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 |
* 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.
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> Executing test function test_AlignedRead_readAligned_SolexaExport ... done successfully.
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< 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.
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> Executing test function test_alphabetOrder ... done successfully.
85c67
< Executing test function test_SRWarn_catch ... done successfully.
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> Executing test function test_countLines ... done successfully.
89c71
< Executing test function test_SRWarn_construction ... done successfully.
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> 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.
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> Executing test function test_SRError_construction ... done successfully.
125d108
< Executing test function test_srdistanceFilter ... done successfully.
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> Executing test function test_SRError_throw ... done successfully.
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< Executing test function test_strandFilter ... done successfully.
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> Executing test function test_SRWarn_catch ... done successfully.
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< Executing test function test_SRList_construction ... done successfully.
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> 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.
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> Executing test function test_alignDataFilter ... done successfully.
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< Executing test function test_ShortReadQ_constructors ... done successfully.
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> Executing test function test_alignQualityFilter ... done successfully.
152d132
< Executing test function test_ShortReadQ_srsort ... done successfully.
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> Executing test function test_chromosomeFilter ... done successfully.
156d136
< Executing test function test_ShortReadQ_subset ... done successfully.
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> Executing test function test_compose ... done successfully.
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< Executing test function test_ShortRead_construction ... done successfully.
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> Executing test function test_nFilter ... done successfully.
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< 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
* 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)