Question: Problems installing v 1.2
0
gravatar for Christopher Wilkinson
16.5 years ago by
Christopher Wilkinson140 wrote:
Hi I've just installed R and have now tried to install bioconductor but have run into several problems I've tried the suggested script (getBioC) but this appears to be failing. Firstly, I'm behind a firewall so have to use password based proxy. I managed to work this out (perhaps a link to the manual pages on how to setup a proxy might not go astray here). I try running the script, it installs the repostools and then appears to hang. It sits at the "synching local package management info" stage and doesn't appear to do anything. I've tried a few times, but always end up doing a Control-C and aborting. I've taken the alternate approach of downloading the Bioconductor_1.2.tar.gz file to try a manual install (R INSTALL Bioconductor_1.2.tar.gz) This appears to work better, until I get to the rhdf5 package where it fails with an configure: error: please specify a valid hdf5 installation with --with-hdf5=DIR ERROR: configure failed for package rhdf5 and I can get no further (no option to skip) I then tried manually installing rhdf5 manually but same error, and even tried hdf5 package but no success. So any suggestions on ways around this. I'm intending to unzip everything and see if I can hack a version minus the rhdf5 package. Cheers Chris Dr Chris Wilkinson Research Officer (Bioinformatics) | Visiting Research Fellow Child Health Research Institute (CHRI) | Microarray Analysis Group 7th floor, Clarence Rieger Building | Room 121 Women's and Children's Hospital | School of Applied Mathematics 72 King William Rd, North Adelaide, 5006 | The University of Adelaide, 5005 Math's Office (Room 121) Ph: 8303 3714 CHRI Office (2nd floor) Ph: 8161 6729 Christopher.Wilkinson@adelaide.edu.au
microarray go rhdf5 repostools • 561 views
ADD COMMENTlink modified 16.5 years ago by A.J. Rossini810 • written 16.5 years ago by Christopher Wilkinson140
Answer: Problems installing v 1.2
0
gravatar for Jeff Gentry
16.5 years ago by
Jeff Gentry3.9k
Jeff Gentry3.9k wrote:
> I try running the script, it installs the repostools and then appears to hang. > It sits at the > "synching local package management info" stage and doesn't appear to do > anything. I suspect that it isn't actually hanging there, it just doesn't report every step. I'll try to put out a more chattery version today to help localize this. > This appears to work better, until I get to the rhdf5 package where it fails > with an > configure: error: please specify a valid hdf5 installation with --with-hdf5=DIR > ERROR: configure failed for package rhdf5 You need the HDF5 libraries: http://hdf.ncsa.uiuc.edu/HDF5/
ADD COMMENTlink written 16.5 years ago by Jeff Gentry3.9k
Answer: Problems installing v 1.2
0
gravatar for David Lapointe
16.5 years ago by
David Lapointe170 wrote:
I had some issues with installing 1.2 ( Linux;Mandrake 9.1) also. Most likely fixable by me. HDF5 did not install (see below) Ruuid had an error in the complilation ( clear.c had a perse error before } type problem) Graphviz I don't have installed ( it seems to want libpng.so.2, I have libpng.so.3 Hah!) XML had an issue trying to find parser.h. So are there pointers to remediating these problems? Can I just reinstall these functions? Overall I like the way everything installs. Also, at the end of the install a message indicate repostools was not updated. Should it have been? David > > You need the HDF5 libraries: http://hdf.ncsa.uiuc.edu/HDF5/ > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo> /bioconductor >
ADD COMMENTlink written 16.5 years ago by David Lapointe170
> HDF5 did not install (see below) You are referring to the actual HDF5 library and not the package (tho obviously the package won't install w/o the library), right? > Ruuid had an error in the complilation ( clear.c had a perse error > before } type problem) I can not replicate this at all, can anyone else? > Graphviz I don't have installed ( it seems to want libpng.so.2, I have > libpng.so.3 Hah!) Again - you are talking about the actual AT&T Graphviz application, correct? If so, this might not be an insurmountable problem, but it is best brought up to the AT&T folks: http://www.research.att.com/sw/tools/graphviz/ > XML had an issue trying to find parser.h. This should be taken up on the R-help list (r-help@stat.math.ethz.ch) > Also, at the end of the install a message indicate repostools was not > updated. Should it have been? It was. That bit is an (admittedly confusing, need to find a way around that) artifact of how getBioC() works. It first downloads reposTools manually, then runs reposTools to update your BioC packages and their dependencies. Since reposTools is already up to date before it starts using the reposTools functions, it appears to the system as if it was not updated. I will set up the getBioC() function to intercept that output from reposTools and have it change this behavior so that it shows up as an updated package. -J
ADD REPLYlink written 16.5 years ago by Jeff Gentry3.9k
Answer: Problems installing v 1.2
0
gravatar for A.J. Rossini
16.5 years ago by
A.J. Rossini810
A.J. Rossini810 wrote:
"Lapointe, David" <david.lapointe@umassmed.edu> writes: > I had some issues with installing 1.2 ( Linux;Mandrake 9.1) also. Most > likely fixable by me. We probably need to mention on the WWW page: > HDF5 did not install (see below) HDF5 libraries -- for all platforms > Ruuid had an error in the complilation ( clear.c had a perse error > before } type problem) glibc-dev packages (not sure what the RPM distro's call them) > Graphviz I don't have installed ( it seems to want libpng.so.2, I have > libpng.so.3 Hah!) where to get graphviz, and that it needs to be a recent version; libpng version is useful. > XML had an issue trying to find parser.h. The range of XML parsers that XML needs (and dev files). I'll get Jeff the Debian versions (in fact, I've got a Debian package just waiting for the 1.2 versions to drop in, so have a sense of the requirements), but it would be nice if others could suggest for other distributions what works... best, -tony -- A.J. Rossini / rossini@u.washington.edu / rossini@scharp.org Biomedical/Health Informatics and Biostatistics, University of Washington. Biostatistics, HVTN/SCHARP, Fred Hutchinson Cancer Research Center. FHCRC: 206-667-7025 (fax=4812)|Voicemail is pretty sketchy/use Email CONFIDENTIALITY NOTICE: This e-mail message and any attachments ... {{dropped}}
ADD COMMENTlink written 16.5 years ago by A.J. Rossini810
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 245 users visited in the last hour