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Package 277/319HostnameOS / ArchBUILDCHECKBUILD BIN
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 
Package: ShortRead
Version: 1.2.1
Command: /home/biocbuild/bbs-2.4-bioc/R/bin/R CMD build ShortRead
StartedAt: 2009-10-20 14:41:50 -0700 (Tue, 20 Oct 2009)
EndedAt: 2009-10-20 14:42:15 -0700 (Tue, 20 Oct 2009)
EllapsedTime: 25.5 seconds
RetCode: 0
Status: OK
PackageFile: ShortRead_1.2.1.tar.gz
PackageFileSize: 1.677 MiB

Command output

* checking for file 'ShortRead/DESCRIPTION' ... OK
* preparing 'ShortRead':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to re-build vignettes
* Installing *source* package 'ShortRead' ...
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for gzeof in -lz... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.4-bioc/R/library/Biostrings/include"   -fpic  -g -O2 -Wall -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.4-bioc/R/library/Biostrings/include"   -fpic  -g -O2 -Wall -c IRanges_stubs.c -o IRanges_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.4-bioc/R/library/Biostrings/include"   -fpic  -g -O2 -Wall -c R_init_ShortRead.c -o R_init_ShortRead.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.4-bioc/R/library/Biostrings/include"   -fpic  -g -O2 -Wall -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 -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.4-bioc/R/library/Biostrings/include"   -fpic  -g -O2 -Wall -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 -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.4-bioc/R/library/Biostrings/include"   -fpic  -g -O2 -Wall -c io_bowtie.c -o io_bowtie.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.4-bioc/R/library/Biostrings/include"   -fpic  -g -O2 -Wall -c io_soap.c -o io_soap.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.4-bioc/R/library/Biostrings/include"   -fpic  -g -O2 -Wall -c pileup.c -o pileup.o
g++ -I/home/biocbuild/bbs-2.4-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.4-bioc/R/library/Biostrings/include"   -fpic  -g -O2 -Wall -c readBfaToc.cc -o readBfaToc.o
g++ -I/home/biocbuild/bbs-2.4-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.4-bioc/R/library/Biostrings/include"   -fpic  -g -O2 -Wall -c read_maq_map.cc -o read_maq_map.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.4-bioc/R/library/Biostrings/include"   -fpic  -g -O2 -Wall -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 -L/usr/local/lib64 -o ShortRead.so 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 -lz -L/home/biocbuild/bbs-2.4-bioc/R/lib -lR
** 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 
  AlignedDataFrame-class            text    html    latex
  AlignedDataFrame                  text    html    latex
  AlignedRead-class                 text    html    latex   example
  AlignedRead                       text    html    latex
  BowtieQA-class                    text    html    latex   example
  ExperimentPath-class              text    html    latex   example
  FastqQA-class                     text    html    latex   example
  Intensity-class                   text    html    latex   example
  MAQMapQA-class                    text    html    latex   example
  QA-class                          text    html    latex   example
  QualityScore-class                text    html    latex   example
  QualityScore                      text    html    latex   example
  RochePath-class                   text    html    latex   example
  RocheSet-class                    text    html    latex   example
  SRFilter-class                    text    html    latex   example
  SRSet-class                       text    html    latex   example
  SRUtil-class                      text    html    latex   example
  ShortRead-class                   text    html    latex   example
  ShortRead-package                 text    html    latex
  ShortReadQ-class                  text    html    latex   example
  SolexaExportQA-class              text    html    latex   example
  SolexaIntensity-class             text    html    latex   example
  SolexaIntensity                   text    html    latex
  SolexaPath-class                  text    html    latex   example
  SolexaSet-class                   text    html    latex   example
  accessors                         text    html    latex   example
  alphabetByCycle                   text    html    latex   example
  alphabetScore                     text    html    latex
  clean                             text    html    latex   example
  countLines                        text    html    latex   example
  deprecated                        text    html    latex
  detail                            text    html    latex   example
  dustyScore                        text    html    latex   example
  pileup                            text    html    latex   example
  polyn                             text    html    latex   example
  qa                                text    html    latex   example
  readAligned                       text    html    latex   example
  readBaseQuality                   text    html    latex   example
  readBfaToc                        text    html    latex
  readFastq                         text    html    latex   example
  readIntensities                   text    html    latex   example
  readPrb                           text    html    latex   example
  readQseq                          text    html    latex   example
  readXStringColumns                text    html    latex   example
  report                            text    html    latex   example
  srFilter                          text    html    latex   example
  srapply                           text    html    latex   example
  srdistance                        text    html    latex   example
  srduplicated                      text    html    latex   example
  tables                            text    html    latex   example
** building package indices ...
* DONE (ShortRead)
* creating vignettes ... OK
* cleaning src
make: Nothing to be done for `clean'.
* removing junk files
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* building 'ShortRead_1.2.1.tar.gz'