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Package 257/294HostnameOS / ArchBUILDCHECKBUILD BIN
ShortRead 1.0.7
Biocore Team c/o BioC user list
Bioconductor Changelog
Snapshot Date: 2009-04-18 11:27:48 -0700 (Sat, 18 Apr 2009)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_3/madman/Rpacks/ShortRead
Last Changed Rev: 37917 / Revision: 38965
Last Changed Date: 2009-03-12 10:45:08 -0700 (Thu, 12 Mar 2009)
wilson2 Linux (openSUSE 11.1) / x86_64  OK  WARNINGS 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  WARNINGS [ OK ]
pitt Mac OS X Tiger (10.4.11) / i386  OK  WARNINGS  OK 
pelham Mac OS X Leopard (10.5.6) / i386  OK  WARNINGS  OK 
Package: ShortRead
Version: 1.0.7
Command: E:\biocbld\bbs-2.3-bioc\R\bin\R.exe CMD INSTALL --build --library=ShortRead.buildbin-libdir ShortRead_1.0.7.tar.gz
StartedAt: 2009-04-18 20:53:53 -0700 (Sat, 18 Apr 2009)
EndedAt: 2009-04-18 20:54:30 -0700 (Sat, 18 Apr 2009)
EllapsedTime: 37.8 seconds
RetCode: 0
Status: OK
PackageFile: ShortRead_1.0.7.zip
PackageFileSize: 2.003 MiB

Command output

installing R.css in E:/biocbld/bbs-2.3-bioc/meat/ShortRead.buildbin-libdir

Using auto-selected zip options ' ShortRead-HELP=ziponly'

---------- Making package ShortRead ------------
  adding build stamp to DESCRIPTION
  installing NAMESPACE file and metadata
  making DLL ...
making Biostrings_stubs.d from Biostrings_stubs.c
making IRanges_stubs.d from IRanges_stubs.c
making R_init_ShortRead.d from R_init_ShortRead.c
making alphabet.d from alphabet.c
making io.d from io.c
making pileup.d from pileup.c
making util.d from util.c
making readBfaToc.d from readBfaToc.cc
making read_maq_map.d from read_maq_map.cc
gcc  -std=gnu99  -IE:/biocbld/bbs-2.3-bioc/R/include -I"E:/biocbld/bbs-2.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.3-bioc/R/library/Biostrings/include"    -O3 -Wall  -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc  -std=gnu99  -IE:/biocbld/bbs-2.3-bioc/R/include -I"E:/biocbld/bbs-2.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.3-bioc/R/library/Biostrings/include"    -O3 -Wall  -c IRanges_stubs.c -o IRanges_stubs.o
gcc  -std=gnu99  -IE:/biocbld/bbs-2.3-bioc/R/include -I"E:/biocbld/bbs-2.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.3-bioc/R/library/Biostrings/include"    -O3 -Wall  -c R_init_ShortRead.c -o R_init_ShortRead.o
gcc  -std=gnu99  -IE:/biocbld/bbs-2.3-bioc/R/include -I"E:/biocbld/bbs-2.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.3-bioc/R/library/Biostrings/include"    -O3 -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  -IE:/biocbld/bbs-2.3-bioc/R/include -I"E:/biocbld/bbs-2.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.3-bioc/R/library/Biostrings/include"    -O3 -Wall  -c io.c -o io.o
gcc  -std=gnu99  -IE:/biocbld/bbs-2.3-bioc/R/include -I"E:/biocbld/bbs-2.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.3-bioc/R/library/Biostrings/include"    -O3 -Wall  -c pileup.c -o pileup.o
gcc  -std=gnu99  -IE:/biocbld/bbs-2.3-bioc/R/include -I"E:/biocbld/bbs-2.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.3-bioc/R/library/Biostrings/include"    -O3 -Wall  -c util.c -o util.o
util.c: In function 'decoder':
util.c:33: warning: 'decode' may be used uninitialized in this function
g++   -IE:/biocbld/bbs-2.3-bioc/R/include -I"E:/biocbld/bbs-2.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.3-bioc/R/library/Biostrings/include"    -O2 -Wall  -c readBfaToc.cc -o readBfaToc.o
In file included from readBfaToc.cc:6:
maqmap_m.h: In function 'int maqmap_read1(void*, maqmap1_T<max_readlen>*)':
maqmap_m.h:65: warning: no return statement in function returning non-void
g++   -IE:/biocbld/bbs-2.3-bioc/R/include -I"E:/biocbld/bbs-2.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.3-bioc/R/library/Biostrings/include"    -O2 -Wall  -c read_maq_map.cc -o read_maq_map.o
In file included from read_maq_map.cc:13:
maqmap_m.h: In function 'int maqmap_read1(void*, maqmap1_T<max_readlen>*)':
maqmap_m.h:65: warning: no return statement in function returning non-void
read_maq_map.cc: In function 'SEXPREC* read_maq_map_B(SEXPREC*, SEXPREC*) [with int max_readlen = 128]':
read_maq_map.cc:178:   instantiated from here
read_maq_map.cc:76: warning: comparison between signed and unsigned integer expressions
read_maq_map.cc: In function 'SEXPREC* read_maq_map_B(SEXPREC*, SEXPREC*) [with int max_readlen = 64]':
read_maq_map.cc:180:   instantiated from here
read_maq_map.cc:76: warning: comparison between signed and unsigned integer expressions
maqmap_m.h: In function 'int maqmap_read1(void*, maqmap1_T<max_readlen>*) [with int max_readlen = 128]':
read_maq_map.cc:104:   instantiated from 'SEXPREC* read_maq_map_B(SEXPREC*, SEXPREC*) [with int max_readlen = 128]'
read_maq_map.cc:178:   instantiated from here
maqmap_m.h:64: warning: no return statement in function returning non-void
maqmap_m.h: In function 'int maqmap_read1(void*, maqmap1_T<max_readlen>*) [with int max_readlen = 64]':
read_maq_map.cc:104:   instantiated from 'SEXPREC* read_maq_map_B(SEXPREC*, SEXPREC*) [with int max_readlen = 64]'
read_maq_map.cc:180:   instantiated from here
maqmap_m.h:64: warning: no return statement in function returning non-void
maqmap_m.h: In function 'int maqmap_read1(void*, maqmap1_T<max_readlen>*) [with int max_readlen = 128]':
maqmap_m.h:64: warning: control reaches end of non-void function
maqmap_m.h: In function 'int maqmap_read1(void*, maqmap1_T<max_readlen>*) [with int max_readlen = 64]':
maqmap_m.h:64: warning: control reaches end of non-void function
windres --preprocessor="gcc -E -xc -DRC_INVOKED" -I E:/biocbld/bbs-2.3-bioc/R/include  -i ShortRead_res.rc -o ShortRead_res.o
g++   -shared -s  -o ShortRead.dll ShortRead.def Biostrings_stubs.o IRanges_stubs.o R_init_ShortRead.o alphabet.o io.o pileup.o util.o readBfaToc.o read_maq_map.o ShortRead_res.o  -LE:/biocbld/bbs-2.3-bioc/R/bin -lRzlib   -lR
  ... DLL made
  installing DLL
  installing R files
  installing inst files
  preparing package ShortRead for lazy loading
Loading required package: IRanges

Attaching package: 'IRanges'


	The following object(s) are masked from package:base :

	 cbind,
	 rbind,
	 sapply 

Loading required package: Biostrings

Attaching package: 'Biostrings'


	The following object(s) are masked from package:base :

	 chartr,
	 order,
	 substr,
	 substring 

Loading required package: Biobase
Loading required package: tools

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.


Attaching package: 'Biobase'


	The following object(s) are masked from package:IRanges :

	 annotation 

Loading required package: lattice
  installing man source files
  installing indices
  installing help
 >>> 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
  ExperimentPath-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
  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
WARNING: \code inside code block in file 'pileup.Rd'
WARNING: \code inside code block in file 'pileup.Rd'
  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
  readPrb                           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
  zipping help files
Microsoft HTML Help Compiler 4.74.8702



Compiling e:\biocbld\bbs-2.3-bioc\meat\R.INSTALL.344\ShortRead\chm\ShortRead.chm





Compile time: 0 minutes, 3 seconds

42	Topics

410	Local links

3	Internet links

1	Graphic





Created e:\biocbld\bbs-2.3-bioc\meat\R.INSTALL.344\ShortRead\chm\ShortRead.chm, 89,242 bytes

Compression decreased file by 160,410 bytes.

  adding MD5 sums

packaged installation of package 'ShortRead' as ShortRead_1.0.7.zip
* DONE (ShortRead)