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BioC 2.14: CHECK report for GenomicAlignments on morelia

This page was generated on 2014-10-08 09:07:13 -0700 (Wed, 08 Oct 2014).

Package 336/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenomicAlignments 1.0.6
Bioconductor Package Maintainer
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/GenomicAlignments
Last Changed Rev: 93517 / Revision: 95116
Last Changed Date: 2014-08-21 16:04:36 -0700 (Thu, 21 Aug 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK 

Summary

Package: GenomicAlignments
Version: 1.0.6
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GenomicAlignments_1.0.6.tar.gz
StartedAt: 2014-10-07 23:03:46 -0700 (Tue, 07 Oct 2014)
EndedAt: 2014-10-07 23:09:40 -0700 (Tue, 07 Oct 2014)
EllapsedTime: 353.2 seconds
RetCode: 0
Status:  OK 
CheckDir: GenomicAlignments.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GenomicAlignments_1.0.6.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/GenomicAlignments.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin13.1.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenomicAlignments/DESCRIPTION’ ... OK
* this is package ‘GenomicAlignments’ version ‘1.0.6’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘BiocGenerics’ ‘IRanges’ ‘GenomicRanges’ ‘Biostrings’ ‘Rsamtools’
  ‘BSgenome’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘GenomicAlignments’ can be installed ... [19s/19s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’ ‘BiocGenerics’ ‘IRanges’ ‘GenomicRanges’ ‘Biostrings’ ‘Rsamtools’
A package should be listed in only one of these fields.
* checking top-level files ... OK
* checking for left-over 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 dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  ‘Biostrings:::.normarg_padding.letter’
  ‘Rsamtools:::.BamViews_delegate’ ‘Rsamtools:::.findMateWithinGroups’
  ‘Rsamtools:::.isValidHit’
  ‘Rsamtools:::.load_bamcols_from_scanBam_res’
  See the note in ?`:::` about the use of this operator.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 ... OK
* checking for missing documentation entries ... OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... [122s/124s] OK
Examples with CPU or elapsed time > 5s
                                 user system elapsed
junctions-methods              34.243  2.338  36.704
sequenceLayer                  16.389  0.945  19.021
summarizeOverlaps-methods      13.043  0.921  14.863
findSpliceOverlaps-methods      9.031  0.516   9.691
readGAlignments                 8.709  0.326   9.046
GAlignmentsList-class           6.272  0.127   6.452
findCompatibleOverlaps-methods  5.180  0.142   5.650
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘GenomicAlignments_unit_tests.R’ [50s/51s]
 [51s/51s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-2.14-bioc/meat/GenomicAlignments.Rcheck/00check.log’
for details.

GenomicAlignments.Rcheck/00install.out:

* installing *source* package ‘GenomicAlignments’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c IRanges_stubs.c -o IRanges_stubs.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c R_init_GenomicAlignments.c -o R_init_GenomicAlignments.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c cigar_utils.c -o cigar_utils.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c encodeOverlaps_methods.c -o encodeOverlaps_methods.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o GenomicAlignments.so IRanges_stubs.o R_init_GenomicAlignments.o cigar_utils.o encodeOverlaps_methods.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.14-bioc/meat/GenomicAlignments.Rcheck/GenomicAlignments/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GenomicAlignments)

GenomicAlignments.Rcheck/GenomicAlignments-Ex.timings:

nameusersystemelapsed
GAlignmentPairs-class4.1130.0334.180
GAlignments-class2.0790.0172.097
GAlignmentsList-class6.2720.1276.452
GappedReads-class0.3040.0060.310
OverlapEncodings-class0.0730.0030.075
cigar-utils0.3180.0080.327
coverage-methods1.1110.0141.125
encodeOverlaps-methods0.0330.0010.034
findCompatibleOverlaps-methods5.1800.1425.650
findMateAlignment0.9440.0270.970
findOverlaps-methods1.8520.0071.862
findSpliceOverlaps-methods9.0310.5169.691
intra-range-methods0.5920.0150.609
junctions-methods34.243 2.33836.704
pileLettersAt1.1560.0121.170
readGAlignments8.7090.3269.046
sequenceLayer16.389 0.94519.021
setops-methods0.3250.0170.344
stackStringsFromBam1.9560.0782.035
summarizeOverlaps-methods13.043 0.92114.863