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BioC 3.0: CHECK report for GenomicRanges on perceval

This page was generated on 2015-04-10 09:54:57 -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: 2015-04-10 02:03:55 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 02:09:04 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 309.0 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
###
##############################################################################
##############################################################################


* 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-darwin10.8.0 (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 ... [18s/26s] 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 ... [54s/61s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
tileGenome               15.229  0.693  15.924
inter-range-methods       7.497  0.185   7.683
mapCoords-methods         7.195  0.371   7.566
makeGRangesFromDataFrame  6.560  0.254  13.635
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘GenomicRanges_unit_tests.R’ [76s/76s]
 [76s/76s] 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
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/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  -mtune=core2 -g -O2 -Wall  -c IRanges_stubs.c -o IRanges_stubs.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/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  -mtune=core2 -g -O2 -Wall  -c R_init_GenomicRanges.c -o R_init_GenomicRanges.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/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  -mtune=core2 -g -O2 -Wall  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/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  -mtune=core2 -g -O2 -Wall  -c transcript_utils.c -o transcript_utils.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -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 -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-class0.5070.0070.514
GRanges-class0.3660.0040.370
GRangesList-class0.7530.0110.964
GRangesMapping-class0.0010.0000.000
GenomicRanges-comparison0.4610.0050.467
SummarizedExperiment-class0.1100.0020.113
constraint0.3780.0070.395
coverage-methods0.5610.0070.567
findOverlaps-methods2.8590.0172.876
inter-range-methods7.4970.1857.683
intra-range-methods0.7140.0350.751
makeGRangesFromDataFrame 6.560 0.25413.635
map-methods0.0000.0000.001
mapCoords-methods7.1950.3717.566
nearest-methods0.9570.0300.987
phicoef0.0030.0000.003
range-squeezers0.0000.0000.001
setops-methods1.3470.0061.353
strand-utils0.0580.0010.060
tile-methods0.0640.0000.065
tileGenome15.229 0.69315.924