[BioC] Is the qrqc package source updated?

Wed Mar 21 05:44:05 CET 2012

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/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
>
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