Hello, I have an odd issue that I have been unable thus far to resolve. Literally overnight it has become impossible to add a lymphGate filter to a workFlow. This is specific for the lymphGate filter only, as any other type of filter works just fine. The error that I am receiving is shown after the Sweave output here. It happens regardless of whether the code is run in Sweave or manually in R. [snip] 10 : echo keep.source term verbatim (label = createWorkFlowBoundaryTransformLogicle) 11 : echo keep.source term verbatim (label = LiveDeadUVFilterAlt) 12 : keep.source term tex (label = summaryLive) 13 : echo keep.source term verbatim pdf (label = plotLiveDead) 14 : keep.source (label = LiveDeadUVFiltercd3) 15 : keep.source (label = plotLiveDeadcd3) 16 : echo keep.source term verbatim (label = singletfilterCreate) 17 : echo keep.source term verbatim pdf (label = plotSingletfilter) 18 : echo keep.source term verbatim (label = lymphocyteFilterCD4CD3) 19 : echo keep.source term verbatim (label = add.lymph.Gate) Error: chunk 19 (label = add.lymph.Gate) Error in function (classes, fdef, mtable) : unable to find an inherited method for function "add", for signature "workFlow", "list" In addition: Warning messages: 1: In readBin(con, dattype, n = (offsets["dataend"] - offsets["datastart"] + : 'signed = FALSE' is only valid for integers of sizes 1 and 2 2: In readBin(con, dattype, n = (offsets["dataend"] - offsets["datastart"] + : 'signed = FALSE' is only valid for integers of sizes 1 and 2 3: In readBin(con, dattype, n = (offsets["dataend"] - offsets["datastart"] + : 'signed = FALSE' is only valid for integers of sizes 1 and 2 4: In readBin(con, dattype, n = (offsets["dataend"] - offsets["datastart"] + : 'signed = FALSE' is only valid for integers of sizes 1 and 2 5: In readBin(con, dattype, n = (offsets["dataend"] - offsets["datastart"] + : 'signed = FALSE' is only valid for integers of sizes 1 and 2 6: In readBin(con, dattype, n = (offsets["dataend"] - offsets["datastart"] + : 'signed = FALSE' is only valid for integers of sizes 1 and 2 7: In readBin(con, dattype, n = (offsets["dataend"] - offsets["datastart"] + : 'signed = FALSE' is only valid for integers of sizes 1 and 2 The only difference overnight is that I 'upgraded' the tcl/tk package on my computer. Since then I have reinstalled R and ran upgrade.packages for both R and Bioconductor, but the problem persists. I suspect I have not provided enough information here. Any ideas on how to figure this out would be greatly appreciated. Thanks, Aric ----------------- sessionInfo() R version 2.13.2 (2011-09-30) Platform: amd64-portbld-freebsd9.0 (64-bit) locale: [1] C attached base packages: [1] splines tools grid stats graphics grDevices utils [8] datasets methods base other attached packages: [1] xtable_1.6-0 Rgraphviz_1.30.1 flowQ_1.12.0 [4] latticeExtra_0.6-19 RColorBrewer_1.0-5 parody_1.10.0 [7] bioDist_1.24.1 KernSmooth_2.23-7 outliers_0.14 [10] flowStats_1.13.0 cluster_1.14.1 mvoutlier_1.9.4 [13] robCompositions_1.5.0 car_2.0-11 survival_2.36-10 [16] nnet_7.3-1 compositions_1.10-2 energy_1.4-0 [19] MASS_7.3-14 boot_1.3-2 tensorA_0.36 [22] rgl_0.92.798 fda_2.2.7 zoo_1.7-6 [25] flowWorkspace_0.99.22 IDPmisc_1.1.16 flowViz_1.16.0 [28] lattice_0.19-33 flowCore_1.18.0 rrcov_1.3-01 [31] pcaPP_1.9-44 mvtnorm_0.9-9991 robustbase_0.7-8 [34] Biobase_2.12.2 XML_3.4-3 RBGL_1.29.0 [37] graph_1.30.0 multicore_0.1-7 Rmpi_0.5-9 [40] fortunes_1.4-2 loaded via a namespace (and not attached): [1] AnnotationDbi_1.14.1 DBI_0.2-5 RSQLite_0.10.0 [4] annotate_1.30.1 feature_1.2.8 geneplotter_1.30.0 [7] ks_1.8.4 stats4_2.13.2

On 11/13/2011 12:08 PM, Aric Gregson wrote: > Hello, > > I have an odd issue that I have been unable thus far to resolve. > Literally overnight it has become impossible to add a lymphGate filter > to a workFlow. This is specific for the lymphGate filter only, as any > other type of filter works just fine. The error that I am receiving is > shown after the Sweave output here. It happens regardless of whether > the code is run in Sweave or manually in R. > > [snip] > 10 : echo keep.source term verbatim (label = > createWorkFlowBoundaryTransformLogicle) > 11 : echo keep.source term verbatim (label = LiveDeadUVFilterAlt) > 12 : keep.source term tex (label = summaryLive) > 13 : echo keep.source term verbatim pdf (label = plotLiveDead) > 14 : keep.source (label = LiveDeadUVFiltercd3) > 15 : keep.source (label = plotLiveDeadcd3) > 16 : echo keep.source term verbatim (label = singletfilterCreate) > 17 : echo keep.source term verbatim pdf (label = plotSingletfilter) > 18 : echo keep.source term verbatim (label = lymphocyteFilterCD4CD3) > 19 : echo keep.source term verbatim (label = add.lymph.Gate) > > Error: chunk 19 (label = add.lymph.Gate) > Error in function (classes, fdef, mtable) : > unable to find an inherited method for function "add", for signature > "workFlow", "list" > In addition: Warning messages: > 1: In readBin(con, dattype, n = (offsets["dataend"] - > offsets["datastart"] + : > 'signed = FALSE' is only valid for integers of sizes 1 and 2 > 2: In readBin(con, dattype, n = (offsets["dataend"] - > offsets["datastart"] + : > 'signed = FALSE' is only valid for integers of sizes 1 and 2 > 3: In readBin(con, dattype, n = (offsets["dataend"] - > offsets["datastart"] + : > 'signed = FALSE' is only valid for integers of sizes 1 and 2 > 4: In readBin(con, dattype, n = (offsets["dataend"] - > offsets["datastart"] + : > 'signed = FALSE' is only valid for integers of sizes 1 and 2 > 5: In readBin(con, dattype, n = (offsets["dataend"] - > offsets["datastart"] + : > 'signed = FALSE' is only valid for integers of sizes 1 and 2 > 6: In readBin(con, dattype, n = (offsets["dataend"] - > offsets["datastart"] + : > 'signed = FALSE' is only valid for integers of sizes 1 and 2 > 7: In readBin(con, dattype, n = (offsets["dataend"] - > offsets["datastart"] + : > 'signed = FALSE' is only valid for integers of sizes 1 and 2 > > > The only difference overnight is that I 'upgraded' the tcl/tk package > on my computer. Since then I have reinstalled R and ran > upgrade.packages for both R and Bioconductor, but the problem persists. > I suspect I have not provided enough information here. Any ideas on how > to figure this out would be greatly appreciated. Hi Aric -- instead of running 'Sweave' on your vignette, trying running 'Stangle'. This produces an R script file that you can step through. Likely you'll get to the code corresponding to chunk 19, and see the error. Likely you can narrow this down to a single function call that causes the problem and, with luck, identify a parameter to a call to add() (probably the second parameter) that is a 'list' rather than what it is supposed to be. But at that point you might be able to give us a simple-to-reproduce example. Martin > > Thanks, Aric > ----------------- > > sessionInfo() > R version 2.13.2 (2011-09-30) > Platform: amd64-portbld-freebsd9.0 (64-bit) > > locale: > [1] C > > attached base packages: > [1] splines tools grid stats graphics grDevices > utils > [8] datasets methods base > > other attached packages: > [1] xtable_1.6-0 Rgraphviz_1.30.1 flowQ_1.12.0 > [4] latticeExtra_0.6-19 RColorBrewer_1.0-5 parody_1.10.0 > [7] bioDist_1.24.1 KernSmooth_2.23-7 outliers_0.14 > [10] flowStats_1.13.0 cluster_1.14.1 mvoutlier_1.9.4 > [13] robCompositions_1.5.0 car_2.0-11 survival_2.36-10 > [16] nnet_7.3-1 compositions_1.10-2 energy_1.4-0 > [19] MASS_7.3-14 boot_1.3-2 tensorA_0.36 > [22] rgl_0.92.798 fda_2.2.7 zoo_1.7-6 > [25] flowWorkspace_0.99.22 IDPmisc_1.1.16 flowViz_1.16.0 > [28] lattice_0.19-33 flowCore_1.18.0 rrcov_1.3-01 > [31] pcaPP_1.9-44 mvtnorm_0.9-9991 robustbase_0.7-8 > [34] Biobase_2.12.2 XML_3.4-3 RBGL_1.29.0 > [37] graph_1.30.0 multicore_0.1-7 Rmpi_0.5-9 > [40] fortunes_1.4-2 > > loaded via a namespace (and not attached): > [1] AnnotationDbi_1.14.1 DBI_0.2-5 RSQLite_0.10.0 > [4] annotate_1.30.1 feature_1.2.8 geneplotter_1.30.0 > [7] ks_1.8.4 stats4_2.13.2 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793