Hi, I've installed R-1.9.0 and Bioconductor 1.3 (default packages) on solaris 8 using gcc3.4.0, and it all went well except for the "affy" library. The affy build seemed OK but there was and error in building the help pages which caused the library install to fail. The relevant section of the getBioC output is shown below. I didn't see anything in the archives that seemed to fit. What is the best way to work around this or to get more useful information about the source of the problem? Thanks -Steve ** help >>> Building/Updating help pages for package 'affy' Formats: text html latex example .setAffyOptions text html latex example AffyBatch-class text html latex example AffyRNAdeg text html latex example ProbeSet-class text html latex example SpikeIn text html latex affy-options text html latex example affy.scalevalue.exprSet text html latex affybatch.example text html latex barplot.ProbeSet text html latex example bg.adjust text html latex bgc text html latex example cdfFromBioC text html latex example cdfenv.example text html latex cleancdfname text html latex example debug.affy123 text html latex expresso text html latex example expressoWidget text html latex example fit.li.wong text html latex example generateExprSet-methods text html latex example generateExprVal-methods text html latex example generateExprVal.method.avgdiff text html latex example generateExprVal.method.playerout text html latex hlog text html latex justrma text html latex example list.celfiles text html latex example loess.normalize text html latex maffy.normalise text html latex example maffy.subset text html latex example mas5 text html latex example mas5calls text html latex example merge.AffyBatch text html latex example multiloess text html latex mva.pairs text html latex example normalize-methods text html latex example normalize text html latex normalize.constant text html latex normalize.contrast text html latex example normalize.invariantset text html latex ERROR: command (e.g. \url) inside \link error: building help failed for package 'affy': No such file or directory for reading errors. ** Removing '/prod/ddm/tools/R/R-1.9.0_Bioconductor-1.3/lib/R/library/affy' ***************************************************************** Steve Roels, Ph.D. Senior Scientist I - Computational Biology Phone: (617) 761-6820 Millennium Pharmaceuticals, Inc. FAX: (617) 577-3555 640 Memorial Drive Email: roels@mpi.com Cambridge, MA 02139-4853 ***************************************************************** This e-mail, including any attachments, is a confidential business communication, and may contain information that is confidential, proprietary and/or privileged. This e-mail is intended only for the individual(s) to whom it is addressed, and may not be saved, copied, printed, disclosed or used by anyone else. If you are not the(an) intended recipient, please immediately delete this e-mail from your computer system and notify the sender. Thank you.

There is something in the archives. https://www.stat.math.ethz.ch/pipermail/bioconductor/2004-April/004549 .html HTH, 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 734-647-5623 >>> "Roels, Steven" <steven.roels@mpi.com> 05/13/04 10:11PM >>> Hi, I've installed R-1.9.0 and Bioconductor 1.3 (default packages) on solaris 8 using gcc3.4.0, and it all went well except for the "affy" library. The affy build seemed OK but there was and error in building the help pages which caused the library install to fail. The relevant section of the getBioC output is shown below. I didn't see anything in the archives that seemed to fit. What is the best way to work around this or to get more useful information about the source of the problem? Thanks -Steve ** help >>> Building/Updating help pages for package 'affy' Formats: text html latex example .setAffyOptions text html latex example AffyBatch-class text html latex example AffyRNAdeg text html latex example ProbeSet-class text html latex example SpikeIn text html latex affy-options text html latex example affy.scalevalue.exprSet text html latex affybatch.example text html latex barplot.ProbeSet text html latex example bg.adjust text html latex bgc text html latex example cdfFromBioC text html latex example cdfenv.example text html latex cleancdfname text html latex example debug.affy123 text html latex expresso text html latex example expressoWidget text html latex example fit.li.wong text html latex example generateExprSet-methods text html latex example generateExprVal-methods text html latex example generateExprVal.method.avgdiff text html latex example generateExprVal.method.playerout text html latex hlog text html latex justrma text html latex example list.celfiles text html latex example loess.normalize text html latex maffy.normalise text html latex example maffy.subset text html latex example mas5 text html latex example mas5calls text html latex example merge.AffyBatch text html latex example multiloess text html latex mva.pairs text html latex example normalize-methods text html latex example normalize text html latex normalize.constant text html latex normalize.contrast text html latex example normalize.invariantset text html latex ERROR: command (e.g. \url) inside \link error: building help failed for package 'affy': No such file or directory for reading errors. ** Removing '/prod/ddm/tools/R/R-1.9.0_Bioconductor-1.3/lib/R/library/affy' ***************************************************************** Steve Roels, Ph.D. Senior Scientist I - Computational Biology Phone: (617) 761-6820 Millennium Pharmaceuticals, Inc. FAX: (617) 577-3555 640 Memorial Drive Email: roels@mpi.com Cambridge, MA 02139-4853 ***************************************************************** This e-mail, including any attachments, is a confidential business communication, and may contain information that is confidential, proprietary and/or privileged. This e-mail is intended only for the individual(s) to whom it is addressed, and may not be saved, copied, printed, disclosed or used by anyone else. If you are not the(an) intended recipient, please immediately delete this e-mail from your computer system and notify the sender. Thank you. _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor