[BioC] Is the qrqc package source updated?

Wed Mar 21 05:35:46 CET 2012

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/libbam.a /Library/Frameworks/R.framework/Versions/2.14/Resources/library/Rsamtools/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/Resources/library/Rsamtools/usrlib/x86_64/libbam.a /Library/Frameworks/R.framework/Versions/2.14/Resources/library/Rsamtools/usrlib/x86_64/libbcf.a /Library/Frameworks/R.framework/Versions/2.14/Resources/library/Rsamtools/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-/RtmpJAbtgf/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/GenomeSequence/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