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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: E:\biocbld\bbs-2.4-bioc\R\bin\R.exe CMD build ShortRead
StartedAt: 2009-10-20 15:28:55 -0700 (Tue, 20 Oct 2009)
EndedAt: 2009-10-20 15:29:41 -0700 (Tue, 20 Oct 2009)
EllapsedTime: 45.7 seconds
RetCode: 0
Status: OK
PackageFile: ShortRead_1.2.1.tar.gz
PackageFileSize: 1.672 MiB

Command output

* checking for file 'ShortRead/DESCRIPTION' ... OK
* preparing 'ShortRead':
* checking DESCRIPTION meta-information ... OK
* cleaning src
make: Nothing to be done for `clean'.
* installing the package to re-build vignettes
* 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-2.4-bioc\meat\ShortRead\chm\ShortRead.chm





Compile time: 0 minutes, 2 seconds

51	Topics

574	Local links

5	Internet links

1	Graphic





Created e:\biocbld\bbs-2.4-bioc\meat\ShortRead\chm\ShortRead.chm, 114,036 bytes

Compression decreased file by 225,516 bytes.

** building package indices ...
** MD5 sums
* 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'