Hi Lauro -- This was a change in the development version of R over the weekend (r32748, 2007-09-04 02:33:30 -0700, I think) and was fixed in the development version of Biobase the same day (r26853, 2007-09-04 16:08:07 -0700; Biobase version 1.15.31). Unfortunately, your machines captured the combination of R and Biobase during the approx. 14 hours when things were not working! The solution is to update Biobase, e.g., > source('http://bioconductor.org/biocLite.R') > biocLite('Biobase') As you found out, using development versions of R and Biobase can have very unfortunate consequences. When offering courses, we try to identify an R snapshot that seems to work, and to use facilities like building and installing packages and course material (and hence building vignettes and exercising the packages on the version of R we will use) to make sure that things will work. Sorry that this happened at such an inopportune time. Martin "Lauro Sumoy Van Dyck" <lauro.sumoy at="" crg.es=""> writes: > Hello, > While conducting a workshop on Bioconductor arrayQC we have > encountered the following error but not on all machines. > > Error in .nextMethod(e1, e2) : > comparison of these types is not implemented > > This error is generated upon trying to generate new objects. > > Could you please help solve this issue? I am told -I am not an R > expert- that there must be a problem associated to handling S4 class > objects. > > Thank you, > > Lauro > > In my particular case this is the session info: >> sessionInfo() > R version 2.6.0 Under development (unstable) (2007-09-04 r42752) > i386-pc-mingw32 > locale: > LC_COLLATE=Spanish_Spain.1252;LC_CTYPE=Spanish_Spain.1252;LC_MONETAR Y=Spanish_Spain.1252;LC_NUMERIC=C;LC_TIME=Spanish_Spain.1252 > attached base packages: > [1] splines tools stats graphics grDevices utils datasets methods base > other attached packages: > [1] arrayQualityMetrics_1.0.17 CCl4_1.0.5 limma_2.11.11 simpleaffy_2.13.01 affyPLM_1.13.6 > [6] gcrma_2.9.1 matchprobes_1.9.10 affydata_1.11.3 RColorBrewer_1.0-1 vsn_3.0.14 > [11] affy_1.15.7 preprocessCore_0.99.12 affyio_1.5.8 genefilter_1.15.11 survival_2.32 > [16] geneplotter_1.15.9 lattice_0.16-4 annotate_1.15.6 AnnotationDbi_0.1.12 RSQLite_0.6-0 > [21] DBI_0.2-3 Biobase_1.15.30 > loaded via a namespace (and not attached): > [1] grid_2.6.0 KernSmooth_2.22-21 > > Commands that generated the same type of error: >> object<-new("AffyBatch") > Error in .nextMethod(e1, e2) : > comparison of these types is not implemented >> object<-new("NChannelSet") > Error in .nextMethod(e1, e2) : > comparison of these types is not implemented > > > Lauro Sumoy > Microarray Laboratory > Bioinformatics and Genomics Program > Center for Genomic Regulation (CRG) > Dr. Aiguader 88 > 08003 Barcelona > Spain > Office Phone: +34-93-316-0125 > CRG Fax: +34-93-316-0099 > e-mail: lauro.sumoy at crg.es > http://www.crg.es <http: www.crg.es=""/> > --------------------------- > Microarray Laboratory Phone: +34-93-316-0126 > Microarray Services Office: +34-93-316-0272 > Microarray Bioinformatics Office: +34-93-316-0238 > Program Secretarial Office: +34-93-316-0110 > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 -- Martin Morgan Bioconductor / Computational Biology http://bioconductor.org

Hi Lauro and others -- To emphasize, the following involves the DEVELOPMENT version of Biobase; users of the released version DO NOT have these problems. My solution (using biocLite) is not correct, for the moment -- the Biobase 'fix' requires the R change, but our build machines do not yet have the updated version of R and so cannot perform the steps to make Biobase available. In theory, the solutions are to use versions of R-devel and Biobase that predate the change, or to use the R-alpha (R-devel has now 'branched' in preparation for the October release) and an svn version of Biobase that post-date the change. Realizing the second option (R-alpha + Biobase from svn) requires the ability to build R and R packages from source. Working combinations of R-alpha and Biobase accessible using biocLite are at least a day away. Martin Martin Morgan <mtmorgan at="" fhcrc.org=""> writes: > Hi Lauro -- > > This was a change in the development version of R over the weekend > (r32748, 2007-09-04 02:33:30 -0700, I think) and was fixed in the > development version of Biobase the same day (r26853, 2007-09-04 > 16:08:07 -0700; Biobase version 1.15.31). Unfortunately, your machines > captured the combination of R and Biobase during the approx. 14 hours > when things were not working! > > The solution is to update Biobase, e.g., > >> source('http://bioconductor.org/biocLite.R') >> biocLite('Biobase') > > As you found out, using development versions of R and Biobase can have > very unfortunate consequences. When offering courses, we try to > identify an R snapshot that seems to work, and to use facilities like > building and installing packages and course material (and hence > building vignettes and exercising the packages on the version of R we > will use) to make sure that things will work. > > Sorry that this happened at such an inopportune time. > > Martin > > "Lauro Sumoy Van Dyck" <lauro.sumoy at="" crg.es=""> writes: > >> Hello, > >> While conducting a workshop on Bioconductor arrayQC we have >> encountered the following error but not on all machines. >> >> Error in .nextMethod(e1, e2) : >> comparison of these types is not implemented >> >> This error is generated upon trying to generate new objects. >> >> Could you please help solve this issue? I am told -I am not an R >> expert- that there must be a problem associated to handling S4 class >> objects. >> >> Thank you, >> >> Lauro >> >> In my particular case this is the session info: >>> sessionInfo() >> R version 2.6.0 Under development (unstable) (2007-09-04 r42752) >> i386-pc-mingw32 >> locale: >> LC_COLLATE=Spanish_Spain.1252;LC_CTYPE=Spanish_Spain.1252;LC_MONETA RY=Spanish_Spain.1252;LC_NUMERIC=C;LC_TIME=Spanish_Spain.1252 >> attached base packages: >> [1] splines tools stats graphics grDevices utils datasets methods base >> other attached packages: >> [1] arrayQualityMetrics_1.0.17 CCl4_1.0.5 limma_2.11.11 simpleaffy_2.13.01 affyPLM_1.13.6 >> [6] gcrma_2.9.1 matchprobes_1.9.10 affydata_1.11.3 RColorBrewer_1.0-1 vsn_3.0.14 >> [11] affy_1.15.7 preprocessCore_0.99.12 affyio_1.5.8 genefilter_1.15.11 survival_2.32 >> [16] geneplotter_1.15.9 lattice_0.16-4 annotate_1.15.6 AnnotationDbi_0.1.12 RSQLite_0.6-0 >> [21] DBI_0.2-3 Biobase_1.15.30 >> loaded via a namespace (and not attached): >> [1] grid_2.6.0 KernSmooth_2.22-21 >> >> Commands that generated the same type of error: >>> object<-new("AffyBatch") >> Error in .nextMethod(e1, e2) : >> comparison of these types is not implemented >>> object<-new("NChannelSet") >> Error in .nextMethod(e1, e2) : >> comparison of these types is not implemented >> >> >> Lauro Sumoy >> Microarray Laboratory >> Bioinformatics and Genomics Program >> Center for Genomic Regulation (CRG) >> Dr. Aiguader 88 >> 08003 Barcelona >> Spain >> Office Phone: +34-93-316-0125 >> CRG Fax: +34-93-316-0099 >> e-mail: lauro.sumoy at crg.es >> http://www.crg.es <http: www.crg.es=""/> >> --------------------------- >> Microarray Laboratory Phone: +34-93-316-0126 >> Microarray Services Office: +34-93-316-0272 >> Microarray Bioinformatics Office: +34-93-316-0238 >> Program Secretarial Office: +34-93-316-0110 >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> 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 > > -- > Martin Morgan > Bioconductor / Computational Biology > http://bioconductor.org > > _______________________________________________ > 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 -- Martin Morgan Bioconductor / Computational Biology http://bioconductor.org