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BioC 3.2: CHECK report for GenomicAlignments on oaxaca

This page was generated on 2016-04-23 10:27:19 -0700 (Sat, 23 Apr 2016).

Package 421/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenomicAlignments 1.6.3
Bioconductor Package Maintainer
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/GenomicAlignments
Last Changed Rev: 112191 / Revision: 116712
Last Changed Date: 2016-01-05 12:51:48 -0800 (Tue, 05 Jan 2016)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: GenomicAlignments
Version: 1.6.3
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GenomicAlignments_1.6.3.tar.gz
StartedAt: 2016-04-23 00:30:56 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 00:36:10 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 314.8 seconds
RetCode: 0
Status:  OK 
CheckDir: GenomicAlignments.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GenomicAlignments_1.6.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/GenomicAlignments.Rcheck’
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenomicAlignments/DESCRIPTION’ ... OK
* this is package ‘GenomicAlignments’ version ‘1.6.3’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘BiocGenerics’ ‘S4Vectors’ ‘IRanges’ ‘GenomeInfoDb’ ‘GenomicRanges’
  ‘SummarizedExperiment’ ‘Biostrings’ ‘Rsamtools’
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 ... [17s/17s] 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’ ‘S4Vectors’ ‘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
'library' or 'require' call to ‘BSgenome’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
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.
* 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 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 ... [106s/119s] OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
junctions-methods          29.563  2.420  38.979
summarizeOverlaps-methods  12.650  1.715  16.902
readGAlignments            13.079  1.253  14.416
sequenceLayer               9.712  1.093  11.509
coordinate-mapping-methods  8.369  0.284   9.638
findSpliceOverlaps-methods  4.673  0.347   5.116
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘GenomicAlignments_unit_tests.R’ [40s/41s]
 [41s/42s] 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
* DONE

Status: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-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/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/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/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/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/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c S4Vectors_stubs.c -o S4Vectors_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/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/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/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c coordinate_mapping_methods.c -o coordinate_mapping_methods.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/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/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/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o GenomicAlignments.so IRanges_stubs.o R_init_GenomicAlignments.o S4Vectors_stubs.o cigar_utils.o coordinate_mapping_methods.o encodeOverlaps_methods.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.2-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-class1.1310.0341.166
GAlignments-class0.4490.0090.457
GAlignmentsList-class3.4530.0863.974
GappedReads-class0.1330.0130.146
OverlapEncodings-class0.0550.0020.080
cigar-utils0.2680.0130.281
coordinate-mapping-methods8.3690.2849.638
coverage-methods3.2930.1623.464
encodeOverlaps-methods0.0300.0000.097
findCompatibleOverlaps-methods0.9440.1121.777
findMateAlignment0.2330.0130.246
findOverlaps-methods0.6110.0180.629
findSpliceOverlaps-methods4.6730.3475.116
intra-range-methods0.2890.0110.300
junctions-methods29.563 2.42038.979
mapCoords-methods0.0000.0010.001
pileLettersAt0.6280.0100.649
readGAlignments13.079 1.25314.416
sequenceLayer 9.712 1.09311.509
setops-methods0.1170.0040.120
stackStringsFromBam1.9200.0391.962
summarizeOverlaps-methods12.650 1.71516.902