Thanks a lot. Yesterday I was unable to get the error because the graphite I downloaded was not the latest version (it had a build failure).
I'll fix clipper asap. Thanks again. Paolo 2017-10-20 10:12 GMT+02:00 Martin Morgan <martin.mor...@roswellpark.org>: > On 10/20/2017 03:43 AM, Paolo Martini wrote: > >> Dear all, >> >> I am the clipper package maintainer. >> According to the "Build/check report" for BioC 3.6, >> the clipper package has an error while compiling the vignette. >> >> I try to reproduce the error in my computer using the devel version but >> the >> R CMD check and installation goes smoothly. >> > > I verified that I'm using devel and my packages are current > > $ R > > R.version.string # 3.4.2 > > BiocInstaller::isDevel() # TRUE > > BiocInstaller::biocValid() # TRUE > > I checked out a fresh copy of clipper, into a temporary directory > > $ git clone https://git.bioconductor.org/packages/clipper > > then installed it > > $ R CMD INSTALL clipper > > I then extracted the R source code of the vignette > > $ cd clipper/vignettes > $ R CMD Stangle clipper.Rnw # could have used knitr::purl() for Rmd > > and tried to run the vignette code > > $ R -f clipper.R > > It fails as on the build system > > > pathwayAnalysis <- pathQ(exp, classes, graph, nperm=100, alphaV=0.05, > b=100) > Error in getExpression(exprs(expr), classes) : Gene names not specified. > Calls: pathQ ... getExpression -> getExpression -> getExpression -> > getExpression > Execution halted > > OK, reproducible without any additional stuff like devtools or RStudio > getting in the way. Time to debug. I started R in my favorite IDE, and > tried to source the vignette > > $ source("clipper.R", echo=TRUE, max=Inf) > > it fails in the same way. I looked for the error, and tried to reproduce > it in a simpler fashion, guessing a bit at what the failing code was trying > to do ('expr' in the traceback() being the function argument 'exp') > > > pathwayAnalysis <- pathQ(exp, classes, graph, nperm=100, alphaV=0.05, > b=100) > Error in getExpression(exprs(expr), classes) : Gene names not specified. > > traceback() > 10: stop("Gene names not specified.") > 9: getExpression(exprs(expr), classes) > 8: getExpression(exprs(expr), classes) > 7: getExpression(expr, classes) > 6: getExpression(expr, classes) > 5: pathQ(exp, classes, graph, nperm = 100, alphaV = 0.05, b = 100) at > clipper.R#95 > 4: eval(ei, envir) > 3: eval(ei, envir) > 2: withVisible(eval(ei, envir)) > 1: source("clipper.R", echo = TRUE, max = Inf) > > clipper:::getExpression(exprs(exp), classes) > Error in clipper:::getExpression(exprs(exp), classes) : > Gene names not specified. > > I found that clipper:::getExpression is and S4 generic, with a likely > method, so set the debugger and tried again > > > clipper:::getExpression > standardGeneric for "getExpression" defined from package "clipper" > > function (expr, classes) > standardGeneric("getExpression") > <environment: 0x11061920> > Methods may be defined for arguments: expr, classes > Use showMethods("getExpression") for currently available ones. > > showMethods(clipper:::getExpression) > Function: getExpression (package clipper) > expr="ExpressionSet", classes="numeric" > expr="matrix", classes="numeric" > > > debug(clipper:::getExpression, signature=c("matrix", "numeric")) > > clipper:::getExpression(exprs(exp), classes) > Tracing clipper:::getExpression(exprs(exp), classes) step 2 > Called from: eval(expr, p) > Browse[1]> n > debug: if (is.null(rownames(expr))) stop("Gene names not specified.") > Browse[2]> rownames(expr) > NULL > Browse[2]> Q > > > > and back at the top level > > > rownames(exprs(exp)) > NULL > > hmm, this looks weird > > > dim(exp) > Features Samples > 0 79 > > In code chunk 3 you'd got the genes from graphite, and > > > head(genes) > [1] "ENTREZID:10000" "ENTREZID:1019" "ENTREZID:1021" > [4] "ENTREZID:1026" "ENTREZID:1029" "ENTREZID:1147" > > in code chunk 10 you'd calculated the intersection of these genes with the > row.names of the sample expression set > > > intersect(genes, row.names(exprs(all))) > character(0) > > and this is because the rownames are in a different format > > > head(row.names(exprs(all))) > [1] "5595" "7075" "1557" "643" "643" "1843" > > I guess this is because graphite or one of it's dependencies has changed, > accidentally or otherwise, the format of the identifiers returned in chunk > 3. Likely the reason that you were not able to reproduce this is because > you were using an out-of-date version of graphite (isDevel() and > biocValid() would have diagnosed this). I don't know whether the resolution > is a bug fix in graphite, or a fix to your own vignette code; it is always > worth pushing the resolution as close to the source of the problem as > possible, so if it's a change in graphite then engage the > maintainer("graphite") in your investigation. > > Martin > > >> Anyone has suggestions on how to debug this? >> >> >> > > This email message may contain legally privileged and/or confidential > information. If you are not the intended recipient(s), or the employee or > agent responsible for the delivery of this message to the intended > recipient(s), you are hereby notified that any disclosure, copying, > distribution, or use of this email message is prohibited. If you have > received this message in error, please notify the sender immediately by > e-mail and delete this email message from your computer. Thank you. > -- ******************************* Paolo Martini c/o Lab Romualdi via U. Bassi 58/b 35121 Padova, Italy Tel: 049 8276319 Fax: 049 8276159 e-mail: paolo.mart...@unipd.it http://romualdi.bio.unipd.it/ ******************************* [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
