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Question: Bioconductor's qvalue package not working on Macs!
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gravatar for Josh B
5.2 years ago by
Josh B30
Josh B30 wrote:
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 [[alternative HTML version deleted]]
ADD COMMENTlink modified 5.2 years ago by Wolfgang Huber13k • written 5.2 years ago by Josh B30
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gravatar for Dan Tenenbaum
5.2 years ago by
Dan Tenenbaum ♦♦ 8.2k
United States
Dan Tenenbaum ♦♦ 8.2k wrote:
Hi Josh, On Tue, Sep 18, 2012 at 1:29 PM, Josh B <joshb41 at="" yahoo.com=""> wrote: > 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! It is difficult to know what's going on because you do not provide any of the output produced by R in response to your commands. Please also send the output of the sessionInfo() command. Dan > > 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 > > [[alternative HTML version deleted]] > > > _______________________________________________ > 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
ADD COMMENTlink written 5.2 years ago by Dan Tenenbaum ♦♦ 8.2k
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gravatar for Wolfgang Huber
5.2 years ago by
EMBL European Molecular Biology Laboratory
Wolfgang Huber13k 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
ADD COMMENTlink written 5.2 years ago by Wolfgang Huber13k
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]]
ADD REPLYlink written 5.2 years ago by Josh B30
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
ADD REPLYlink written 5.2 years ago by Benilton Carvalho4.2k
Dear Ben (and others who responded), I figured out my problem! I did not have the Tcl/Tk libraries installed. They used to be included as part of the OS X installation, but now they are not. So now they must be installed separately. For others who encounter my problem: First download the *signed* version of the latest R installation package. Then, if you look very carefully at the same screen where you downloaded the latest R installation package, you'll see the following text: "This package only contains the R framework, 32-bit GUI (R.app) and 64-bit GUI (R64.app). For Tcl/Tk libraries (needed if you want to use tcltk) and GNU Fortran (needed if you want to compile packages from sources that contain FORTRAN code) please see the tools directory." Click on the link in that text to download the package containing the Tcl/Tk libraries, and then install the package. Voila! It will work! I thank all of you who took the time to respond to my query. You got me pointed in the right direction. Your feedback was vital. Sincerely, Josh ________________________________ From: Benilton Carvalho <beniltoncarvalho@gmail.com> To: Wolfgang Huber <whuber@embl.de> Cc: bioconductor@r-project.org Sent: Wednesday, September 19, 2012 4:52 AM [[elided Yahoo spam]] 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@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. >> [[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 _______________________________________________ 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]]
ADD REPLYlink written 5.2 years ago by Josh B30
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