crlmm error in Mac OS
1
0
Entering edit mode
@steven-buechler-4530
Last seen 9.6 years ago
Before using crlmm in the oligo package for a research project I executed the following commands copied from the vignette and received the error reported below. Any suggestions would be appreciated. Steven Buechler buechler.1 at nd.edi ***** > library(oligo) > library("hapmap100kxba") > pathCelFiles <- system.file("celFiles", package = "hapmap100kxba") > fullFilenames <- list.celfiles(path = pathCelFiles, + full.names = TRUE) > outputDir <- file.path(getwd(), "crlmmTest") > crlmm(fullFilenames, outputDir, verbose = FALSE) Error: !(missing(tmpdir) | file.exists(tmpdir)) is not TRUE > tempdir() [1] "/var/folders/uA/uAFdydnnHIiHJBV4o2gC-E+++TI/-Tmp-//RtmpH9vgb7" > traceback() 4: stop(paste(ch, " is not ", if (length(r) > 1L) "all ", "TRUE", sep = ""), call. = FALSE) 3: stopifnot(!(missing(tmpdir) | file.exists(tmpdir))) 2: justCRLMMv3(filenames, outdir, batch_size = batch_size, recalibrate = recalibrate, minLLRforCalls = minLLRforCalls, balance = balance, verbose = verbose) 1: crlmm(fullFilenames, outputDir, verbose = FALSE) > sessionInfo() R version 2.12.2 (2011-02-25) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] tools stats graphics grDevices utils datasets [7] methods base other attached packages: [1] pd.mapping50k.xba240_1.1.0 RSQLite_0.9-4 [3] DBI_0.2-5 hapmap100kxba_1.3.3 [5] ff_2.2-1 bit_1.1-6 [7] oligo_1.14.0 oligoClasses_1.12.2 [9] Biobase_2.10.0 loaded via a namespace (and not attached): [1] affxparser_1.22.1 affyio_1.18.0 [3] Biostrings_2.18.4 IRanges_1.8.9 [5] preprocessCore_1.12.0 splines_2.12.2 >
oligo crlmm oligo crlmm • 1.1k views
ADD COMMENT
0
Entering edit mode
@vincent-j-carey-jr-4
Last seen 15 days ago
United States
I cannot confirm this with the sessionInfo shown below. [code from vignette...] > crlmm(fullFilenames, outputDir, verbose = FALSE) Loading required package: DBI Removing temporary files ... OK. > sessionInfo() R version 2.12.2 Patched (2011-03-03 r54672) Platform: x86_64-apple-darwin10.4.0/x86_64 (64-bit) locale: [1] C attached base packages: [1] stats graphics grDevices datasets tools utils methods [8] base other attached packages: [1] pd.mapping50k.xba240_1.1.0 RSQLite_0.9-4 [3] DBI_0.2-5 hapmap100kxba_1.3.3 [5] oligo_1.14.0 oligoClasses_1.12.1 [7] Biobase_2.10.0 weaver_1.16.0 [9] codetools_0.2-5 digest_0.4.2 loaded via a namespace (and not attached): [1] Biostrings_2.18.2 IRanges_1.8.7 affxparser_1.22.0 [4] affyio_1.18.0 preprocessCore_1.12.0 splines_2.12.2 On Sat, Mar 5, 2011 at 2:16 PM, Steven Buechler <buechler.1 at="" nd.edu=""> wrote: > Before using crlmm in the oligo package for a research project I executed the following commands copied from the vignette and received the error reported below. Any suggestions would be appreciated. > > Steven Buechler > buechler.1 at nd.edi > > ***** > >> library(oligo) >> library("hapmap100kxba") >> pathCelFiles <- system.file("celFiles", package = "hapmap100kxba") >> fullFilenames <- list.celfiles(path = pathCelFiles, > + full.names = TRUE) >> outputDir <- file.path(getwd(), "crlmmTest") > >> crlmm(fullFilenames, outputDir, verbose = FALSE) > Error: !(missing(tmpdir) | file.exists(tmpdir)) is not TRUE > >> tempdir() > [1] "/var/folders/uA/uAFdydnnHIiHJBV4o2gC-E+++TI/-Tmp-//RtmpH9vgb7" >> traceback() > 4: stop(paste(ch, " is not ", if (length(r) > 1L) "all ", "TRUE", > ? ? ? sep = ""), call. = FALSE) > 3: stopifnot(!(missing(tmpdir) | file.exists(tmpdir))) > 2: justCRLMMv3(filenames, outdir, batch_size = batch_size, recalibrate = recalibrate, > ? ? ? minLLRforCalls = minLLRforCalls, balance = balance, verbose = verbose) > 1: crlmm(fullFilenames, outputDir, verbose = FALSE) >> sessionInfo() > R version 2.12.2 (2011-02-25) > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > locale: > [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] tools ? ? stats ? ? graphics ?grDevices utils ? ? datasets > [7] methods ? base > > other attached packages: > [1] pd.mapping50k.xba240_1.1.0 RSQLite_0.9-4 > [3] DBI_0.2-5 ? ? ? ? ? ? ? ? ?hapmap100kxba_1.3.3 > [5] ff_2.2-1 ? ? ? ? ? ? ? ? ? bit_1.1-6 > [7] oligo_1.14.0 ? ? ? ? ? ? ? oligoClasses_1.12.2 > [9] Biobase_2.10.0 > > loaded via a namespace (and not attached): > [1] affxparser_1.22.1 ? ? affyio_1.18.0 > [3] Biostrings_2.18.4 ? ? IRanges_1.8.9 > [5] preprocessCore_1.12.0 splines_2.12.2 >> > > > _______________________________________________ > 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 >
ADD COMMENT
0
Entering edit mode
Hi Vince, Steven, The error message is not helping but it seems that crlmm() won't write to an output dir that already exists. So you just need to delete the folder pointed by 'outputDir' (set by you to 'file.path(getwd(), "crlmmTest")'), or set it to another location. H. On 03/05/2011 12:56 PM, Vincent Carey wrote: > I cannot confirm this with the sessionInfo shown below. > > [code from vignette...] >> crlmm(fullFilenames, outputDir, verbose = FALSE) > Loading required package: DBI > Removing temporary files ... OK. >> sessionInfo() > R version 2.12.2 Patched (2011-03-03 r54672) > Platform: x86_64-apple-darwin10.4.0/x86_64 (64-bit) > > locale: > [1] C > > attached base packages: > [1] stats graphics grDevices datasets tools utils methods > [8] base > > other attached packages: > [1] pd.mapping50k.xba240_1.1.0 RSQLite_0.9-4 > [3] DBI_0.2-5 hapmap100kxba_1.3.3 > [5] oligo_1.14.0 oligoClasses_1.12.1 > [7] Biobase_2.10.0 weaver_1.16.0 > [9] codetools_0.2-5 digest_0.4.2 > > loaded via a namespace (and not attached): > [1] Biostrings_2.18.2 IRanges_1.8.7 affxparser_1.22.0 > [4] affyio_1.18.0 preprocessCore_1.12.0 splines_2.12.2 > > > On Sat, Mar 5, 2011 at 2:16 PM, Steven Buechler<buechler.1 at="" nd.edu=""> wrote: >> Before using crlmm in the oligo package for a research project I executed the following commands copied from the vignette and received the error reported below. Any suggestions would be appreciated. >> >> Steven Buechler >> buechler.1 at nd.edi >> >> ***** >> >>> library(oligo) >>> library("hapmap100kxba") >>> pathCelFiles<- system.file("celFiles", package = "hapmap100kxba") >>> fullFilenames<- list.celfiles(path = pathCelFiles, >> + full.names = TRUE) >>> outputDir<- file.path(getwd(), "crlmmTest") >> >>> crlmm(fullFilenames, outputDir, verbose = FALSE) >> Error: !(missing(tmpdir) | file.exists(tmpdir)) is not TRUE >> >>> tempdir() >> [1] "/var/folders/uA/uAFdydnnHIiHJBV4o2gC-E+++TI/-Tmp-//RtmpH9vgb7" >>> traceback() >> 4: stop(paste(ch, " is not ", if (length(r)> 1L) "all ", "TRUE", >> sep = ""), call. = FALSE) >> 3: stopifnot(!(missing(tmpdir) | file.exists(tmpdir))) >> 2: justCRLMMv3(filenames, outdir, batch_size = batch_size, recalibrate = recalibrate, >> minLLRforCalls = minLLRforCalls, balance = balance, verbose = verbose) >> 1: crlmm(fullFilenames, outputDir, verbose = FALSE) >>> sessionInfo() >> R version 2.12.2 (2011-02-25) >> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) >> >> locale: >> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 >> >> attached base packages: >> [1] tools stats graphics grDevices utils datasets >> [7] methods base >> >> other attached packages: >> [1] pd.mapping50k.xba240_1.1.0 RSQLite_0.9-4 >> [3] DBI_0.2-5 hapmap100kxba_1.3.3 >> [5] ff_2.2-1 bit_1.1-6 >> [7] oligo_1.14.0 oligoClasses_1.12.2 >> [9] Biobase_2.10.0 >> >> loaded via a namespace (and not attached): >> [1] affxparser_1.22.1 affyio_1.18.0 >> [3] Biostrings_2.18.4 IRanges_1.8.9 >> [5] preprocessCore_1.12.0 splines_2.12.2 >>> >> >> >> _______________________________________________ >> 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 >> > > _______________________________________________ > 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 -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319
ADD REPLY

Login before adding your answer.

Traffic: 718 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6