Hello All, I am trying to take advantage of some of the plotting options in the qrqc package but I am getting an error (related to the "new" Illumina quality scores) that seems to have come up last month (in the archives). I tried to install with type = source but that did not fix the error. Thanks for any suggestions. Best, Noah > source("http://bioconductor.org/biocLite.R") BiocInstaller version 1.2.1, ?biocLite for help > biocLite("qrqc", type = "source") BioC_mirror: 'http://www.bioconductor.org' Using R version 2.14, BiocInstaller version 1.2.1. Installing package(s) 'qrqc' trying URL 'http://www.bioconductor.org/packages/2.9/bioc/src/contrib/ qrqc_1.2.0.tar.gz' Content type 'application/x-gzip' length 213683 bytes (208 Kb) opened URL ================================================== downloaded 208 Kb * installing *source* package ?qrqc? ... ** libs *** arch - i386 gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/ Resources/library/Rsamtools/include" -fPIC -g -O2 -c R_init_io.c -o R_init_io.o gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/ Resources/library/Rsamtools/include" -fPIC -g -O2 -c io.c -o io.o gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o qrqc.so R_init_io.o io.o -lz /Library/Frameworks/R .framework/Versions/2.14/Resources/library/Rsamtools/usrlib/i386/libba m.a /Library/Frameworks/R.framework/Versions/2.14/Resources/library/Rs amtools/usrlib/i386/libbcf.a /Library/Frameworks/R.framework/Versions/ 2.14/Resources/library/Rsamtools/usrlib/i386/libtabix.a -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/2.14/Resources/ library/qrqc/libs/i386 *** arch - x86_64 gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/ Resources/library/Rsamtools/include" -fPIC -g -O2 -c R_init_io.c -o R_init_io.o gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/ Resources/library/Rsamtools/include" -fPIC -g -O2 -c io.c -o io.o gcc -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o qrqc.so R_init_io.o io.o -lz /Library/Frameworks/R.framework/Versions/2.14/Res ources/library/Rsamtools/usrlib/x86_64/libbam.a /Library/Frameworks/R. framework/Versions/2.14/Resources/library/Rsamtools/usrlib/x86_64/libb cf.a /Library/Frameworks/R.framework/Versions/2.14/Resources/library/R samtools/usrlib/x86_64/libtabix.a -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/2.14/Resources/ library/qrqc/libs/x86_64 ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ... *** tangling vignette sources ... ?qrqc.Rnw? ** testing if installed package can be loaded *** arch - i386 *** arch - x86_64 * DONE (qrqc) The downloaded packages are in ?/private/var/folders/14/14lHU6sYHXWDo48Jc3Lq++lgIs+/-Tmp-/Rtm pJAbtgf/downloaded_packages? > library(qrqc) Loading required package: Rsamtools Loading required package: IRanges Attaching package: ?IRanges? The following object(s) are masked from ?package:base?: cbind, eval, intersect, Map, mapply, order, paste, pmax, pmax.int, pmin, pmin.int, rbind, rep.int, setdiff, table, union Loading required package: GenomicRanges Loading required package: Biostrings Loading required package: tools > tempSeqs <- readSeqFile(filename = "/Users/ndowell/Documents/Catrox/ GenomeSequence/RawData/ShotgunPEmarch2012/Fastq/run248.PEIi- 4_TGACCA_L003_R1.fastq") Error in readSeqFile(filename = "/Users/ndowell/Documents/Catrox/Genom eSequence/RawData/ShotgunPEmarch2012/Fastq/run248.PEIi- 4_TGACCA_L003_R1.fastq") : base quality out of range (0 <= b <= 62) encountered: 35 > s.fastq <- readSeqFile(system.file('extdata', 'test.fastq', package='qrqc')) > qualPlot(s.fastq) Error: could not find function "qualPlot" > sessionInfo() R version 2.14.1 (2011-12-22) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] tools stats graphics grDevices utils datasets methods base other attached packages: [1] qrqc_1.2.0 Rsamtools_1.6.3 Biostrings_2.22.0 GenomicRanges_1.6.7 IRanges_1.12.6 BiocInstaller_1.2.1 loaded via a namespace (and not attached): [1] bitops_1.0-4.1 brew_1.0-6 BSgenome_1.22.0 evaluate_0.4.1 plyr_1.7.1 RCurl_1.91-1 reshape_0.8.4 rtracklayer_1.14.4 [9] stringr_0.6 testthat_0.6 XML_3.9-4 xtable_1.7-0 zlibbioc_1.0.1 Noah L. Dowell, Postdoctoral fellow Howard Hughes Medical Institute University of Wisconsin Department of Genetics 1525 Linden Drive Madison, WI 53706 608-265-2004 (lab) ndowell at wisc.edu

On Tue, Mar 20, 2012 at 9:35 PM, NDowell <ndowell at="" wisc.edu=""> wrote: > Hello All, > > > I am trying to take advantage of some of the plotting options in the qrqc package but I am getting an error (related to the "new" Illumina quality scores) that seems to have come up last month (in the archives). ?I tried to install with type = source but that did not fix the error. ?Thanks for any suggestions. Hi Noah, The qualPlot function exists in the devel branch, so you can't get to it with R-2.14. Install R-2.15 alpha (or wait for 2.15.0 and Bioconductor 2.10 in early April). Then just biocLite("qrqc") You won't need 'type="source"'. Dan > > > Best, > > Noah > > >> source("http://bioconductor.org/biocLite.R") > BiocInstaller version 1.2.1, ?biocLite for help >> ? ? biocLite("qrqc", type = "source") > BioC_mirror: 'http://www.bioconductor.org' > Using R version 2.14, BiocInstaller version 1.2.1. > Installing package(s) 'qrqc' > trying URL 'http://www.bioconductor.org/packages/2.9/bioc/src/contri b/qrqc_1.2.0.tar.gz' > Content type 'application/x-gzip' length 213683 bytes (208 Kb) > opened URL > ================================================== > downloaded 208 Kb > > * installing *source* package ?qrqc? ... > ** libs > *** arch - i386 > gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/ Resources/library/Rsamtools/include" ? -fPIC ?-g -O2 -c R_init_io.c -o R_init_io.o > gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/ Resources/library/Rsamtools/include" ? -fPIC ?-g -O2 -c io.c -o io.o > gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o qrqc.so R_init_io.o io.o -lz /Library/Frameworks/R.framework/Versions/2.14/Res ources/library/Rsamtools/usrlib/i386/libbam.a /Library/Frameworks/R.fr amework/Versions/2.14/Resources/library/Rsamtools/usrlib/i386/libbcf.a /Library/Frameworks/R.framework/Versions/2.14/Resources/library/Rsamto ols/usrlib/i386/libtabix.a -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation > installing to /Library/Frameworks/R.framework/Versions/2.14/Resource s/library/qrqc/libs/i386 > *** arch - x86_64 > gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/ Resources/library/Rsamtools/include" ? -fPIC ?-g -O2 -c R_init_io.c -o R_init_io.o > gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/ Resources/library/Rsamtools/include" ? -fPIC ?-g -O2 -c io.c -o io.o > gcc -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o qrqc.so R_init_io.o io.o -lz /Library/Frameworks/R.framework/Versions/2.14/Res ources/library/Rsamtools/usrlib/x86_64/libbam.a /Library/Frameworks/R. framework/Versions/2.14/Resources/library/Rsamtools/usrlib/x86_64/libb cf.a /Library/Frameworks/R.framework/Versions/2.14/Resources/library/R samtools/usrlib/x86_64/libtabix.a -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation > installing to /Library/Frameworks/R.framework/Versions/2.14/Resource s/library/qrqc/libs/x86_64 > ** R > ** inst > ** preparing package for lazy loading > ** help > *** installing help indices > ** building package indices ... > *** tangling vignette sources ... > ? ?qrqc.Rnw? > ** testing if installed package can be loaded > *** arch - i386 > *** arch - x86_64 > > * DONE (qrqc) > > The downloaded packages are in > ? ? ? ??/private/var/folders/14/14lHU6sYHXWDo48Jc3Lq++lgIs+/-Tmp-/Rt mpJAbtgf/downloaded_packages? >> library(qrqc) > Loading required package: Rsamtools > Loading required package: IRanges > > Attaching package: ?IRanges? > > The following object(s) are masked from ?package:base?: > > ? ?cbind, eval, intersect, Map, mapply, order, paste, pmax, pmax.int, pmin, pmin.int, rbind, rep.int, setdiff, table, union > > Loading required package: GenomicRanges > Loading required package: Biostrings > Loading required package: tools >> tempSeqs <- readSeqFile(filename = "/Users/ndowell/Documents/Catrox /GenomeSequence/RawData/ShotgunPEmarch2012/Fastq/run248.PEIi- 4_TGACCA_L003_R1.fastq") > Error in readSeqFile(filename = "/Users/ndowell/Documents/Catrox/Gen omeSequence/RawData/ShotgunPEmarch2012/Fastq/run248.PEIi- 4_TGACCA_L003_R1.fastq") : > ?base quality out of range (0 <= b <= 62) encountered: 35 > > > > > >> s.fastq <- readSeqFile(system.file('extdata', 'test.fastq', package='qrqc')) >> qualPlot(s.fastq) > Error: could not find function "qualPlot" > > > > > >> sessionInfo() > R version 2.14.1 (2011-12-22) > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > locale: > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] tools ? ? stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base > > other attached packages: > [1] qrqc_1.2.0 ? ? ? ? ?Rsamtools_1.6.3 ? ? Biostrings_2.22.0 ? GenomicRanges_1.6.7 IRanges_1.12.6 ? ? ?BiocInstaller_1.2.1 > > loaded via a namespace (and not attached): > ?[1] bitops_1.0-4.1 ? ? brew_1.0-6 ? ? ? ? BSgenome_1.22.0 ? ?evaluate_0.4.1 ? ? plyr_1.7.1 ? ? ? ? RCurl_1.91-1 ? ? ? reshape_0.8.4 ? ? ?rtracklayer_1.14.4 > ?[9] stringr_0.6 ? ? ? ?testthat_0.6 ? ? ? XML_3.9-4 ? ? ? ? ?xtable_1.7-0 ? ? ? zlibbioc_1.0.1 > > Noah L. Dowell, Postdoctoral fellow > Howard Hughes Medical Institute > University of Wisconsin > Department of Genetics > 1525 Linden Drive > Madison, WI 53706 > 608-265-2004?(lab) > ndowell at wisc.edu > > _______________________________________________ > 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