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 'E:/biocbld/bbs-2.3-bioc/meat/ShortRead.Rcheck'
* using R version 2.8.1 (2008-12-22)
* using session charset: ISO8859-1
* 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'
WARNING: \code inside code block in file 'pileup.Rd'
See 'E:/biocbld/bbs-2.3-bioc/meat/ShortRead.Rcheck/00install.out' for details.
* checking package directory ... OK
* checking for portable file names ... 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 ...
make[1]: Entering directory `/cygdrive/e/biocbld/bbs-2.3-bioc/meat/ShortRead.Rcheck/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
<
81,84c63
< Executing test function test_alphabetOrder ... Timing stopped at: 0.02 0 0.02
< Error in checkEquals(srorder(sread(rfq)), order(as.character(sread(rfq)))) :
< Mean relative difference: 0.4435591
< done successfully.
---
> Executing test function test_alphabetOrder ... done successfully.
96c75
< Executing test function test_readFastq_errors ... Timing stopped at: 0 0 0
---
> Executing test function test_readFastq_errors ... Timing stopped at: 0 0 0.001
107,110d85
< Executing test function test_ShortRead_construction ... done successfully.
<
<
<
126a102,105
> Executing test function test_ShortRead_construction ... done successfully.
>
>
>
187,190c166
< Executing test function test_SRVector_construction ... Timing stopped at: 0 0 0
< Error in as.vector(x, "list") :
< cannot coerce type 'S4' to vector of type 'list'
< done successfully.
---
> Executing test function test_SRVector_construction ... done successfully.
OK
make[1]: Leaving directory `/cygdrive/e/biocbld/bbs-2.3-bioc/meat/ShortRead.Rcheck/tests'
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
E:/biocbld/bbs-2.3-bioc/meat/ShortRead.Rcheck/00check.log
for details
installing R.css in E:/biocbld/bbs-2.3-bioc/meat/ShortRead.Rcheck
---------- 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
Microsoft HTML Help Compiler 4.74.8702
Compiling e:\biocbld\bbs-2.3-bioc\meat\ShortRead.Rcheck\00_pkg_src\ShortRead\chm\ShortRead.chm
Compile time: 0 minutes, 0 seconds
42 Topics
410 Local links
3 Internet links
1 Graphic
Created e:\biocbld\bbs-2.3-bioc\meat\ShortRead.Rcheck\00_pkg_src\ShortRead\chm\ShortRead.chm, 89,240 bytes
Compression decreased file by 160,412 bytes.
adding MD5 sums
* DONE (ShortRead)