ShortRead 1.5.8
Biocore Team c/o BioC user list
| Bioconductor Changelog | | Snapshot Date: 2009-12-07 11:32:00 -0800 (Mon, 07 Dec 2009) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ShortRead | | Last Changed Rev: 43433 / Revision: 43434 | | Last Changed Date: 2009-12-07 09:13:58 -0800 (Mon, 07 Dec 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-2.6-bioc/meat/ShortRead.Rcheck'
* using R version 2.11.0 Under development (unstable) (2009-10-22 r50179)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ShortRead/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ShortRead' version '1.5.8'
* 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'
.read_cif_or_cnf_file: no visible binding for global variable 'vers'
* checking Rd files ... OK
* checking Rd metadata ... 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' ...19,23d18
< 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
<
OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK
* install options are ' --no-html'
* installing *source* package 'ShortRead' ...
** libs
making DLL ...
gcc -I"e:/biocbld/bbs-2.6-bioc/R/include" -I"e:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -I"e:/biocbld/bbs-2.6-bioc/R/library/Biostrings/include" -O3 -Wall -std=gnu99 -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -I"e:/biocbld/bbs-2.6-bioc/R/include" -I"e:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -I"e:/biocbld/bbs-2.6-bioc/R/library/Biostrings/include" -O3 -Wall -std=gnu99 -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I"e:/biocbld/bbs-2.6-bioc/R/include" -I"e:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -I"e:/biocbld/bbs-2.6-bioc/R/library/Biostrings/include" -O3 -Wall -std=gnu99 -c R_init_ShortRead.c -o R_init_ShortRead.o
gcc -I"e:/biocbld/bbs-2.6-bioc/R/include" -I"e:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -I"e:/biocbld/bbs-2.6-bioc/R/library/Biostrings/include" -O3 -Wall -std=gnu99 -c alphabet.c -o alphabet.o
alphabet.c: In function 'alphabet_as_int':
alphabet.c:190: warning: 'ians' may be used uninitialized in this function
gcc -I"e:/biocbld/bbs-2.6-bioc/R/include" -I"e:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -I"e:/biocbld/bbs-2.6-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:118: warning: 'bytes_read' may be used uninitialized in this function
gcc -I"e:/biocbld/bbs-2.6-bioc/R/include" -I"e:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -I"e:/biocbld/bbs-2.6-bioc/R/library/Biostrings/include" -O3 -Wall -std=gnu99 -c io_bowtie.c -o io_bowtie.o
gcc -I"e:/biocbld/bbs-2.6-bioc/R/include" -I"e:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -I"e:/biocbld/bbs-2.6-bioc/R/library/Biostrings/include" -O3 -Wall -std=gnu99 -c io_soap.c -o io_soap.o
gcc -I"e:/biocbld/bbs-2.6-bioc/R/include" -I"e:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -I"e:/biocbld/bbs-2.6-bioc/R/library/Biostrings/include" -O3 -Wall -std=gnu99 -c pileup.c -o pileup.o
g++ -I"e:/biocbld/bbs-2.6-bioc/R/include" -I"e:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -I"e:/biocbld/bbs-2.6-bioc/R/library/Biostrings/include" -O2 -Wall -c readBfaToc.cc -o readBfaToc.o
g++ -I"e:/biocbld/bbs-2.6-bioc/R/include" -I"e:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -I"e:/biocbld/bbs-2.6-bioc/R/library/Biostrings/include" -O2 -Wall -c read_maq_map.cc -o read_maq_map.o
gcc -I"e:/biocbld/bbs-2.6-bioc/R/include" -I"e:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -I"e:/biocbld/bbs-2.6-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:95: warning: 'strand' may be used uninitialized in this function
util.c: In function 'encoder':
util.c:59: warning: 'encode' may be used uninitialized in this function
util.c: In function 'decoder':
util.c:43: warning: 'decode' may be used uninitialized in this function
gcc -I"e:/biocbld/bbs-2.6-bioc/R/include" -I"e:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -I"e:/biocbld/bbs-2.6-bioc/R/library/Biostrings/include" -O3 -Wall -std=gnu99 -c xsnap.c -o xsnap.o
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 xsnap.o -lRzlib -Le:/biocbld/bbs-2.6-bioc/R/bin -lR
... done
** R
** inst
** preparing package for lazy loading
Attaching package: 'IRanges'
The following object(s) are masked from package:base :
Map,
cbind,
mapply,
order,
pmax,
pmax.int,
pmin,
pmin.int,
rbind,
rep.int,
table
** help
*** installing help indices
** building package indices ...
** MD5 sums
* DONE (ShortRead)