Dear Wolfgang, Thank you for your reply. This is very strange! I cannot get qvalue to work on any of three different Macs (running either OSX Mountain Lion or Lion.) The error messages are the same on all three machines, even after I uninstall R and re-install. Here is the full output from my session, including the crash: > source("http://bioconductor.org/biocLite.R") BiocInstaller version 1.4.7, ?biocLite for help > biocLite("qvalue") BioC_mirror: http://bioconductor.org Using R version 2.15, BiocInstaller version 1.4.7. Warning: unable to access index for repository http://brainarray.mbni. med.umich.edu/bioc/bin/macosx/leopard/contrib/2.15 Installing package(s) 'qvalue' Warning: unable to access index for repository http://brainarray.mbni. med.umich.edu/bioc/bin/macosx/leopard/contrib/2.15 trying URL 'http://www.bioconductor.org/packages/2.10/bioc/bin/macosx/ leopard/contrib/2.15/qvalue_1.30.0.tgz' Content type 'application/x-gzip' length 553875 bytes (540 Kb) opened URL ================================================== downloaded 540 Kb The downloaded binary packages are in /var/folders/yx/wxbjjl592j775_b0fgrdry440000gn/T//RtmpG3UNv7/downloade d_packages Warning: unable to access index for repository http://brainarray.mbni. med.umich.edu/bioc/bin/macosx/leopard/contrib/2.15 > library(qvalue) Loading Tcl/Tk interface ...  *** caught segfault *** address 0x70000000c, cause 'memory not mapped' Traceback:  1: sys.parent()  2: sys.function(sys.parent())  3: formals(sys.function(sys.parent()))  4: match.arg(encoding)  5: match(match.arg(encoding), c("", "bytes", "UTF-8"))  6: textConnection("rval", "w", local = TRUE)  7: capture.output(print(args(sessionInfo)))  8: paste(capture.output(print(args(sessionInfo))), collapse = "")  9: gsub("\\s+", " ", paste(capture.output(print(args(sessionInfo))), collapse = "")) 10: doTryCatch(return(expr), name, parentenv, handler) 11: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 12: tryCatchList(expr, classes, parentenv, handlers) 13: tryCatch(expr, error = function(e) {    call <- conditionCall(e) if (!is.null(call)) {        if (identical(call[[1L]], quote(doTryCatch)))             call <- sys.call(-4L)        dcall <- deparse(call)[1L]        prefix <- paste("Error in", dcall, ": ") LONG <- 75L        msg <- conditionMessage(e)        sm <- strsplit(msg, "\n")[[1L]]        w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")        if is.na(w))             w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],                 type = "b") if (w > LONG)             prefix <- paste0(prefix, "\n  ")    } else prefix <- "Error : "    msg <- paste0(prefix, conditionMessage(e), "\n")    .Internal(seterrmessage(msg[1L]))    if (!silent && identical(getOption("show.error.messages"),         TRUE)) {        cat(msg, file = stderr())  .Internal(printDeferredWarnings())    }    invisible(structure(msg, class = "try-error", condition = e))}) 14: try(gsub("\\s+", " ", paste(capture.output(print(args(sessionInfo))),     collapse = "")), silent = TRUE) Possible actions: 1: abort (with core dump, if enabled) 2: normal R exit 3: exit R without saving workspace 4: exit R saving workspace > sessionInfo() ________________________________ From: Wolfgang Huber <whuber@embl.de> To: bioconductor@r-project.org Sent: Wednesday, September 19, 2012 1:47 AM [[elided Yahoo spam]] Josh, the qvalue package and in particular the code you list below works perfectly well (the GUI opens and responds) on the machine I have just tested it with (OS X 10.8.1 (12B19)). Perhaps your installation of R is broken? > sessionInfo() R Under development (unstable) (2012-09-18 r60759) Platform: x86_64-apple-darwin12.1.0/x86_64 (64-bit) locale: [1] C attached base packages: [1] stats    graphics  grDevices utils    datasets  methods  base other attached packages: [1] qvalue_1.31.0        BiocInstaller_1.5.12 fortunes_1.5-0 loaded via a namespace (and not attached): [1] tcltk_2.16.0 tools_2.16.0 PS in·duc·tion; noun, the inference of a general statement from a finite set of examples.     Best wishes     Wolfgang Sep/18/12 10:29 PM, Josh B scripsit: > Dear listserv members, > > I have discovered that the qvalue package no longer works on Macs, at > least those running OS X Lion or Mountain Lion. I have tried multiple > different machines, and in each case, the qvalue package fails to > load properly and R crashes when I attempt to use the "qvalue()" > command. > > Is there something I am doing wrong, or can someone verify that I am > right? This is a serious problem for me. > > Here is the exact code I am running (please note that changing the > Bioconductor mirror does NOT help): > > Source("http://bioconductor.org/biocLite.R") biocLite("qvalue") #this > generates many indecipherable warnings library(qvalue) #now this part > coming up here is the specific part that causes the crash: > > qvalue() #boom, that's it, R shuts down. #Please note that changing > the Bioconductor mirror does not help: > > chooseBioCmirror() #choose whichever mirror you like > > Source("http://bioconductor.org/biocLite.R") biocLite("qvalue") > #again, many indecipherable warnings library(qvalue) qvalue() #boom, > R shuts down again, same as before > > If you run my code, above, you will find this exact same problem on > ANY Mac running OSX Lion or Mountain Lion. But is there any way to > get qvalue working on my Mac? I very much need it. > [[elided Yahoo spam]] > > Sincerely, Josh Banta, Ph.D > > Assistant Professor Department of Biology The University of Texas at > Tyler Tyler, TX 75799 Tel: (903) 565-5655 > http://plantevolutionaryecology.org > -- Best wishes     Wolfgang Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber _______________________________________________ Bioconductor mailing list Bioconductor@r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]

Idem for a machine on 10.6.8 running the latest stable R release. > sessionInfo() R version 2.15.1 Patched (2012-09-03 r60555) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages: [1] stats graphics grDevices datasets utils methods base other attached packages: [1] qvalue_1.30.0 RColorBrewer_1.0-5 BiocInstaller_1.4.7 loaded via a namespace (and not attached): [1] tcltk_2.15.1 tools_2.15.1 On 19 September 2012 07:47, Wolfgang Huber <whuber at="" embl.de=""> wrote: > Josh, > > the qvalue package and in particular the code you list below works perfectly > well (the GUI opens and responds) on the machine I have just tested it with > (OS X 10.8.1 (12B19)). Perhaps your installation of R is broken? > >> sessionInfo() > R Under development (unstable) (2012-09-18 r60759) > Platform: x86_64-apple-darwin12.1.0/x86_64 (64-bit) > > locale: > [1] C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] qvalue_1.31.0 BiocInstaller_1.5.12 fortunes_1.5-0 > > loaded via a namespace (and not attached): > [1] tcltk_2.16.0 tools_2.16.0 > > PS in?duc?tion; noun, the inference of a general statement from a finite set > of examples. > > Best wishes > Wolfgang > > > Sep/18/12 10:29 PM, Josh B scripsit: > >> Dear listserv members, >> >> I have discovered that the qvalue package no longer works on Macs, at >> least those running OS X Lion or Mountain Lion. I have tried multiple >> different machines, and in each case, the qvalue package fails to >> load properly and R crashes when I attempt to use the "qvalue()" >> command. >> >> Is there something I am doing wrong, or can someone verify that I am >> right? This is a serious problem for me. >> >> Here is the exact code I am running (please note that changing the >> Bioconductor mirror does NOT help): >> >> Source("http://bioconductor.org/biocLite.R") biocLite("qvalue") #this >> generates many indecipherable warnings library(qvalue) #now this part >> coming up here is the specific part that causes the crash: >> >> qvalue() #boom, that's it, R shuts down. #Please note that changing >> the Bioconductor mirror does not help: >> >> chooseBioCmirror() #choose whichever mirror you like >> >> Source("http://bioconductor.org/biocLite.R") biocLite("qvalue") >> #again, many indecipherable warnings library(qvalue) qvalue() #boom, >> R shuts down again, same as before >> >> If you run my code, above, you will find this exact same problem on >> ANY Mac running OSX Lion or Mountain Lion. But is there any way to >> get qvalue working on my Mac? I very much need it. >> >> Thank you in advance! >> >> Sincerely, Josh Banta, Ph.D >> >> Assistant Professor Department of Biology The University of Texas at >> Tyler Tyler, TX 75799 Tel: (903) 565-5655 >> http://plantevolutionaryecology.org >> > > -- > Best wishes > Wolfgang > > Wolfgang Huber > EMBL > http://www.embl.de/research/units/genome_biology/huber > > > _______________________________________________ > 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