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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: /Library/Frameworks/R.framework/Versions/2.8/Resources/bin/R CMD check --no-vignettes ShortRead_1.0.7.tar.gz
StartedAt: 2009-04-18 17:59:53 -0700 (Sat, 18 Apr 2009)
EndedAt: 2009-04-18 18:02:47 -0700 (Sat, 18 Apr 2009)
EllapsedTime: 174.2 seconds
RetCode: 0
Status: WARNINGS
CheckDir: ShortRead.Rcheck
Warnings: 1

Command output

* checking for working pdflatex ... OK
* using log directory '/Users/biocbuild/bbs-2.3-bioc/meat/ShortRead.Rcheck'
* using R version 2.8.1 (2008-12-22)
* using session charset: ASCII
* checking for file 'ShortRead/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ShortRead' version '1.0.7'
* 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 ... WARNING
Found the following significant warnings:
  WARNING: \code inside code block in file 'pileup.Rd'
See '/Users/biocbuild/bbs-2.3-bioc/meat/ShortRead.Rcheck/00install.out' for details.
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... 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 ... OK
* checking Rd files ... 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
* creating ShortRead-Ex.R ... OK
* checking examples ... OK
* checking tests ...
  Running 'runalltests.R'
  Comparing 'runalltests.Rout' to 'runalltests.Rout.save' ...5,8c5
< Attaching package: 'IRanges'
< 
< 
< 	The following object(s) are masked from package:base :
---
> Welcome to Bioconductor
10,12c7,9
< 	 cbind,
< 	 rbind,
< 	 sapply 
---
>   Vignettes contain introductory material. To view, type
>   'openVignette()'. To cite Bioconductor, see
>   'citation("Biobase")' and for packages 'citation(pkgname)'.
25,39d21
< 
< 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 
< 
61c43
< Executing test function test_AlignedRead_readAligned_SolexaExport  ...  done successfully.
---
> Executing test function test_AlignedRead_readAligned_run_as_factor  ...  done successfully.
65c47
< Executing test function test_AlignedRead_readAligned_SolexaExport_filter  ...  done successfully.
---
> Executing test function test_AlignedRead_readAligned_SolexaExport  ...  done successfully.
69c51
< Executing test function test_AlignedRead_readAligned_run_as_factor  ...  done successfully.
---
> Executing test function test_AlignedRead_readAligned_SolexaExport_filter  ...  done successfully.
77c59
< Executing test function test_SRError_construction  ...  done successfully.
---
> Executing test function test_alphabetByCycle  ...  done successfully.
81c63
< Executing test function test_SRError_throw  ...  done successfully.
---
> Executing test function test_alphabetOrder  ...  done successfully.
85c67
< Executing test function test_SRWarn_catch  ...  done successfully.
---
> Executing test function test_countLines  ...  done successfully.
89c71
< Executing test function test_SRWarn_construction  ...  done successfully.
---
> Executing test function test_mark_field  ...  done successfully.
93c75,76
< Executing test function test_SRWarn_throw  ...  done successfully.
---
> Executing test function test_readFastq_errors  ... Timing stopped at: 0 0 0.001 
> Error in checkTrue(FALSE) : Test not TRUE.
94a78
>  done successfully.
97d80
< Executing test function test_alignDataFilter  ...  done successfully.
98a82
> Executing test function test_readXStringColumns_toIUPAC  ...  done successfully.
101d84
< Executing test function test_alignQualityFilter  ...  done successfully.
102a86
> Executing test function test_ShortReadQ_clean  ...  done successfully.
105d88
< Executing test function test_chromosomeFilter  ...  done successfully.
106a90
> Executing test function test_ShortReadQ_constructors  ...  done successfully.
109d92
< Executing test function test_compose  ...  done successfully.
110a94
> Executing test function test_ShortReadQ_srsort  ...  done successfully.
113d96
< Executing test function test_nFilter  ...  done successfully.
114a98
> Executing test function test_ShortReadQ_subset  ...  done successfully.
117d100
< Executing test function test_polynFilter  ...  done successfully.
118a102
> Executing test function test_ShortRead_construction  ...  done successfully.
121d104
< Executing test function test_srFilter  ...  done successfully.
122a106
> Executing test function test_SRError_construction  ...  done successfully.
125d108
< Executing test function test_srdistanceFilter  ...  done successfully.
126a110
> Executing test function test_SRError_throw  ...  done successfully.
129d112
< Executing test function test_strandFilter  ...  done successfully.
130a114
> Executing test function test_SRWarn_catch  ...  done successfully.
133d116
< Executing test function test_SRList_construction  ...  done successfully.
134a118
> Executing test function test_SRWarn_construction  ...  done successfully.
137,140d120
< Executing test function test_SRVector_construction  ... Timing stopped at: 0.003 0 0.003 
< Error in as.vector(x, "list") : 
<   cannot coerce type 'S4' to vector of type 'list'
<  done successfully.
141a122
> Executing test function test_SRWarn_throw  ...  done successfully.
144d124
< Executing test function test_ShortReadQ_clean  ...  done successfully.
145a126
> Executing test function test_alignDataFilter  ...  done successfully.
148d128
< Executing test function test_ShortReadQ_constructors  ...  done successfully.
149a130
> Executing test function test_alignQualityFilter  ...  done successfully.
152d132
< Executing test function test_ShortReadQ_srsort  ...  done successfully.
153a134
> Executing test function test_chromosomeFilter  ...  done successfully.
156d136
< Executing test function test_ShortReadQ_subset  ...  done successfully.
157a138
> Executing test function test_compose  ...  done successfully.
160d140
< Executing test function test_ShortRead_construction  ...  done successfully.
161a142
> Executing test function test_nFilter  ...  done successfully.
164d144
< Executing test function test_alphabetByCycle  ...  done successfully.
165a146
> Executing test function test_polynFilter  ...  done successfully.
168,171d148
< Executing test function test_alphabetOrder  ... Timing stopped at: 0.018 0.013 0.032 
< Error in checkEquals(srorder(sread(rfq)), order(as.character(sread(rfq)))) : 
<   Mean relative difference: 0.4951691
<  done successfully.
172a150
> Executing test function test_srdistanceFilter  ...  done successfully.
175d152
< Executing test function test_countLines  ...  done successfully.
176a154
> Executing test function test_srFilter  ...  done successfully.
179d156
< Executing test function test_mark_field  ...  done successfully.
180a158
> Executing test function test_strandFilter  ...  done successfully.
183,184d160
< Executing test function test_readFastq_errors  ... Timing stopped at: 0 0 0 
< Error in checkTrue(FALSE) : Test not TRUE.
186c162
<  done successfully.
---
> Executing test function test_SRList_construction  ...  done successfully.
190c166
< Executing test function test_readXStringColumns_toIUPAC  ...  done successfully.
---
> Executing test function test_SRVector_construction  ...  done successfully.
 OK
 OK
* checking package vignettes in 'inst/doc' ... OK
* creating ShortRead-manual.tex ... OK
* checking ShortRead-manual.tex using pdflatex ... OK

WARNING: There was 1 warning, see
  /Users/biocbuild/bbs-2.3-bioc/meat/ShortRead.Rcheck/00check.log
for details

ShortRead.Rcheck/00install.out:

* 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
** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/Biostrings/include"   -fPIC  -g -O2 -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/Biostrings/include"   -fPIC  -g -O2 -c IRanges_stubs.c -o IRanges_stubs.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/Biostrings/include"   -fPIC  -g -O2 -c R_init_ShortRead.c -o R_init_ShortRead.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/Biostrings/include"   -fPIC  -g -O2 -c alphabet.c -o alphabet.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/Biostrings/include"   -fPIC  -g -O2 -c io.c -o io.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/Biostrings/include"   -fPIC  -g -O2 -c pileup.c -o pileup.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/Biostrings/include"   -fPIC  -g -O2 -c readBfaToc.cc -o readBfaToc.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/Biostrings/include"   -fPIC  -g -O2 -c read_maq_map.cc -o read_maq_map.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/Biostrings/include"   -fPIC  -g -O2 -c util.c -o util.o
g++ -arch i386 -dynamiclib -Wl,-headerpad_max_install_names -mmacosx-version-min=10.4 -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o ShortRead.so Biostrings_stubs.o IRanges_stubs.o R_init_ShortRead.o alphabet.o io.o pileup.o readBfaToc.o read_maq_map.o util.o -lz   -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** R
** inst
** preparing package 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
** help
 >>> 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
  ExperimentPath-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
  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
WARNING: \code inside code block in file 'pileup.Rd'
  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
  readPrb                           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)