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BioC 3.0: CHECK report for GenomicRanges on oaxaca

This page was generated on 2015-04-10 10:04:01 -0700 (Fri, 10 Apr 2015).

Package 370/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenomicRanges 1.18.4
Bioconductor Package Maintainer
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/GenomicRanges
Last Changed Rev: 98053 / Revision: 102249
Last Changed Date: 2015-01-05 23:48:41 -0800 (Mon, 05 Jan 2015)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  WARNINGS 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  WARNINGS  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  WARNINGS  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ WARNINGS ] OK 

Summary

Package: GenomicRanges
Version: 1.18.4
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GenomicRanges_1.18.4.tar.gz
StartedAt: 2015-04-09 23:57:06 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-10 00:01:17 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 251.2 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: GenomicRanges.Rcheck
Warnings: 2

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GenomicRanges_1.18.4.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/GenomicRanges.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenomicRanges/DESCRIPTION’ ... OK
* this is package ‘GenomicRanges’ version ‘1.18.4’
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘GenomicRanges’ can be installed ... [14s/15s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 ... 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 ... WARNING
Rd files with duplicated alias 'tile,GenomicRanges-method':
  ‘GRanges-class.Rd’ ‘tile-methods.Rd’
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 classes:
  ‘DelegatingGenomicRanges’
Undocumented S4 methods:
  generic 'ranges' and siglist 'DelegatingGenomicRanges'
  generic 'seqinfo' and siglist 'DelegatingGenomicRanges'
  generic 'seqinfo' and siglist 'List'
  generic 'seqinfo' and siglist 'RangedData'
  generic 'seqinfo' and siglist 'RangesList'
  generic 'seqinfo<-' and siglist 'List'
  generic 'seqinfo<-' and siglist 'RangedData'
  generic 'seqnames' and siglist 'DelegatingGenomicRanges'
  generic 'seqnames' and siglist 'RangedData'
  generic 'seqnames' and siglist 'RangesList'
  generic 'strand' and siglist 'DelegatingGenomicRanges'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See 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 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 ... [41s/47s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
tileGenome               8.460  0.332   8.860
mapCoords-methods        6.178  0.253   6.438
makeGRangesFromDataFrame 5.667  0.177  12.190
inter-range-methods      5.507  0.113   5.683
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘GenomicRanges_unit_tests.R’ [58s/60s]
 [58s/60s] 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

WARNING: There were 2 warnings.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/GenomicRanges.Rcheck/00check.log’
for details.

GenomicRanges.Rcheck/00install.out:

* installing *source* package ‘GenomicRanges’ ...
** 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/S4Vectors/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/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c R_init_GenomicRanges.c -o R_init_GenomicRanges.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/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.1/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/3.1/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c transcript_utils.c -o transcript_utils.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 GenomicRanges.so IRanges_stubs.o R_init_GenomicRanges.o S4Vectors_stubs.o transcript_utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.0-bioc/meat/GenomicRanges.Rcheck/GenomicRanges/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 (GenomicRanges)

GenomicRanges.Rcheck/GenomicRanges-Ex.timings:

nameusersystemelapsed
GIntervalTree-class0.5510.0080.559
GRanges-class0.3870.0030.392
GRangesList-class0.7500.0080.757
GRangesMapping-class0.0030.0000.004
GenomicRanges-comparison0.4160.0030.419
SummarizedExperiment-class0.1190.0020.120
constraint0.5310.0040.536
coverage-methods0.3510.0060.360
findOverlaps-methods2.8660.0112.884
inter-range-methods5.5070.1135.683
intra-range-methods0.5240.0040.530
makeGRangesFromDataFrame 5.667 0.17712.190
map-methods0.0010.0000.001
mapCoords-methods6.1780.2536.438
nearest-methods1.0280.0111.039
phicoef0.0040.0000.004
range-squeezers0.0000.0000.001
setops-methods1.3990.0041.404
strand-utils0.0570.0010.058
tile-methods0.0730.0010.074
tileGenome8.4600.3328.860