Question: Building BioC 2.2 with R 2.7.0
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gravatar for Atro Tossavainen
11.5 years ago by
Atro Tossavainen160 wrote:
I've successfully built R 2.7.0 for x86 Linux (RHEL4), x86_64 Linux (RHEL4), Solaris 8 SPARC and IRIX 6.5. The Bioconductor installation process works fine on x86_64 Linux and IRIX. Building annaffy fails on x86 Linux, and building annaffy and simpleaffy fail on Solaris 8. In both cases, the annaffy error message is as follows: Loading required package: GO.db Loading required package: AnnotationDbi Loading required package: DBI Loading required package: RSQLite Error in sqliteExecStatement(con, statement, bind.data) : RS-DBI driver: (error in statement: no such table: metadata) Error : .onLoad failed in 'loadNamespace' for 'GO.db' Error: package 'GO.db' could not be loaded Execution halted ERROR: lazy loading failed for package 'annaffy' ** Removing '/.../R/2.7.0/lib/R/library/annaffy' The simpleaffy installation attempt ends with: Loading required package: splines Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared library '/.../R/2.7.0/lib/R/library/genefilter/libs/genefilter.so': ld.so.1: /.../R/2.7.0/lib. at sys/R/bin/exec/R: fatal: relocation error: file /.../R/2.7.0/lib/R/library/genefilter/libs/genefilter.so: symbol __1cDstdJexceptionG__vtbl_: referenced symbol not found Error: package 'genefilter' could not be loaded Execution halted ERROR: lazy loading failed for package 'simpleaffy' ** Removing '/.../R/2.7.0/lib/R/library/simpleaffy' All help appreciated. -- Atro Tossavainen (Mr.) / The Institute of Biotechnology at Systems Analyst, Techno-Amish & / the University of Helsinki, Finland, +358-9-19158939 UNIX Dinosaur / employs me, but my opinions are my own. < URL : http : / / www . helsinki . fi / %7E atossava / > NO FILE ATTACHMENTS
go annaffy simpleaffy • 767 views
ADD COMMENTlink modified 11.5 years ago by Groot, Philip de630 • written 11.5 years ago by Atro Tossavainen160
Answer: Building BioC 2.2 with R 2.7.0
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gravatar for Kasper Daniel Hansen
11.5 years ago by
United States
Kasper Daniel Hansen6.4k wrote:
The first thing to understand is that in some case R CMD INSTALL can seem sucessful, but when you to to do the librray command from within R it fails, ie. R> library(SOMEPACKAGE) This typically happens when a package is dynamically linked to something that R cannot find when it tries to load the package. Now, the slightly confusing issue that may happen is that when package XX depends on package YY, R will try to load the YY package when it tries to install XX. So if YY has the problem I just mention you will not discover it when you install YY but rather when you install something that depends on YY. See below for rest of comments On May 26, 2008, at 4:03 AM, Atro Tossavainen wrote: > I've successfully built R 2.7.0 for x86 Linux (RHEL4), x86_64 Linux > (RHEL4), Solaris 8 SPARC and IRIX 6.5. The Bioconductor installation > process works fine on x86_64 Linux and IRIX. > > Building annaffy fails on x86 Linux, and building annaffy and > simpleaffy > fail on Solaris 8. In both cases, the annaffy error message is as > follows: > > Loading required package: GO.db > Loading required package: AnnotationDbi > Loading required package: DBI > Loading required package: RSQLite > Error in sqliteExecStatement(con, statement, bind.data) : > RS-DBI driver: (error in statement: no such table: metadata) > Error : .onLoad failed in 'loadNamespace' for 'GO.db' > Error: package 'GO.db' could not be loaded > Execution halted > ERROR: lazy loading failed for package 'annaffy' > ** Removing '/.../R/2.7.0/lib/R/library/annaffy' Here it seems like you GO.db installation is wrong. This is not a dynamically linked issue, but something else. My guess is that you have some version mismatch. > > The simpleaffy installation attempt ends with: > > Loading required package: splines > Error in dyn.load(file, DLLpath = DLLpath, ...) : > unable to load shared library '/.../R/2.7.0/lib/R/library/ > genefilter/libs/genefilter.so': > ld.so.1: /.../R/2.7.0/lib. at sys/R/bin/exec/R: fatal: relocation > error: file /.../R/2.7.0/lib/R/library/genefilter/libs/ > genefilter.so: symbol __1cDstdJexceptionG__vtbl_: referenced symbol > not found > Error: package 'genefilter' could not be loaded > Execution halted > ERROR: lazy loading failed for package 'simpleaffy' > ** Removing '/.../R/2.7.0/lib/R/library/simpleaffy' Looking at the error, it happens when you try to load genefilter. I will bet that if you open up R and do R> library(genefilter) you will get the same error. Now, why genefilter does not install properly, I have no idea about. > All help appreciated. > > -- > Atro Tossavainen (Mr.) / The Institute of > Biotechnology at > Systems Analyst, Techno-Amish & / the University of Helsinki, > Finland, > +358-9-19158939 UNIX Dinosaur / employs me, but my opinions are > my own. > < URL : http : / / www . helsinki . fi / %7E atossava / > NO FILE > ATTACHMENTS > > _______________________________________________ > 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
ADD COMMENTlink written 11.5 years ago by Kasper Daniel Hansen6.4k
Hi all, Kasper Daniel Hansen wrote: > The first thing to understand is that in some case R CMD INSTALL can > seem sucessful, but when you to to do the librray command from within R > it fails, ie. > > R> library(SOMEPACKAGE) > > This typically happens when a package is dynamically linked to something > that R cannot find when it tries to load the package. Now, the slightly > confusing issue that may happen is that when package XX depends on > package YY, R will try to load the YY package when it tries to install > XX. So if YY has the problem I just mention you will not discover it > when you install YY but rather when you install something that depends > on YY. > > See below for rest of comments > > On May 26, 2008, at 4:03 AM, Atro Tossavainen wrote: > >> I've successfully built R 2.7.0 for x86 Linux (RHEL4), x86_64 Linux >> (RHEL4), Solaris 8 SPARC and IRIX 6.5. The Bioconductor installation >> process works fine on x86_64 Linux and IRIX. >> >> Building annaffy fails on x86 Linux, and building annaffy and simpleaffy >> fail on Solaris 8. In both cases, the annaffy error message is as >> follows: >> >> Loading required package: GO.db >> Loading required package: AnnotationDbi >> Loading required package: DBI >> Loading required package: RSQLite >> Error in sqliteExecStatement(con, statement, bind.data) : >> RS-DBI driver: (error in statement: no such table: metadata) My guess is that Kasper is pretty close, but that the real culprit is RSQLite. But without a complete log of what did and did not install we won't know. So, if you could, please try library(RSQLite) and library(GO) and let us know which of them fails? Depending on the outcome of that, you might then try to install as described on the download instructions - via biocLite (as you may also have version mismatches, which we can't know about from the output given). If you did not use biocLite please do, it is intended to help avoid just these issues. >> Error : .onLoad failed in 'loadNamespace' for 'GO.db' >> Error: package 'GO.db' could not be loaded >> Execution halted >> ERROR: lazy loading failed for package 'annaffy' >> ** Removing '/.../R/2.7.0/lib/R/library/annaffy' > > Here it seems like you GO.db installation is wrong. This is not a > dynamically linked issue, but something else. My guess is that you have > some version mismatch. > >> >> The simpleaffy installation attempt ends with: >> >> Loading required package: splines >> Error in dyn.load(file, DLLpath = DLLpath, ...) : >> unable to load shared library >> '/.../R/2.7.0/lib/R/library/genefilter/libs/genefilter.so': >> ld.so.1: /.../R/2.7.0/lib. at sys/R/bin/exec/R: fatal: relocation error: >> file /.../R/2.7.0/lib/R/library/genefilter/libs/genefilter.so: symbol >> __1cDstdJexceptionG__vtbl_: referenced symbol not found >> Error: package 'genefilter' could not be loaded >> Execution halted >> ERROR: lazy loading failed for package 'simpleaffy' >> ** Removing '/.../R/2.7.0/lib/R/library/simpleaffy' This looks a lot like you did not reinstall genefilter, or if you did, then perhaps you did not use biocLite. Using ldd on R/2.7.0/lib/R/library/genefilter/libs/genefilter.so might reveal what library is missing - but it is typically hard to get this kind of failure, without doing fairly odd things, and the best advice is to do something like: biocLite("genefilter") and then see if it fails to install properly - report back if it fails, with complete details of what you typed and what you got - and we might be able to help. best wishes Robert > > Looking at the error, it happens when you try to load genefilter. I will > bet that if you open up R and do > R> library(genefilter) > you will get the same error. > > Now, why genefilter does not install properly, I have no idea about. > > >> All help appreciated. >> >> -- >> Atro Tossavainen (Mr.) / The Institute of Biotechnology at >> Systems Analyst, Techno-Amish & / the University of Helsinki, >> Finland, >> +358-9-19158939 UNIX Dinosaur / employs me, but my opinions are >> my own. >> < URL : http : / / www . helsinki . fi / %7E atossava / > NO FILE >> ATTACHMENTS >> >> _______________________________________________ >> 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 > > _______________________________________________ > 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 > -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 rgentlem at fhcrc.org
ADD REPLYlink written 11.5 years ago by rgentleman5.5k
Thanks all for your help so far. > My guess is that Kasper is pretty close, but that the real culprit is > RSQLite. But without a complete log of what did and did not install we > won't know. > > So, if you could, please try > library(RSQLite) Loading RSQLite on both Solaris 8 and x86 Linux (RHEL4) produces the expected results: Loading required package: DBI (back to prompt) > and > > library(GO) Error in library(GO) : there is no package called 'GO' That's in fact what it says on the other platforms as well where the whole installation of Bioconductor seemed to work properly. But now that GO has finished installing on the other two, I see that --------- The package 'GO' is deprecated and will not be supported in the future. Instead we strongly reccomend that you should start using the 'GO.db' package. --------- Oh well. However, trying to execute library(GO.db) fails on the two platforms as described earlier: > library(GO.db) Loading required package: AnnotationDbi Loading required package: Biobase Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation(pkgname)'. Loading required package: DBI Loading required package: RSQLite Error in sqliteExecStatement(con, statement, bind.data) : RS-DBI driver: (error in statement: no such table: metadata) Error : .onLoad failed in 'loadNamespace' for 'GO.db' Error: package/namespace load failed for 'GO.db' (The error message is identical on both. Loading GO.db works fine on IRIX and x86_64 RHEL4, as stated before.) > Depending on the outcome of that, you might then try to install as > described on the download instructions - via biocLite (as you may also > have version mismatches, which we can't know about from the output given). I'm installing from scratch. I always do. The directory that I installed R 2.7.0 into has no previous content at all, so although I've got a working copy of an earlier version of R and associated Bioconductor somewhere, they're elsewhere and should not be being looked into at all. I wouldn't even dream of trying to upgrade over a known working configuration, that's suicidal. :-) > If you did not use biocLite please do, it is intended to help avoid > just these issues. I did precisely that: source("http://bioconductor.org/biocLite.R") biocLite() and NOTHING else to begin with. > > Here it seems like you GO.db installation is wrong. This is not a > > dynamically linked issue, but something else. My guess is that you have > > some version mismatch. It shouldn't be possible. I'll try to reinstall GO.db on the affected platforms with biocLite("GO.db") and see how it goes. It works now. I don't understand why, but it's good enough. > This looks a lot like you did not reinstall genefilter, or if you > did, then perhaps you did not use biocLite. I did (assuming "biocLite()" does), and I did. > Using ldd on > R/2.7.0/lib/R/library/genefilter/libs/genefilter.so > might reveal what library is missing All library references in genefilter.so resolve properly. > biocLite("genefilter") > > and then see if it fails to install properly - report back if it > fails, with complete details of what you typed and what you got - and we > might be able to help. I'll try that and report back. -- Atro Tossavainen (Mr.) / The Institute of Biotechnology at Systems Analyst, Techno-Amish & / the University of Helsinki, Finland, +358-9-19158939 UNIX Dinosaur / employs me, but my opinions are my own. < URL : http : / / www . helsinki . fi / %7E atossava / > NO FILE ATTACHMENTS
ADD REPLYlink written 11.5 years ago by Atro Tossavainen160
Answer: Building BioC 2.2 with R 2.7.0
0
gravatar for Groot, Philip de
11.5 years ago by
Groot, Philip de630 wrote:
Hello all, I encountered the same problem with genefilter. Genefilter depends on tkWidgets which in turn depends on access to the x-server (stupid, but this is true for several Bioconductor packages now; it's rather annoying). So: use the xhost command to properly arrange your X display properties and the genefilter problem might be solved. Regards, Dr. Philip de Groot Wageningen University ________________________________ From: Robert Gentleman [mailto:rgentlem@fhcrc.org] Sent: Mon 26/05/2008 10:36 PM To: Kasper Daniel Hansen Cc: Atro.Tossavainen at helsinki.fi; bioconductor at stat.math.ethz.ch Subject: Re: [BioC] Building BioC 2.2 with R 2.7.0 Hi all, Kasper Daniel Hansen wrote: > The first thing to understand is that in some case R CMD INSTALL can > seem sucessful, but when you to to do the librray command from within R > it fails, ie. > > R> library(SOMEPACKAGE) > > This typically happens when a package is dynamically linked to something > that R cannot find when it tries to load the package. Now, the slightly > confusing issue that may happen is that when package XX depends on > package YY, R will try to load the YY package when it tries to install > XX. So if YY has the problem I just mention you will not discover it > when you install YY but rather when you install something that depends > on YY. > > See below for rest of comments > > On May 26, 2008, at 4:03 AM, Atro Tossavainen wrote: > >> I've successfully built R 2.7.0 for x86 Linux (RHEL4), x86_64 Linux >> (RHEL4), Solaris 8 SPARC and IRIX 6.5. The Bioconductor installation >> process works fine on x86_64 Linux and IRIX. >> >> Building annaffy fails on x86 Linux, and building annaffy and simpleaffy >> fail on Solaris 8. In both cases, the annaffy error message is as >> follows: >> >> Loading required package: GO.db >> Loading required package: AnnotationDbi >> Loading required package: DBI >> Loading required package: RSQLite >> Error in sqliteExecStatement(con, statement, bind.data) : >> RS-DBI driver: (error in statement: no such table: metadata) My guess is that Kasper is pretty close, but that the real culprit is RSQLite. But without a complete log of what did and did not install we won't know. So, if you could, please try library(RSQLite) and library(GO) and let us know which of them fails? Depending on the outcome of that, you might then try to install as described on the download instructions - via biocLite (as you may also have version mismatches, which we can't know about from the output given). If you did not use biocLite please do, it is intended to help avoid just these issues. >> Error : .onLoad failed in 'loadNamespace' for 'GO.db' >> Error: package 'GO.db' could not be loaded >> Execution halted >> ERROR: lazy loading failed for package 'annaffy' >> ** Removing '/.../R/2.7.0/lib/R/library/annaffy' > > Here it seems like you GO.db installation is wrong. This is not a > dynamically linked issue, but something else. My guess is that you have > some version mismatch. > >> >> The simpleaffy installation attempt ends with: >> >> Loading required package: splines >> Error in dyn.load(file, DLLpath = DLLpath, ...) : >> unable to load shared library >> '/.../R/2.7.0/lib/R/library/genefilter/libs/genefilter.so': >> ld.so.1: /.../R/2.7.0/lib. at sys/R/bin/exec/R: fatal: relocation error: >> file /.../R/2.7.0/lib/R/library/genefilter/libs/genefilter.so: symbol >> __1cDstdJexceptionG__vtbl_: referenced symbol not found >> Error: package 'genefilter' could not be loaded >> Execution halted >> ERROR: lazy loading failed for package 'simpleaffy' >> ** Removing '/.../R/2.7.0/lib/R/library/simpleaffy' This looks a lot like you did not reinstall genefilter, or if you did, then perhaps you did not use biocLite. Using ldd on R/2.7.0/lib/R/library/genefilter/libs/genefilter.so might reveal what library is missing - but it is typically hard to get this kind of failure, without doing fairly odd things, and the best advice is to do something like: biocLite("genefilter") and then see if it fails to install properly - report back if it fails, with complete details of what you typed and what you got - and we might be able to help. best wishes Robert > > Looking at the error, it happens when you try to load genefilter. I will > bet that if you open up R and do > R> library(genefilter) > you will get the same error. > > Now, why genefilter does not install properly, I have no idea about. > > >> All help appreciated. >> >> -- >> Atro Tossavainen (Mr.) / The Institute of Biotechnology at >> Systems Analyst, Techno-Amish & / the University of Helsinki, >> Finland, >> +358-9-19158939 UNIX Dinosaur / employs me, but my opinions are >> my own. >> < URL : http : / / www . helsinki . fi / %7E atossava / > NO FILE >> ATTACHMENTS >> >> _______________________________________________ >> 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 > > _______________________________________________ > 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 > -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 rgentlem at fhcrc.org
ADD COMMENTlink written 11.5 years ago by Groot, Philip de630
> I encountered the same problem with genefilter. Genefilter depends on > tkWidgets which in turn depends on access to the x-server (stupid, but > this is true for several Bioconductor packages now; it's rather annoying). > So: use the xhost command to properly arrange your X display properties > and the genefilter problem might be solved. I neglected to mention (as I didn't see it being related at all) that all of my sessions always have X forwarding via ssh enabled. If this was the issue, I would have had the same problem on all platforms, and furthermore, I am able to run other X programs from the Solaris host on my desktop without issues. Whatever it is, it's not this. Now that you mention it, however, I need to point out that raw X11 on the network using xauth (bad) or xhost (really, really bad) is some- thing that, in my ever so humble opinion, should have died out in 1995 or so when Tatu Yl?nen published ssh. I don't know why people still insist on shooting themselves in the foot by running raw X11 on the network without SSH protection, nor do I particularly need to know. -- Atro Tossavainen (Mr.) / The Institute of Biotechnology at Systems Analyst, Techno-Amish & / the University of Helsinki, Finland, +358-9-19158939 UNIX Dinosaur / employs me, but my opinions are my own. < URL : http : / / www . helsinki . fi / %7E atossava / > NO FILE ATTACHMENTS
ADD REPLYlink written 11.5 years ago by Atro Tossavainen160
Here's the line that generated genefilter.so: (I'm using Sun's Studio 11 compilers and enabled the use of the sunperf library while building R.) CC -G -o genefilter.so half_range_mode.o init.o nd.o pAUC.o rowPAUCs.o rowttests.o ttest.o -R/opt/SUNWspro/lib/v8plus:/opt/SUNWspro/lib:/opt/ SUNWspro/lib/v8plus:/opt/SUNWspro/lib -L/opt/SUNWspro/lib/v8plus -L/opt/SUNWspro/prod/lib/v8plus -L/opt/SUNWspro/lib -L/opt/SUNWspro/prod/lib -L/usr/ccs/lib -lfui -lfai -lfai2 -lfsumai -lfprodai -lfminlai -lfmaxlai -lfminvai -lfmaxvai -lfsu -lsunmath -lmtsk -lm I think all of the various -R, -L and -l parameters should have been reduced into "-library=sunperf" above. It might not be an issue. I removed the existing genefilter installation and tried building again simply with biocLite("genefilter"), which resulted in exactly the same problem. I also tried building the .so by hand: CC -G -o genefilter.so half_range_mode.o init.o nd.o pAUC.o rowPAUCs.o rowttests.o ttest.o -library=sunperf which resulted in exactly the same problem when loading via > library(genefilter) Loading required package: Biobase Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation(pkgname)'. Loading required package: survival Loading required package: splines Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared library '/.../R/2.7.0/lib/R/library/genefilter/libs/genefilter.so': ld.so.1: /.../R/2.7.0/lib/R/bin/exec/R: fatal: relocation error: file /.../R/2.7.0/lib/R/library/genefilter/libs/genefilter.so: symbol __1cDstdJexceptionG__vtbl_: referenced symbol not found Error: package/namespace load failed for 'genefilter' -- Atro Tossavainen (Mr.) / The Institute of Biotechnology at Systems Analyst, Techno-Amish & / the University of Helsinki, Finland, +358-9-19158939 UNIX Dinosaur / employs me, but my opinions are my own. < URL : http : / / www . helsinki . fi / %7E atossava / > NO FILE ATTACHMENTS
ADD REPLYlink written 11.5 years ago by Atro Tossavainen160
Hi Atro, Thanks for all your efforts in trouble shooting. If I understand, the GO issue is now resolved but genefilter is still problematic. Could you try using gcc to compile rather than sunperf? It looks like there are some header file issues that may be complicating the issue and it will take a few days to fix them and test properly (given a bunch of other constraints). best wishes Robert Atro Tossavainen wrote: > Here's the line that generated genefilter.so: > > (I'm using Sun's Studio 11 compilers and enabled the use of the sunperf > library while building R.) > > CC -G -o genefilter.so half_range_mode.o init.o nd.o pAUC.o rowPAUCs.o rowttests.o ttest.o -R/opt/SUNWspro/lib/v8plus:/opt/SUNWspr o/lib:/opt/SUNWspro/lib/v8plus:/opt/SUNWspro/lib -L/opt/SUNWspro/lib/v8plus -L/opt/SUNWspro/prod/lib/v8plus -L/opt/SUNWspro/lib -L/opt/SUNWspro/prod/lib -L/usr/ccs/lib -lfui -lfai -lfai2 -lfsumai -lfprodai -lfminlai -lfmaxlai -lfminvai -lfmaxvai -lfsu -lsunmath -lmtsk -lm > > I think all of the various -R, -L and -l parameters should have been > reduced into "-library=sunperf" above. It might not be an issue. > > I removed the existing genefilter installation and tried building again > simply with biocLite("genefilter"), which resulted in exactly the same > problem. I also tried building the .so by hand: > > CC -G -o genefilter.so half_range_mode.o init.o nd.o pAUC.o rowPAUCs.o rowttests.o ttest.o -library=sunperf > > which resulted in exactly the same problem when loading via > >> library(genefilter) > Loading required package: Biobase > Loading required package: tools > > Welcome to Bioconductor > > Vignettes contain introductory material. To view, type > 'openVignette()'. To cite Bioconductor, see > 'citation("Biobase")' and for packages 'citation(pkgname)'. > > Loading required package: survival > Loading required package: splines > Error in dyn.load(file, DLLpath = DLLpath, ...) : > unable to load shared library '/.../R/2.7.0/lib/R/library/genefilter/libs/genefilter.so': > ld.so.1: /.../R/2.7.0/lib/R/bin/exec/R: fatal: relocation error: file /.../R/2.7.0/lib/R/library/genefilter/libs/genefilter.so: symbol __1cDstdJexceptionG__vtbl_: referenced symbol not found > Error: package/namespace load failed for 'genefilter' > -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 rgentlem at fhcrc.org
ADD REPLYlink written 11.5 years ago by rgentleman5.5k
Robert, > Thanks for all your efforts in trouble shooting. If I understand, > the GO issue is now resolved but genefilter is still problematic. Yes indeed. > Could you try using gcc to compile rather than sunperf? As the Bioconductor packages are built with whatever was used to compile R itself, this meant having to compile R from scratch with gcc, which I wasn't really looking forward to. However, at the moment, that looks like the only way I could get a working genefilter going on Solaris/SPARC, and I also found I could substitute the gcc-compiled genefilter.so for the Sun Studio generated one in the otherwise Sun Studio generated install. While this is far from practical, it at least allowed me to have a working set of R and Bioconductor for Solaris/SPARC for now. > > ld.so.1: /.../R/2.7.0/lib/R/bin/exec/R: fatal: relocation error: file /.../R/2.7.0/lib/R/library/genefilter/libs/genefilter.so: symbol __1cDstdJexceptionG__vtbl_: referenced symbol not found As far as I can guess, this might mean that g++ was used to compile something somewhere even though I've specified Sun Studio all along. I'd need to rebuild all of R once more and log everything to verify. -- Atro Tossavainen (Mr.) / The Institute of Biotechnology at Systems Analyst, Techno-Amish & / the University of Helsinki, Finland, +358-9-19158939 UNIX Dinosaur / employs me, but my opinions are my own. < URL : http : / / www . helsinki . fi / %7E atossava / > NO FILE ATTACHMENTS
ADD REPLYlink written 11.5 years ago by Atro Tossavainen160
Hi, I'm seeking help here regarding updating the Rcurl for macOSX to a newer version so it'll accomodate to bioconductor 2.7. The current version of Rcurl 0.8-1 (in bioconductor 2.7 for macOSX) is built for bioconductor 2.6; Is there anyone who could help to put the bioconductor 2.7 compatible version of Rcurl into the database? So we could use packages depending on Rcurl? Any kind help is greatly appreciated! Thanks in advance. yan Atro Tossavainen wrote: >Robert, > > > >> Thanks for all your efforts in trouble shooting. If I understand, >>the GO issue is now resolved but genefilter is still problematic. >> >> > >Yes indeed. > > > >> Could you try using gcc to compile rather than sunperf? >> >> > >As the Bioconductor packages are built with whatever was used to compile >R itself, this meant having to compile R from scratch with gcc, which >I wasn't really looking forward to. However, at the moment, that looks >like the only way I could get a working genefilter going on Solaris/SPARC, >and I also found I could substitute the gcc-compiled genefilter.so for >the Sun Studio generated one in the otherwise Sun Studio generated >install. While this is far from practical, it at least allowed me to >have a working set of R and Bioconductor for Solaris/SPARC for now. > > > >>> ld.so.1: /.../R/2.7.0/lib/R/bin/exec/R: fatal: relocation error: file /.../R/2.7.0/lib/R/library/genefilter/libs/genefilter.so: symbol __1cDstdJexceptionG__vtbl_: referenced symbol not found >>> >>> > >As far as I can guess, this might mean that g++ was used to compile >something somewhere even though I've specified Sun Studio all along. >I'd need to rebuild all of R once more and log everything to verify. > > >
ADD REPLYlink written 11.5 years ago by yan zhou80
Hi, > I'm seeking help here regarding updating the Rcurl for macOSX to a > newer version so it'll accomodate to bioconductor 2.7. The current > version of Rcurl 0.8-1 (in bioconductor 2.7 for macOSX) is built for > bioconductor 2.6; Is there anyone who could help to put the > bioconductor 2.7 compatible version of Rcurl into the database? So > we could use packages depending on Rcurl? Any kind help is greatly > appreciated! When this was brought up earlier, I think the consensus was that since this isn't a bioconductor hosted package, you'd better inquire over at R-help. That said, someone also suggested earlier to install it straight from the source via this incantation: > install.packages("RCurl", repos = "http://www.omegahat.org/R") I don't think that worked for me, and I ended up d/ling the source package and installing it manually, by first d/ling it and uncompressing it. You'll get an RCurl folder. At the command line, you can then: $ R CMD BUILD RCurl $ R CMD CHECK RCurl_0.9-3.tar.gz $ R CMD INSTALL RCurl_0.9-3.tar.gz I'm not sure if this is the best way, but I seem to have a fully functioning RCurl again since the biomaRt package relies on that, and that works now. Btw - you can get RCurl here: http://www.omegahat.org/RCurl/ HTH, -steve
ADD REPLYlink written 11.5 years ago by Steve Lianoglou12k
Steve and Yan, We just uploaded source, Windows binary, and MacOS X Tiger binary packages for RCurl 0.9-3 to the Bioconductor CRAN-like repository http://bioconductor.org/packages/2.2/extra. This repository is make available when you use R 2.7.0 and type source("http://bioconductor.org/biocLite.R") biocLite("RCurl") Let me know if this meets your needs. Cheers, Patrick Steve Lianoglou wrote: > Hi, > >> I'm seeking help here regarding updating the Rcurl for macOSX to a >> newer version so it'll accomodate to bioconductor 2.7. The current >> version of Rcurl 0.8-1 (in bioconductor 2.7 for macOSX) is built for >> bioconductor 2.6; Is there anyone who could help to put the >> bioconductor 2.7 compatible version of Rcurl into the database? So we >> could use packages depending on Rcurl? Any kind help is greatly >> appreciated! > > When this was brought up earlier, I think the consensus was that since > this isn't a bioconductor hosted package, you'd better inquire over at > R-help. > > That said, someone also suggested earlier to install it straight from > the source via this incantation: > > > install.packages("RCurl", repos = "http://www.omegahat.org/R") > > I don't think that worked for me, and I ended up d/ling the source > package and installing it manually, by first d/ling it and > uncompressing it. You'll get an RCurl folder. At the command line, you > can then: > > $ R CMD BUILD RCurl > $ R CMD CHECK RCurl_0.9-3.tar.gz > $ R CMD INSTALL RCurl_0.9-3.tar.gz > > I'm not sure if this is the best way, but I seem to have a fully > functioning RCurl again since the biomaRt package relies on that, and > that works now. > > Btw - you can get RCurl here: http://www.omegahat.org/RCurl/ > > HTH, > -steve > > _______________________________________________ > 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
ADD REPLYlink written 11.5 years ago by Patrick Aboyoun1.6k
Patrick and Steve, Thank you for all your kind help. I installed using source. It works fine. yan Patrick Aboyoun wrote: > Steve and Yan, > We just uploaded source, Windows binary, and MacOS X Tiger binary > packages for RCurl 0.9-3 to the Bioconductor CRAN-like repository > http://bioconductor.org/packages/2.2/extra. This repository is make > available when you use R 2.7.0 and type > > source("http://bioconductor.org/biocLite.R") > biocLite("RCurl") > > Let me know if this meets your needs. > > > Cheers, > Patrick > > > > Steve Lianoglou wrote: > >> Hi, >> >>> I'm seeking help here regarding updating the Rcurl for macOSX to a >>> newer version so it'll accomodate to bioconductor 2.7. The current >>> version of Rcurl 0.8-1 (in bioconductor 2.7 for macOSX) is built for >>> bioconductor 2.6; Is there anyone who could help to put the >>> bioconductor 2.7 compatible version of Rcurl into the database? So >>> we could use packages depending on Rcurl? Any kind help is greatly >>> appreciated! >> >> >> When this was brought up earlier, I think the consensus was that >> since this isn't a bioconductor hosted package, you'd better inquire >> over at R-help. >> >> That said, someone also suggested earlier to install it straight from >> the source via this incantation: >> >> > install.packages("RCurl", repos = "http://www.omegahat.org/R") >> >> I don't think that worked for me, and I ended up d/ling the source >> package and installing it manually, by first d/ling it and >> uncompressing it. You'll get an RCurl folder. At the command line, >> you can then: >> >> $ R CMD BUILD RCurl >> $ R CMD CHECK RCurl_0.9-3.tar.gz >> $ R CMD INSTALL RCurl_0.9-3.tar.gz >> >> I'm not sure if this is the best way, but I seem to have a fully >> functioning RCurl again since the biomaRt package relies on that, and >> that works now. >> >> Btw - you can get RCurl here: http://www.omegahat.org/RCurl/ >> >> HTH, >> -steve >> >> _______________________________________________ >> 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 > >
ADD REPLYlink written 11.5 years ago by yan zhou80
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