentry wrote: > >>> I've gotten this error a few times. Each time I rerun >>> getBioC("exprs") , it get past it and then it happens again. >>> >> >> >> Yes ... I've gotten a rash of these reports, have not been able to >> personally reproduce it. Originally the first couple of people were >> using >> Mac OS X, so thought it was a problem specific to that OS, but now >> have a >> few people using Win32 and Unix machines. I'm a bit baffled as everyone >> is using release side stuff, and nothing should have changed there, but >> clearly something is not right. Will let folks know ASAP when I figure >> something out. >> >> Thanks >> -J >> >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor
ADD REPLYlink written 13.0 years ago by James W. MacDonald44k
Hello Group, How can I get RefSeq accession IDs instead of LocusLink IDs. >get("1000_at", env=hguav2LOCUSID) [1] 5595 Instead of one single probe, how can I get all 12,625 in RefSeq accession ID for hguav952. env=hguav2REFSEQ isnt working. Please help. Thank you. Robert Baertsch <baertsch@soe.ucsc.edu> wrote: While you are at it, can you please allow people to install R without being root? Our sysadmin will install only RPMs and since bioconductor has no RPMS, all of the R users need to compile the source for R. It is a real pain and many long time R users are frustrated by it. What do you guys have to do something special? Every other unix app in the world has an RPM. RPM good. installation scripts bad. Get the picture. Jeff Gentry wrote: >>I've gotten this error a few times. Each time I rerun getBioC("exprs") , >>it get past it and then it happens again. >> >> > >Yes ... I've gotten a rash of these reports, have not been able to >personally reproduce it. Originally the first couple of people were using >Mac OS X, so thought it was a problem specific to that OS, but now have a >few people using Win32 and Unix machines. I'm a bit baffled as everyone >is using release side stuff, and nothing should have changed there, but >clearly something is not right. Will let folks know ASAP when I figure >something out. > >Thanks >-J > > _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor --------------------------------- [[alternative HTML version deleted]]
ADD REPLYlink written 13.0 years ago by Ranga Chari40
You can download pre-compiled .rpm for R from CRAN eg. http://www.cran.mirrors.pair.com/bin/linux/ You should also note that not everybody in the world uses an RPM based Linux distribution. As for installing BioC as a non root user. Try setting the R_LIBS environment variable eg for bash export R_LIBS=/home/myaccount/MyRpacks thanks, Ben On Tue, 2004-08-24 at 11:10, Robert Baertsch wrote: > While you are at it, can you please allow people to install R without > being root? Our sysadmin will install only RPMs and since bioconductor > has no RPMS, all of the R users need to compile the source for R. > > It is a real pain and many long time R users are frustrated by it. What > do you guys have to do something special? Every other unix app in the > world has an RPM. > > RPM good. > installation scripts bad. > > Get the picture. > > Jeff Gentry wrote: > > >>I've gotten this error a few times. Each time I rerun getBioC("exprs") , > >>it get past it and then it happens again. > >> > >> > > > >Yes ... I've gotten a rash of these reports, have not been able to > >personally reproduce it. Originally the first couple of people were using > >Mac OS X, so thought it was a problem specific to that OS, but now have a > >few people using Win32 and Unix machines. I'm a bit baffled as everyone > >is using release side stuff, and nothing should have changed there, but > >clearly something is not right. Will let folks know ASAP when I figure > >something out. > > > >Thanks > >-J > > > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- Ben Bolstad <bolstad@stat.berkeley.edu> http://www.stat.berkeley.edu/~bolstad
ADD REPLYlink written 13.0 years ago by Ben Bolstad1.1k
thanks Ben, export R_LIBS sounds like a good solution. I will try it. Ben Bolstad wrote: >You can download pre-compiled .rpm for R from CRAN eg. > >http://www.cran.mirrors.pair.com/bin/linux/ > >You should also note that not everybody in the world uses an RPM based >Linux distribution. > >As for installing BioC as a non root user. Try setting the R_LIBS >environment variable eg for bash > >export R_LIBS=/home/myaccount/MyRpacks > >thanks, > >Ben > > > >On Tue, 2004-08-24 at 11:10, Robert Baertsch wrote: > > >>While you are at it, can you please allow people to install R without >>being root? Our sysadmin will install only RPMs and since bioconductor >>has no RPMS, all of the R users need to compile the source for R. >> >>It is a real pain and many long time R users are frustrated by it. What >>do you guys have to do something special? Every other unix app in the >>world has an RPM. >> >>RPM good. >>installation scripts bad. >> >>Get the picture. >> >>Jeff Gentry wrote: >> >> >> >>>>I've gotten this error a few times. Each time I rerun getBioC("exprs") , >>>>it get past it and then it happens again. >>>> >>>> >>>> >>>> >>>Yes ... I've gotten a rash of these reports, have not been able to >>>personally reproduce it. Originally the first couple of people were using >>>Mac OS X, so thought it was a problem specific to that OS, but now have a >>>few people using Win32 and Unix machines. I'm a bit baffled as everyone >>>is using release side stuff, and nothing should have changed there, but >>>clearly something is not right. Will let folks know ASAP when I figure >>>something out. >>> >>>Thanks >>>-J >>> >>> >>> >>> >>_______________________________________________ >>Bioconductor mailing list >>Bioconductor@stat.math.ethz.ch >>https://stat.ethz.ch/mailman/listinfo/bioconductor >> >>
ADD REPLYlink written 13.0 years ago by Robert Baertsch60
0
gravatar for A.J. Rossini
13.0 years ago by
A.J. Rossini810
A.J. Rossini810 wrote:
You can compile R without being root. Why not just do that? i.e. unpack, then ./configure --prefix=/home/your/placement/directory for example... best, -tony Robert Baertsch <baertsch@soe.ucsc.edu> writes: > While you are at it, can you please allow people to install R without > being root? Our sysadmin will install only RPMs and since > bioconductor has no RPMS, all of the R users need to compile the > source for R. > > It is a real pain and many long time R users are frustrated by it. > What do you guys have to do something special? Every other unix app in > the world has an RPM. > > RPM good. > installation scripts bad. > > Get the picture. > > Jeff Gentry wrote: > >>> I've gotten this error a few times. Each time I rerun >>> getBioC("exprs") , it get past it and then it happens again. >>> >>> >> >>Yes ... I've gotten a rash of these reports, have not been able to >>personally reproduce it. Originally the first couple of people were using >>Mac OS X, so thought it was a problem specific to that OS, but now have a >>few people using Win32 and Unix machines. I'm a bit baffled as everyone >>is using release side stuff, and nothing should have changed there, but >>clearly something is not right. Will let folks know ASAP when I figure >>something out. >> >>Thanks >>-J >> >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > -- Anthony Rossini Research Associate Professor rossini@u.washington.edu http://www.analytics.washington.edu/ Biomedical and Health Informatics University of Washington Biostatistics, SCHARP/HVTN Fred Hutchinson Cancer Research Center UW (Tu/Th/F): 206-616-7630 FAX=206-543-3461 | Voicemail is unreliable FHCRC (M/W): 206-667-7025 FAX=206-667-4812 | use Email CONFIDENTIALITY NOTICE: This e-mail message and any attachme...{{dropped}}
ADD COMMENTlink written 13.0 years ago by A.J. Rossini810
We have R installed with RPMs (by root), sorry for the confusion. My request was for a RPM install of bioconductor. I guess that is not possible. When I tried to install bioconductor myself, I got a permission problem with /usr/lib since it is root owned. Can someone tell my how to use the .libPath command to get around that? Better yet, it would be nice if these incantations were on the bioconductor website. -Robert A.J. Rossini wrote: >You can compile R without being root. Why not just do that? > >i.e. > > unpack, then ./configure --prefix=/home/your/placement/directory > >for example... > >best, >-tony > > >Robert Baertsch <baertsch@soe.ucsc.edu> writes: > > > >>While you are at it, can you please allow people to install R without >>being root? Our sysadmin will install only RPMs and since >>bioconductor has no RPMS, all of the R users need to compile the >>source for R. >> >>It is a real pain and many long time R users are frustrated by it. >>What do you guys have to do something special? Every other unix app in >>the world has an RPM. >> >>RPM good. >>installation scripts bad. >> >>Get the picture. >> >>Jeff Gentry wrote: >> >> >> >>>>I've gotten this error a few times. Each time I rerun >>>>getBioC("exprs") , it get past it and then it happens again. >>>> >>>> >>>> >>>> >>>Yes ... I've gotten a rash of these reports, have not been able to >>>personally reproduce it. Originally the first couple of people were using >>>Mac OS X, so thought it was a problem specific to that OS, but now have a >>>few people using Win32 and Unix machines. I'm a bit baffled as everyone >>>is using release side stuff, and nothing should have changed there, but >>>clearly something is not right. Will let folks know ASAP when I figure >>>something out. >>> >>>Thanks >>>-J >>> >>> >>> >>> >>_______________________________________________ >>Bioconductor mailing list >>Bioconductor@stat.math.ethz.ch >>https://stat.ethz.ch/mailman/listinfo/bioconductor >> >> >> > > >
ADD REPLYlink written 13.0 years ago by Robert Baertsch60
Robert Baertsch wrote: > We have R installed with RPMs (by root), sorry for the confusion. My > request was for a RPM install of bioconductor. I guess that is not > possible. > > When I tried to install bioconductor myself, I got a permission problem > with /usr/lib since it is root owned. > > Can someone tell my how to use the .libPath command to get around that? .libPaths("/somewhere/you/have/write/access") Note that this only affects the current R session. You will have to either follow Ben Bolstad's suggestion or put the .libPath() command in either an .Rprofile or .First file. Please see ?.libPaths and ?.Rprofile for more information. Best, Jim -- James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109
ADD REPLYlink written 13.0 years ago by James W. MacDonald44k
0
gravatar for A.J. Rossini
13.0 years ago by
A.J. Rossini810
A.J. Rossini810 wrote:
Robert Baertsch <baertsch@soe.ucsc.edu> writes: > Better yet, it would be nice if these incantations were on the > bioconductor website. We are waiting for someone to write them! Alternatively, I thought that a BioC-installer package for Debian exists (at least on the recent Quantian bootable DVDs, I think). best, -tony -- Anthony Rossini Research Associate Professor rossini@u.washington.edu http://www.analytics.washington.edu/ Biomedical and Health Informatics University of Washington Biostatistics, SCHARP/HVTN Fred Hutchinson Cancer Research Center UW (Tu/Th/F): 206-616-7630 FAX=206-543-3461 | Voicemail is unreliable FHCRC (M/W): 206-667-7025 FAX=206-667-4812 | use Email CONFIDENTIALITY NOTICE: This e-mail message and any attachme...{{dropped}}
ADD COMMENTlink written 13.0 years ago by A.J. Rossini810
0
gravatar for michael watson IAH-C
13.0 years ago by
michael watson IAH-C3.4k wrote:
>RPM good. >installation scripts bad. >Get the picture. To be honest, I've had nothing but trouble with RPMs and always install from source. The Marlboro man wouldn't use RPMs. John Wayne wouldn't use RPMs. Be a real man, install from source ;-)
ADD COMMENTlink written 13.0 years ago by michael watson IAH-C3.4k
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