I have posted this problem earlier, but there was no response. Hence, I'm posting this again. I have installed R version 2.3.1, on Mac (OS 10.4.7, on an Intel CoreDuo iMac). When I try to install bioconductor -- following instructions, using biocLite() -- it downloads the packages mentioned on the install page. However, the instatllation does not complete. I get the following message after the downloads are complete: ------ The downloaded packages are in /tmp/RtmpJdBYlA/downloaded_packages Warning messages: 1: number of rows of result is not a multiple of vector length (arg 2) in: cbind(1, res0, Repository = repos) 2: cannot create HTML package index in: make.packages.html() ------ I have tried installation with only one package (affy), and still face the same problem. The entire log for affy is as follows: -------- > source("http://www.bioconductor.org/biocLite.R") > biocLite(c("affy")) Running getBioC version 0.1.6 with R version 2.3.1 Running biocinstall version 1.8.4 with R version 2.3.1 Your version of R requires version 1.8 of Bioconductor. trying URL 'http://bioconductor.org/packages/1.8/bioc/bin/macosx/i386/contrib/2.3 /affy_1.10.0.tgz' Content type 'application/x-gzip' length 1733585 bytes opened URL ================================================== downloaded 1692Kb The downloaded packages are in /tmp/RtmpJdBYlA/downloaded_packages Warning messages: 1: number of rows of result is not a multiple of vector length (arg 2) in: cbind(1, res0, Repository = repos) 2: cannot create HTML package index in: make.packages.html() --------- Please help. Debashis Bhattacharya.

Seth Falcon has already answered your question (yesterday). Please read it before you post again. Thanks, H. Debashis Bhattacharya wrote: > I have posted this problem earlier, but there was no response. Hence, > I'm posting this again. > > I have installed R version 2.3.1, on Mac (OS 10.4.7, on an Intel CoreDuo > iMac). > > When I try to install bioconductor -- following instructions, using > biocLite() -- it downloads > the packages mentioned on the install page. However, the instatllation > does not complete. > > I get the following message after the downloads are complete: > > ------ > The downloaded packages are in > /tmp/RtmpJdBYlA/downloaded_packages > Warning messages: > 1: number of rows of result > is not a multiple of vector length (arg 2) in: cbind(1, res0, > Repository = repos) > 2: cannot create HTML package index in: make.packages.html() > ------ > > I have tried installation with only one package (affy), and still face > the same problem. The entire log > for affy is as follows: > > -------- > > source("http://www.bioconductor.org/biocLite.R") > > biocLite(c("affy")) > Running getBioC version 0.1.6 with R version 2.3.1 > Running biocinstall version 1.8.4 with R version 2.3.1 > Your version of R requires version 1.8 of Bioconductor. > trying URL > 'http://bioconductor.org/packages/1.8/bioc/bin/macosx/i386/contrib/2 .3/affy_1.10.0.tgz' > > Content type 'application/x-gzip' length 1733585 bytes > opened URL > ================================================== > downloaded 1692Kb > > > The downloaded packages are in > /tmp/RtmpJdBYlA/downloaded_packages > Warning messages: > 1: number of rows of result > is not a multiple of vector length (arg 2) in: cbind(1, res0, > Repository = repos) > 2: cannot create HTML package index in: make.packages.html() > --------- > > Please help. > > > > Debashis Bhattacharya. > > _______________________________________________ > 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 > > -- ------------------------ Hervé Pagès E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319

Hi Debashis, I had the same issue, and raised it here back in July See e.g. https://stat.ethz.ch/pipermail/bioconductor/2006-July/013691.html It appears that your download and installation did work alright. Two warnings were issued, but no errors. Warning 1: Warning messages: 1: number of rows of result is not a multiple of vector length (arg 2) in: cbind(1, res0, Repository = repos) The first warning occurs when an empty package repository is in place in BioC, usually because a package had errors in testing and did not compile. This is reportedly fixed in the upcoming release of R, but not in the current release. Simon Urbanek reported: "For the record, the other warning mentioned appears when installing from empty repositories - it is not Mac specific. (The lindsey repository is empty on Bioc, because none of the packages compiles). I have now also committed the fix (thanks to Seth for the correct analysis and fix)." Warning 2: Warning messages: 2: cannot create HTML package index in: make.packages.html() If you run > help.start() before you run > source("http://www.bioconductor.org/biocLite.R") > biocLite(c("affy")) then I believe you should not see the second warning, as help.start() will create the directories and files that biocLite() is trying to modify. biocLite() wants to add help information to the help HTML package index, but that index is not in place until help.start() sets it all up. Simon Urbanek reported: "Yes, it fails because it expects the help system to have created them already and you're not supposed to mess with that manually. (Again, this is not Mac-specific - until help.start is invoked, the directories are not there on any unix)." Try loading and running some examples for the packages you've installed, they should work alright. Hopefully these warnings will no longer appear in the next release of R, as they continue to confuse new users who are earnestly striving to ensure that software was properly downloaded and installed. Best regards Steven McKinney Statistician Molecular Oncology and Breast Cancer Program British Columbia Cancer Research Centre email: smckinney at bccrc.ca tel: 604-675-8000 x7561 BCCRC Molecular Oncology 675 West 10th Ave, Floor 4 Vancouver B.C. V5Z 1L3 Canada -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch on behalf of Debashis Bhattacharya Sent: Tue 8/29/2006 11:20 AM To: bioconductor at stat.math.ethz.ch Subject: [BioC] Bioconductor installation problem on Mac I have posted this problem earlier, but there was no response. Hence, I'm posting this again. I have installed R version 2.3.1, on Mac (OS 10.4.7, on an Intel CoreDuo iMac). When I try to install bioconductor -- following instructions, using biocLite() -- it downloads the packages mentioned on the install page. However, the instatllation does not complete. I get the following message after the downloads are complete: ------ The downloaded packages are in /tmp/RtmpJdBYlA/downloaded_packages Warning messages: 1: number of rows of result is not a multiple of vector length (arg 2) in: cbind(1, res0, Repository = repos) 2: cannot create HTML package index in: make.packages.html() ------ I have tried installation with only one package (affy), and still face the same problem. The entire log for affy is as follows: -------- > source("http://www.bioconductor.org/biocLite.R") > biocLite(c("affy")) Running getBioC version 0.1.6 with R version 2.3.1 Running biocinstall version 1.8.4 with R version 2.3.1 Your version of R requires version 1.8 of Bioconductor. trying URL 'http://bioconductor.org/packages/1.8/bioc/bin/macosx/i386/contrib/2.3 /affy_1.10.0.tgz' Content type 'application/x-gzip' length 1733585 bytes opened URL ================================================== downloaded 1692Kb The downloaded packages are in /tmp/RtmpJdBYlA/downloaded_packages Warning messages: 1: number of rows of result is not a multiple of vector length (arg 2) in: cbind(1, res0, Repository = repos) 2: cannot create HTML package index in: make.packages.html() --------- Please help. Debashis Bhattacharya. _______________________________________________ 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