ShortRead 1.11.23
Biocore Team c/o BioC user list
| Snapshot Date: 2011-07-06 19:21:50 -0700 (Wed, 06 Jul 2011) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ShortRead | | Last Changed Rev: 56598 / Revision: 56603 | | Last Changed Date: 2011-07-06 15:55:59 -0700 (Wed, 06 Jul 2011) |
| wilson2 | Linux (openSUSE 11.4) / x86_64 | OK | WARNINGS | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | WARNINGS | OK |
| gewurz | Windows Server 2008 R2 Enterprise (64-bit) / x64 | OK | WARNINGS | OK |
| moscato1 | Windows Server 2008 R2 Enterprise (64-bit) / x64 | OK | WARNINGS | OK |
| pitt | Mac OS X Leopard (10.5.8) / i386 | OK | [ WARNINGS ] | OK |
* using log directory '/Users/biocbuild/bbs-2.9-bioc/meat/ShortRead.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-06-22 r56208)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'ShortRead/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ShortRead' version '1.11.23'
* checking package name space information ... OK
* checking package dependencies ... NOTE
Packages which this enhances but not available for checking:
'Rmpi' 'multicore'
* checking if this is a source package ... OK
* checking whether package 'ShortRead' can be installed ... WARNING
Found the following significant warnings:
Warning: Class "AssayData" is defined (with package slot 'Biobase') but no metadata object found to revise subclass information---not exported? Making a copy in package 'ShortRead'
See '/Users/biocbuild/bbs-2.9-bioc/meat/ShortRead.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
installed size is 5.2Mb
sub-directories of 1Mb or more:
doc 2.3Mb
extdata 1.3Mb
* 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
.coverage_viewer: no visible binding for global variable 'group'
.multicoverage_viewer: no visible global function definition for
'.getData<-'
.multicoverage_viewer: no visible binding for global variable 'lv'
.multicoverage_viewer: no visible binding for global variable 'group'
.multicoverage_viewer: no visible binding for global variable 'sv'
.plotCycleBaseCall: no visible binding for global variable 'Base'
.plotNucleotideCount: no visible binding for global variable
'Nucleotide'
.plotReadCount: no visible binding for global variable 'Census'
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link(s) in documentation object '/Users/biocbuild/bbs-2.9-bioc/meat/ShortRead.Rcheck/00_pkg_src/ShortRead/man/Snapshot-class.Rd':
'Snapshot-class'
See the information in section 'Cross-references' of the 'Writing R
Extensions' manual.
* checking for missing documentation entries ... WARNING
Undocumented code objects:
'GappedReads' 'qname' 'qseq' 'readGappedReads'
Undocumented S4 classes:
'AssayData' 'GappedReads' 'Snapshot' 'trellis'
Undocumented S4 methods:
generic 'SnapshotFunctionList' and siglist 'SnapshotFunction'
generic '[' and siglist 'GappedReads,ANY,ANY'
generic 'c' and siglist 'GappedReads'
generic 'narrow' and siglist 'GappedReads'
generic 'qname' and siglist 'GappedReads'
generic 'qseq' and siglist 'GappedReads'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See the chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... 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) and $(LAPACK_LIBS) ... OK
* checking sizes of PDF files under 'inst/doc' ... NOTE
'qpdf' made some significant size reductions:
compacted 'ShortRead_and_HilbertVis.pdf' from 1277Kb to 598Kb
consider running tools::compactPDF() on these files
* checking examples ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running 'ShortRead_unit_tests.R'
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK
WARNING: There were 3 warnings, see
'/Users/biocbuild/bbs-2.9-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 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... 4
checking for gzeof in -lz... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
*** arch - i386
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -fPIC -g -O2 -Wall -pedantic -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -fPIC -g -O2 -Wall -pedantic -c IRanges_stubs.c -o IRanges_stubs.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -fPIC -g -O2 -Wall -pedantic -c R_init_ShortRead.c -o R_init_ShortRead.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -fPIC -g -O2 -Wall -pedantic -c alphabet.c -o alphabet.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -fPIC -g -O2 -Wall -pedantic -c io.c -o io.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -fPIC -g -O2 -Wall -pedantic -c io_bowtie.c -o io_bowtie.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -fPIC -g -O2 -Wall -pedantic -c io_soap.c -o io_soap.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -fPIC -g -O2 -Wall -pedantic -c pileup.c -o pileup.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/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=4 -DHAVE_LIBZ=1 -fPIC -g -O2 -Wall -fasm-blocks -c readBfaToc.cc -o readBfaToc.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/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=4 -DHAVE_LIBZ=1 -fPIC -g -O2 -Wall -fasm-blocks -c read_maq_map.cc -o read_maq_map.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -fPIC -g -O2 -Wall -pedantic -c sampler.c -o sampler.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -fPIC -g -O2 -Wall -pedantic -c trim.c -o trim.o
trim.c: In function 'trim_tails':
trim.c:25: warning: ignoring #pragma omp parallel
trim.c:42: warning: ignoring #pragma omp parallel
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -fPIC -g -O2 -Wall -pedantic -c util.c -o util.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -fPIC -g -O2 -Wall -pedantic -c xsnap.c -o xsnap.o
g++-4.2 -arch i386 -dynamiclib -Wl,-headerpad_max_install_names -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 io_bowtie.o io_soap.o pileup.o readBfaToc.o read_maq_map.o sampler.o trim.o util.o xsnap.o -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.9-bioc/meat/ShortRead.Rcheck/ShortRead/libs/i386
** R
** inst
** preparing package for lazy loading
Attaching package: 'IRanges'
The following object(s) are masked from 'package:base':
Map, cbind, eval, intersect, mapply, order, paste, pmax, pmax.int,
pmin, pmin.int, rbind, rep.int, setdiff, table, union
Loading required package: RColorBrewer
Warning: Class "AssayData" is defined (with package slot 'Biobase') but no metadata object found to revise subclass information---not exported? Making a copy in package 'ShortRead'
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
'Overview.Rnw'
** testing if installed package can be loaded
* DONE (ShortRead)