ShortRead 1.2.1
Biocore Team c/o BioC user list
| Bioconductor Changelog | | Snapshot Date: 2009-10-20 11:27:33 -0700 (Tue, 20 Oct 2009) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_4/madman/Rpacks/ShortRead | | Last Changed Rev: 39750 / Revision: 42512 | | Last Changed Date: 2009-05-27 20:44:43 -0700 (Wed, 27 May 2009) |
| wilson1 | Linux (openSUSE 11.1) / x86_64 | OK | OK | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | [ OK ] | OK |
| pitt | Mac OS X Tiger (10.4.11) / i386 | OK | OK | OK |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* checking for working pdflatex ... OK
* using log directory 'E:/biocbld/bbs-2.4-bioc/meat/ShortRead.Rcheck'
* using R version 2.9.2 (2009-08-24)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ShortRead/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ShortRead' version '1.2.1'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'ShortRead' can be installed ... OK
* 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 name space can be loaded with stated dependencies ... 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
.plotCycleBaseCall: no visible binding for global variable 'Base'
* checking Rd files ... OK
* checking Rd files against version 2 parser ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... 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 ... OK
* checking examples ... OK
* checking tests ...
Running 'runalltests.R'
Comparing 'runalltests.Rout' to 'runalltests.Rout.save' ...19,22c19
< Error in checkEquals(srorder(sread(rfq)), order(as.character(sread(rfq)))) :
< Mean relative difference: 0.4435591
< Error in checkIdentical(exp, res) : FALSE
< Error in checkTrue(FALSE) : Test not TRUE
---
> Error in checkTrue(FALSE) : Test not TRUE.
OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK
* Installing *source* package 'ShortRead' ...
** libs
making DLL ...
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -I"e:/biocbld/bbs-2.4-bioc/R/library/IRanges/include" -I"e:/biocbld/bbs-2.4-bioc/R/library/Biostrings/include" -O3 -Wall -std=gnu99 -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -I"e:/biocbld/bbs-2.4-bioc/R/library/IRanges/include" -I"e:/biocbld/bbs-2.4-bioc/R/library/Biostrings/include" -O3 -Wall -std=gnu99 -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -I"e:/biocbld/bbs-2.4-bioc/R/library/IRanges/include" -I"e:/biocbld/bbs-2.4-bioc/R/library/Biostrings/include" -O3 -Wall -std=gnu99 -c R_init_ShortRead.c -o R_init_ShortRead.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -I"e:/biocbld/bbs-2.4-bioc/R/library/IRanges/include" -I"e:/biocbld/bbs-2.4-bioc/R/library/Biostrings/include" -O3 -Wall -std=gnu99 -c alphabet.c -o alphabet.o
alphabet.c: In function 'alphabet_as_int':
alphabet.c:195: warning: 'ians' may be used uninitialized in this function
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -I"e:/biocbld/bbs-2.4-bioc/R/library/IRanges/include" -I"e:/biocbld/bbs-2.4-bioc/R/library/Biostrings/include" -O3 -Wall -std=gnu99 -c io.c -o io.o
io.c: In function '_count_ipar_int_recs':
io.c:125: warning: suggest parentheses around assignment used as truth value
io.c:136: warning: suggest parentheses around assignment used as truth value
io.c:142: warning: suggest parentheses around assignment used as truth value
io.c:117: warning: 'bytes_read' may be used uninitialized in this function
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -I"e:/biocbld/bbs-2.4-bioc/R/library/IRanges/include" -I"e:/biocbld/bbs-2.4-bioc/R/library/Biostrings/include" -O3 -Wall -std=gnu99 -c io_bowtie.c -o io_bowtie.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -I"e:/biocbld/bbs-2.4-bioc/R/library/IRanges/include" -I"e:/biocbld/bbs-2.4-bioc/R/library/Biostrings/include" -O3 -Wall -std=gnu99 -c io_soap.c -o io_soap.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -I"e:/biocbld/bbs-2.4-bioc/R/library/IRanges/include" -I"e:/biocbld/bbs-2.4-bioc/R/library/Biostrings/include" -O3 -Wall -std=gnu99 -c pileup.c -o pileup.o
g++ -I"e:/biocbld/bbs-2.4-bioc/R/include" -I"e:/biocbld/bbs-2.4-bioc/R/library/IRanges/include" -I"e:/biocbld/bbs-2.4-bioc/R/library/Biostrings/include" -O2 -Wall -c readBfaToc.cc -o readBfaToc.o
g++ -I"e:/biocbld/bbs-2.4-bioc/R/include" -I"e:/biocbld/bbs-2.4-bioc/R/library/IRanges/include" -I"e:/biocbld/bbs-2.4-bioc/R/library/Biostrings/include" -O2 -Wall -c read_maq_map.cc -o read_maq_map.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -I"e:/biocbld/bbs-2.4-bioc/R/library/IRanges/include" -I"e:/biocbld/bbs-2.4-bioc/R/library/Biostrings/include" -O3 -Wall -std=gnu99 -c util.c -o util.o
util.c: In function '_char_as_strand_int':
util.c:69: warning: 'strand' may be used uninitialized in this function
util.c: In function 'decoder':
util.c:33: warning: 'decode' may be used uninitialized in this function
g++ -shared -s -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 util.o -lRzlib -Le:/biocbld/bbs-2.4-bioc/R/bin -lR
... done
** R
** inst
** preparing package for lazy loading
Attaching package: 'IRanges'
The following object(s) are masked from package:base :
cbind,
duplicated,
order,
pmax,
pmax.int,
pmin,
pmin.int,
rank,
rbind,
rep.int,
sapply,
sort,
table,
unique
Warning in .reportSuperclassConflicts(Class, classDef@contains, where) :
unable to find a consistent ordering of superclasses for class "ArrayIntensity": order chosen is inconsistent with the superclasses of "array"
** help
*** installing help indices
>>> Building/Updating help pages for package 'ShortRead'
Formats: text html latex example chm
AlignedDataFrame-class text html latex chm
AlignedDataFrame text html latex chm
AlignedRead-class text html latex example chm
AlignedRead text html latex chm
BowtieQA-class text html latex example chm
ExperimentPath-class text html latex example chm
FastqQA-class text html latex example chm
Intensity-class text html latex example chm
MAQMapQA-class text html latex example chm
QA-class text html latex example chm
QualityScore-class text html latex example chm
QualityScore text html latex example chm
RochePath-class text html latex example chm
RocheSet-class text html latex example chm
SRFilter-class text html latex example chm
SRSet-class text html latex example chm
SRUtil-class text html latex example chm
ShortRead-class text html latex example chm
ShortRead-package text html latex chm
ShortReadQ-class text html latex example chm
SolexaExportQA-class text html latex example chm
SolexaIntensity-class text html latex example chm
SolexaIntensity text html latex chm
SolexaPath-class text html latex example chm
SolexaSet-class text html latex example chm
accessors text html latex example chm
alphabetByCycle text html latex example chm
alphabetScore text html latex chm
clean text html latex example chm
countLines text html latex example chm
deprecated text html latex chm
detail text html latex example chm
dustyScore text html latex example chm
pileup text html latex example chm
polyn text html latex example chm
qa text html latex example chm
readAligned text html latex example chm
readBaseQuality text html latex example chm
readBfaToc text html latex chm
readFastq text html latex example chm
readIntensities text html latex example chm
readPrb text html latex example chm
readQseq text html latex example chm
readXStringColumns text html latex example chm
report text html latex example chm
srFilter text html latex example chm
srapply text html latex example chm
srdistance text html latex example chm
srduplicated text html latex example chm
tables text html latex example chm
Microsoft HTML Help Compiler 4.74.8702
Compiling e:\biocbld\BBS-2~1.4-B\meat\SHORTR~1.RCH\00_PKG~1\SHORTR~1\chm\ShortRead.chm
Compile time: 0 minutes, 1 second
51 Topics
574 Local links
5 Internet links
1 Graphic
Created e:\biocbld\BBS-2~1.4-B\meat\SHORTR~1.RCH\00_PKG~1\SHORTR~1\chm\ShortRead.chm, 114,036 bytes
Compression decreased file by 225,516 bytes.
** building package indices ...
** MD5 sums
* DONE (ShortRead)