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Package 309/353HostnameOS / ArchBUILDCHECKBUILD BIN
ShortRead 1.4.0
Biocore Team c/o BioC user list
Snapshot Date: 2010-04-02 23:28:25 -0700 (Fri, 02 Apr 2010)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_5/madman/Rpacks/ShortRead
Last Changed Rev: 42684 / Revision: 45705
Last Changed Date: 2009-10-27 16:33:29 -0700 (Tue, 27 Oct 2009)
wilson2 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 
Package: ShortRead
Version: 1.4.0
Command: E:\biocbld\bbs-2.5-bioc\R\bin\R.exe CMD check --no-vignettes ShortRead_1.4.0.tar.gz
StartedAt: 2010-04-03 06:25:11 -0700 (Sat, 03 Apr 2010)
EndedAt: 2010-04-03 06:28:08 -0700 (Sat, 03 Apr 2010)
EllapsedTime: 176.8 seconds
RetCode: 0
Status: OK
CheckDir: ShortRead.Rcheck
Warnings: 0

Command output

* checking for working pdflatex ... OK
* using log directory 'E:/biocbld/bbs-2.5-bioc/meat/ShortRead.Rcheck'
* using R version 2.10.1 (2009-12-14)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ShortRead/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ShortRead' version '1.4.0'
* 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 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

ShortRead.Rcheck/00install.out:

* install options are ' --no-html'

* installing *source* package 'ShortRead' ...
** libs
  making DLL ...
gcc -I"e:/biocbld/bbs-2.5-bioc/R/include"   -I"e:/biocbld/bbs-2.5-bioc/R/library/IRanges/include" -I"e:/biocbld/bbs-2.5-bioc/R/library/Biostrings/include"     -O3 -Wall  -std=gnu99 -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -I"e:/biocbld/bbs-2.5-bioc/R/include"   -I"e:/biocbld/bbs-2.5-bioc/R/library/IRanges/include" -I"e:/biocbld/bbs-2.5-bioc/R/library/Biostrings/include"     -O3 -Wall  -std=gnu99 -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I"e:/biocbld/bbs-2.5-bioc/R/include"   -I"e:/biocbld/bbs-2.5-bioc/R/library/IRanges/include" -I"e:/biocbld/bbs-2.5-bioc/R/library/Biostrings/include"     -O3 -Wall  -std=gnu99 -c R_init_ShortRead.c -o R_init_ShortRead.o
gcc -I"e:/biocbld/bbs-2.5-bioc/R/include"   -I"e:/biocbld/bbs-2.5-bioc/R/library/IRanges/include" -I"e:/biocbld/bbs-2.5-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-2.5-bioc/R/include"   -I"e:/biocbld/bbs-2.5-bioc/R/library/IRanges/include" -I"e:/biocbld/bbs-2.5-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-2.5-bioc/R/include"   -I"e:/biocbld/bbs-2.5-bioc/R/library/IRanges/include" -I"e:/biocbld/bbs-2.5-bioc/R/library/Biostrings/include"     -O3 -Wall  -std=gnu99 -c io_bowtie.c -o io_bowtie.o
gcc -I"e:/biocbld/bbs-2.5-bioc/R/include"   -I"e:/biocbld/bbs-2.5-bioc/R/library/IRanges/include" -I"e:/biocbld/bbs-2.5-bioc/R/library/Biostrings/include"     -O3 -Wall  -std=gnu99 -c io_soap.c -o io_soap.o
gcc -I"e:/biocbld/bbs-2.5-bioc/R/include"   -I"e:/biocbld/bbs-2.5-bioc/R/library/IRanges/include" -I"e:/biocbld/bbs-2.5-bioc/R/library/Biostrings/include"     -O3 -Wall  -std=gnu99 -c pileup.c -o pileup.o
g++ -I"e:/biocbld/bbs-2.5-bioc/R/include"   -I"e:/biocbld/bbs-2.5-bioc/R/library/IRanges/include" -I"e:/biocbld/bbs-2.5-bioc/R/library/Biostrings/include"     -O2 -Wall  -c readBfaToc.cc -o readBfaToc.o
g++ -I"e:/biocbld/bbs-2.5-bioc/R/include"   -I"e:/biocbld/bbs-2.5-bioc/R/library/IRanges/include" -I"e:/biocbld/bbs-2.5-bioc/R/library/Biostrings/include"     -O2 -Wall  -c read_maq_map.cc -o read_maq_map.o
gcc -I"e:/biocbld/bbs-2.5-bioc/R/include"   -I"e:/biocbld/bbs-2.5-bioc/R/library/IRanges/include" -I"e:/biocbld/bbs-2.5-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-2.5-bioc/R/include"   -I"e:/biocbld/bbs-2.5-bioc/R/library/IRanges/include" -I"e:/biocbld/bbs-2.5-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-2.5-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)