ShortRead 1.5.8
Biocore Team c/o BioC user list
| Bioconductor Changelog | | Snapshot Date: 2009-12-07 11:32:00 -0800 (Mon, 07 Dec 2009) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ShortRead | | Last Changed Rev: 43433 / Revision: 43434 | | Last Changed Date: 2009-12-07 09:13:58 -0800 (Mon, 07 Dec 2009) |
| wilson1 | Linux (openSUSE 11.1) / x86_64 | OK | [ OK ] | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | OK | OK |
| pitt | Mac OS X Tiger (10.4.11) / i386 | OK | OK | OK |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* checking for working pdflatex ... OK
* using log directory '/loc/home/biocbuild/bbs-2.6-bioc/meat/ShortRead.Rcheck'
* using R version 2.11.0 Under development (unstable) (2009-11-10 r50388)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ShortRead/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ShortRead' version '1.5.8'
* 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 ... OK
* 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 package can be unloaded cleanly ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking whether the name space can be unloaded cleanly ... 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 ... NOTE
.plotCycleBaseCall: no visible binding for global variable 'Base'
.read_cif_or_cnf_file: no visible binding for global variable 'vers'
* checking Rd files ... OK
* checking Rd metadata ... 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
* checking examples ... OK
* checking tests ...
Running 'runalltests.R'
Comparing 'runalltests.Rout' to 'runalltests.Rout.save' ...21,22d20
< Error in checkTrue(FALSE) : Test not TRUE
<
OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK
* install options are ' --no-html'
* 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 how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking size of unsigned long... 8
checking for gzeof in -lz... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.6-bioc/R/library/Biostrings/include" -fpic -g -O2 -Wall -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.6-bioc/R/library/Biostrings/include" -fpic -g -O2 -Wall -c IRanges_stubs.c -o IRanges_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.6-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-2.6-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.6-bioc/R/library/Biostrings/include" -fpic -g -O2 -Wall -c alphabet.c -o alphabet.o
alphabet.c: In function 'alphabet_as_int':
alphabet.c:190: warning: 'ians' may be used uninitialized in this function
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.6-bioc/R/library/Biostrings/include" -fpic -g -O2 -Wall -c io.c -o io.o
io.c: In function '_count_ipar_int_recs':
io.c:118: warning: 'bytes_read' may be used uninitialized in this function
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.6-bioc/R/library/Biostrings/include" -fpic -g -O2 -Wall -c io_bowtie.c -o io_bowtie.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.6-bioc/R/library/Biostrings/include" -fpic -g -O2 -Wall -c io_soap.c -o io_soap.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.6-bioc/R/library/Biostrings/include" -fpic -g -O2 -Wall -c pileup.c -o pileup.o
g++ -I/home/biocbuild/bbs-2.6-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.6-bioc/R/library/Biostrings/include" -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DSIZEOF_UNSIGNED_LONG=8 -DHAVE_LIBZ=1 -fpic -g -O2 -Wall -c readBfaToc.cc -o readBfaToc.o
g++ -I/home/biocbuild/bbs-2.6-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.6-bioc/R/library/Biostrings/include" -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DSIZEOF_UNSIGNED_LONG=8 -DHAVE_LIBZ=1 -fpic -g -O2 -Wall -c read_maq_map.cc -o read_maq_map.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.6-bioc/R/library/Biostrings/include" -fpic -g -O2 -Wall -c util.c -o util.o
util.c: In function '_char_as_strand_int':
util.c:95: warning: 'strand' may be used uninitialized in this function
util.c: In function 'encoder':
util.c:59: warning: 'encode' may be used uninitialized in this function
util.c: In function 'decoder':
util.c:43: warning: 'decode' may be used uninitialized in this function
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.6-bioc/R/library/Biostrings/include" -fpic -g -O2 -Wall -c xsnap.c -o xsnap.o
g++ -shared -L/usr/local/lib64 -o ShortRead.so Biostrings_stubs.o IRanges_stubs.o R_init_ShortRead.o alphabet.o io.o io_bowtie.o io_soap.o pileup.o readBfaToc.o read_maq_map.o util.o xsnap.o -lz -L/home/biocbuild/bbs-2.6-bioc/R/lib -lR
** R
** inst
** preparing package for lazy loading
Attaching package: 'IRanges'
The following object(s) are masked from package:base :
Map,
cbind,
mapply,
order,
pmax,
pmax.int,
pmin,
pmin.int,
rbind,
rep.int,
table
** help
*** installing help indices
** building package indices ...
* DONE (ShortRead)