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 '/loc/home/biocbuild/bbs-2.3-bioc/meat/ShortRead.Rcheck'
* using R version 2.8.1 (2008-12-22)
* using session charset: UTF-8
* 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 '/loc/home/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 ...
make[1]: Entering directory `/loc/home/biocbuild/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 :
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< annotation
<
93c75
< 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
184,187c166
< Executing test function test_SRVector_construction ... Timing stopped at: 0 0 0.002
< 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 `/loc/home/biocbuild/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
/loc/home/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
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.3-bioc/R/library/Biostrings/include" -fpic -g -O2 -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 -I/home/biocbuild/bbs-2.3-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.3-bioc/R/library/Biostrings/include" -fpic -g -O2 -Wall -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.3-bioc/R/library/Biostrings/include" -fpic -g -O2 -Wall -c io.c -o io.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.3-bioc/R/library/Biostrings/include" -fpic -g -O2 -Wall -c IRanges_stubs.c -o IRanges_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.3-bioc/R/library/Biostrings/include" -fpic -g -O2 -Wall -c pileup.c -o pileup.o
g++ -I/home/biocbuild/bbs-2.3-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.3-bioc/R/library/Biostrings/include" -fpic -g -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++ -I/home/biocbuild/bbs-2.3-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.3-bioc/R/library/Biostrings/include" -fpic -g -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:65: 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:65: 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:65: 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:65: warning: control reaches end of non-void function
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.3-bioc/R/library/Biostrings/include" -fpic -g -O2 -Wall -c R_init_ShortRead.c -o R_init_ShortRead.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.3-bioc/R/library/Biostrings/include" -fpic -g -O2 -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++ -shared -L/usr/local/lib64 -o ShortRead.so alphabet.o Biostrings_stubs.o io.o IRanges_stubs.o pileup.o readBfaToc.o read_maq_map.o R_init_ShortRead.o util.o -lz -L/home/biocbuild/bbs-2.3-bioc/R/lib -lR
** 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)