Package: ShortRead

Version: 1.11.23

Command: D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch ShortRead_1.11.23.tar.gz

StartedAt: 2011-07-07 06:17:01 -0700 (Thu, 07 Jul 2011)

EndedAt: 2011-07-07 06:21:26 -0700 (Thu, 07 Jul 2011)

EllapsedTime: 265.9 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: ShortRead.Rcheck

Warnings: 3

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/ShortRead.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-06-03 r56036)
* using platform: x86_64-pc-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ShortRead/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ShortRead' version '1.11.23'
* checking package name space information ... OK
* checking package dependencies ... NOTE
Packages which this enhances but not available for checking:
  'Rmpi' 'multicore'
* checking if this is a source package ... OK
* checking whether package 'ShortRead' can be installed ... WARNING
Found the following significant warnings:
  Warning: Class "AssayData" is defined (with package slot 'Biobase') but no metadata object found to revise subclass information---not exported?  Making a copy in package 'ShortRead'
See 'D:/biocbld/bbs-2.9-bioc/meat/ShortRead.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc       2.3Mb
    extdata   1.3Mb
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking whether the name space can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.coverage_viewer: no visible binding for global variable 'group'
.multicoverage_viewer: no visible global function definition for
  '.getData<-'
.multicoverage_viewer: no visible binding for global variable 'lv'
.multicoverage_viewer: no visible binding for global variable 'group'
.multicoverage_viewer: no visible binding for global variable 'sv'
.plotCycleBaseCall: no visible binding for global variable 'Base'
.plotNucleotideCount: no visible binding for global variable
  'Nucleotide'
.plotReadCount: no visible binding for global variable 'Census'
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link(s) in documentation object 'D:/biocbld/bbs-2.9-bioc/meat/ShortRead.Rcheck/00_pkg_src/ShortRead/man/Snapshot-class.Rd':
  'Snapshot-class'

See the information in section 'Cross-references' of the 'Writing R
Extensions' manual.

* checking for missing documentation entries ... WARNING
Undocumented code objects:
  'GappedReads' 'qname' 'qseq' 'readGappedReads'
Undocumented S4 classes:
  'AssayData' 'GappedReads' 'Snapshot' 'trellis'
Undocumented S4 methods:
  generic 'SnapshotFunctionList' and siglist 'SnapshotFunction'
  generic '[' and siglist 'GappedReads,ANY,ANY'
  generic 'c' and siglist 'GappedReads'
  generic 'narrow' and siglist 'GappedReads'
  generic 'qname' and siglist 'GappedReads'
  generic 'qseq' and siglist 'GappedReads'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See the chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking examples ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'ShortRead_unit_tests.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There were 3 warnings, see
  'D:/biocbld/bbs-2.9-bioc/meat/ShortRead.Rcheck/00check.log'
for details

* installing *source* package 'ShortRead' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
x86_64-w64-mingw32-gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include"      -O2 -Wall  -std=gnu99 -c Biostrings_stubs.c -o Biostrings_stubs.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include"      -O2 -Wall  -std=gnu99 -c IRanges_stubs.c -o IRanges_stubs.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include"      -O2 -Wall  -std=gnu99 -c R_init_ShortRead.c -o R_init_ShortRead.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include"      -O2 -Wall  -std=gnu99 -c alphabet.c -o alphabet.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include"      -O2 -Wall  -std=gnu99 -c io.c -o io.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include"      -O2 -Wall  -std=gnu99 -c io_bowtie.c -o io_bowtie.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include"      -O2 -Wall  -std=gnu99 -c io_soap.c -o io_soap.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include"      -O2 -Wall  -std=gnu99 -c pileup.c -o pileup.o
x86_64-w64-mingw32-g++  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include"      -O2 -Wall  -c readBfaToc.cc -o readBfaToc.o
x86_64-w64-mingw32-g++  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include"      -O2 -Wall  -c read_maq_map.cc -o read_maq_map.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include"      -O2 -Wall  -std=gnu99 -c sampler.c -o sampler.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include"      -O2 -Wall  -std=gnu99 -c trim.c -o trim.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include"      -O2 -Wall  -std=gnu99 -c util.c -o util.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include"      -O2 -Wall  -std=gnu99 -c xsnap.c -o xsnap.o
x86_64-w64-mingw32-g++ -shared -s -static-libgcc -o ShortRead.dll tmp.def Biostrings_stubs.o IRanges_stubs.o R_init_ShortRead.o alphabet.o io.o io_bowtie.o io_soap.o pileup.o readBfaToc.o read_maq_map.o sampler.o trim.o util.o xsnap.o -LD:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LD:/biocbld/BBS-2˜1.9-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.9-bioc/meat/ShortRead.Rcheck/ShortRead/libs/x64
** R
** inst
** preparing package for lazy loading

Attaching package: 'IRanges'

The following object(s) are masked from 'package:base':

    Map, cbind, eval, intersect, mapply, order, paste, pmax, pmax.int,
    pmin, pmin.int, rbind, rep.int, setdiff, table, union

Loading required package: RColorBrewer
Warning: Class "AssayData" is defined (with package slot 'Biobase') but no metadata object found to revise subclass information---not exported?  Making a copy in package 'ShortRead'
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'Overview.Rnw' 
** testing if installed package can be loaded

* DONE (ShortRead)

name	user	system	elapsed
AlignedRead-class	0.83	0.31	1.14
BAMQA-class	0	0	0
BowtieQA-class	0	0	0
ExperimentPath-class	0	0	0
FastqQA-class	0	0	0
Intensity-class	0.33	0.00	0.40
MAQMapQA-class	0	0	0
QA-class	0	0	0
QualityScore-class	0	0	0
QualityScore	0.02	0.00	0.01
RochePath-class	0	0	0
RocheSet-class	0	0	0
RtaIntensity-class	0.07	0.00	0.08
RtaIntensity	0.04	0.00	0.03
SRFilter-class	0	0	0
SRFilterResult-class	0.08	0.00	0.07
SRSet-class	0	0	0
SRUtil-class	0.02	0.00	0.02
Sampler-class	0.46	0.17	0.64
ShortRead-class	0.08	0.00	0.08
ShortReadQ-class	0.63	0.33	0.95
Snapshot-class	1.83	0.02	1.88
SnapshotFunction-class	0	0	0
SolexaExportQA-class	0	0	0
SolexaIntensity-class	0.17	0.01	0.18
SolexaPath-class	0.28	0.27	0.55
SolexaSet-class	0.09	0.00	0.09
SpTrellis-class	0.02	0.00	0.02
accessors	0	0	0
alphabetByCycle	0.22	0.28	0.50
clean	0	0	0
countLines	0.00	0.02	0.02
deprecated	0	0	0
dustyScore	0.48	0.31	0.80
polyn	0	0	0
qa	0.92	0.52	1.44
readAligned	0.83	0.67	1.50
readBaseQuality	0.11	0.08	0.18
readFasta	0.06	0.00	0.16
readFastq	0.50	0.56	1.06
readIntensities	0.16	0.00	0.16
readPrb	0.08	0.00	0.08
readQseq	0.14	0.17	0.31
readXStringColumns	0.45	0.65	1.09
renew	0.28	0.23	0.52
report	0	0	0
srFilter	0.81	0.41	1.22
srapply	0	0	0
srdistance	0.32	0.21	0.53
srduplicated	0.37	0.30	0.67
tables	0.35	0.16	0.50
trimTails	0	0	0