GenomicRanges 1.8.13
Bioconductor Package Maintainer
| Snapshot Date: 2012-09-23 17:01:39 -0700 (Sun, 23 Sep 2012) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_10/madman/Rpacks/GenomicRanges | | Last Changed Rev: 68848 / Revision: 69725 | | Last Changed Date: 2012-08-27 13:46:58 -0700 (Mon, 27 Aug 2012) |
| lamb2 | Linux (openSUSE 11.4) / x86_64 | OK | WARNINGS | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | WARNINGS | OK |
| petty | Mac OS X Leopard (10.5.8) / i386 | OK | [ WARNINGS ] | OK |
* using log directory '/Users/biocbuild/bbs-2.10-bioc/meat/GenomicRanges.Rcheck'
* using R version 2.15.1 (2012-06-22)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'GenomicRanges/DESCRIPTION' ... OK
* this is package 'GenomicRanges' version '1.8.13'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking whether package 'GenomicRanges' can be installed ... OK
* checking installed package size ... 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 namespace can be loaded with stated dependencies ... OK
* checking whether the namespace 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link(s) in documentation object '/Users/biocbuild/bbs-2.10-bioc/meat/GenomicRanges.Rcheck/00_pkg_src/GenomicRanges/man/encodeOverlaps-methods.Rd':
'[IRanges]{Hits}'
Missing link(s) in documentation object '/Users/biocbuild/bbs-2.10-bioc/meat/GenomicRanges.Rcheck/00_pkg_src/GenomicRanges/man/findOverlaps-methods.Rd':
'[IRanges]{Hits}'
See the information in section 'Cross-references' of the 'Writing R
Extensions' manual.
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
generic '$<-' and siglist 'SummarizedExperiment'
generic '[[<-' and siglist 'GRangesList,ANY,ANY'
generic '[[<-' and siglist 'SummarizedExperiment,ANY,missing'
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 use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running 'GenomicRanges_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 2 warnings.
See
'/Users/biocbuild/bbs-2.10-bioc/meat/GenomicRanges.Rcheck/00check.log'
for details.
* installing *source* package 'GenomicRanges' ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -fPIC -g -O2 -Wall -pedantic -c IRanges_stubs.c -o IRanges_stubs.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -fPIC -g -O2 -Wall -pedantic -c R_init_GenomicRanges.c -o R_init_GenomicRanges.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -fPIC -g -O2 -Wall -pedantic -c cigar_utils.c -o cigar_utils.o
cigar_utils.c: In function 'ref_locs_to_query_locs':
cigar_utils.c:1096: warning: 'n' may be used uninitialized in this function
cigar_utils.c: In function 'cigar_to_width':
cigar_utils.c:763: warning: 'width' may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -fPIC -g -O2 -Wall -pedantic -c transcript_utils.c -o transcript_utils.o
transcript_utils.c: In function 'tlocs2rlocs':
transcript_utils.c:119: warning: 'end' may be used uninitialized in this function
transcript_utils.c:119: note: 'end' was declared here
transcript_utils.c:119: warning: 'start' may be used uninitialized in this function
transcript_utils.c:119: note: 'start' was declared here
transcript_utils.c:208: warning: 'nlocs' may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o GenomicRanges.so IRanges_stubs.o R_init_GenomicRanges.o cigar_utils.o transcript_utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.10-bioc/meat/GenomicRanges.Rcheck/GenomicRanges/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
'GenomicRangesIntroduction.Rnw'
'GenomicRangesUseCases.Rnw'
'OverlapEncodings.Rnw'
'summarizeOverlaps.Rnw'
** testing if installed package can be loaded
* DONE (GenomicRanges)