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Package 224/553HostnameOS / ArchBUILDCHECKBUILD BIN
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 

Summary

Package: GenomicRanges
Version: 1.8.13
Command: /home/biocbuild/bbs-2.10-bioc/R/bin/R CMD check --no-vignettes --timings GenomicRanges_1.8.13.tar.gz
StartedAt: 2012-09-24 01:07:32 -0700 (Mon, 24 Sep 2012)
EndedAt: 2012-09-24 01:10:51 -0700 (Mon, 24 Sep 2012)
EllapsedTime: 198.7 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: GenomicRanges.Rcheck
Warnings: 2

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.10-bioc/meat/GenomicRanges.Rcheck’
* using R version 2.15.1 (2012-06-22)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 ‘/loc/home/biocbuild/bbs-2.10-bioc/meat/GenomicRanges.Rcheck/00_pkg_src/GenomicRanges/man/encodeOverlaps-methods.Rd’:
  ‘[IRanges]{Hits}’

Missing link(s) in documentation object ‘/loc/home/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 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
  ‘/loc/home/biocbuild/bbs-2.10-bioc/meat/GenomicRanges.Rcheck/00check.log’
for details.

GenomicRanges.Rcheck/00install.out:

* installing *source* package ‘GenomicRanges’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/IRanges/include"   -fpic  -g -O2  -Wall -c IRanges_stubs.c -o IRanges_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/IRanges/include"   -fpic  -g -O2  -Wall -c R_init_GenomicRanges.c -o R_init_GenomicRanges.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/IRanges/include"   -fpic  -g -O2  -Wall -c cigar_utils.c -o cigar_utils.o
cigar_utils.c: In function ‘cigar_to_width’:
cigar_utils.c:763:23: warning: ‘width’ may be used uninitialized in this function
cigar_utils.c: In function ‘ref_locs_to_query_locs’:
cigar_utils.c:1096:9: warning: ‘n’ may be used uninitialized in this function
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/IRanges/include"   -fpic  -g -O2  -Wall -c transcript_utils.c -o transcript_utils.o
transcript_utils.c: In function ‘tlocs2rlocs’:
transcript_utils.c:208:44: warning: ‘nlocs’ may be used uninitialized in this function
gcc -std=gnu99 -shared -L/usr/local/lib64 -o GenomicRanges.so IRanges_stubs.o R_init_GenomicRanges.o cigar_utils.o transcript_utils.o -L/home/biocbuild/bbs-2.10-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.10-bioc/meat/GenomicRanges.Rcheck/GenomicRanges/libs
** 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)

GenomicRanges.Rcheck/GenomicRanges-Ex.timings:

nameusersystemelapsed
GRanges-class1.4040.0241.430
GRangesList-class1.2200.0041.251
GappedAlignmentPairs-class3.7720.0803.955
GappedAlignments-class1.1600.0081.166
GenomicRanges-comparison1.3320.0001.330
Seqinfo-class0.0600.0080.067
SummarizedExperiment-class0.0600.0000.057
cigar-utils0.4320.0160.455
constraint1.0080.0001.008
countGenomicOverlaps000
coverage-methods1.4480.0161.465
encodeOverlaps-methods000
findOverlaps-methods3.5410.0243.568
seqinfo0.0040.0000.006
seqlevels-utils0.4720.0120.485
setops-methods2.8000.0162.822
strand-utils0.0080.0000.011
summarizeOverlaps7.3960.1327.544