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BioC 3.0: CHECK report for GenomicRanges on zin1

This page was generated on 2015-04-10 09:38:52 -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: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings GenomicRanges_1.18.4.tar.gz
StartedAt: 2015-04-10 00:23:40 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 00:27:11 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 211.1 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: GenomicRanges.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings GenomicRanges_1.18.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/GenomicRanges.Rcheck’
* using R version 3.1.3 (2015-03-09)
* 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 ‘1.18.4’
* 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 ... [12s/13s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [37s/47s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
tileGenome               9.169  0.168   9.424
inter-range-methods      5.208  0.084   5.739
makeGRangesFromDataFrame 5.029  0.168  13.085
mapCoords-methods        4.880  0.060   5.484
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘GenomicRanges_unit_tests.R’ [49s/52s]
 [49s/52s] 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
  ‘/home/biocbuild/bbs-3.0-bioc/meat/GenomicRanges.Rcheck/00check.log’
for details.

GenomicRanges.Rcheck/00install.out:

* installing *source* package ‘GenomicRanges’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include"   -fpic  -g -O2  -Wall -c IRanges_stubs.c -o IRanges_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-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-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include"   -fpic  -g -O2  -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-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:143:38: warning: ‘end’ may be used uninitialized in this function [-Wuninitialized]
transcript_utils.c:120:24: note: ‘end’ was declared here
transcript_utils.c:143:38: warning: ‘start’ may be used uninitialized in this function [-Wuninitialized]
transcript_utils.c:120:17: note: ‘start’ was declared here
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.0-bioc/R/lib -L/usr/local/lib -o GenomicRanges.so IRanges_stubs.o R_init_GenomicRanges.o S4Vectors_stubs.o transcript_utils.o -L/home/biocbuild/bbs-3.0-bioc/R/lib -lR
installing to /home/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-class0.5280.0000.536
GRanges-class0.3280.0040.337
GRangesList-class0.6520.0040.669
GRangesMapping-class0.0000.0000.001
GenomicRanges-comparison0.3680.0000.371
SummarizedExperiment-class0.1000.0000.102
constraint0.3520.0000.356
coverage-methods0.4360.0040.469
findOverlaps-methods2.4760.0042.508
inter-range-methods5.2080.0845.739
intra-range-methods0.4240.0040.541
makeGRangesFromDataFrame 5.029 0.16813.085
map-methods000
mapCoords-methods4.8800.0605.484
nearest-methods0.8600.0120.875
phicoef0.0040.0000.003
range-squeezers0.0000.0000.001
setops-methods1.1560.0081.168
strand-utils0.0480.0000.049
tile-methods0.0560.0000.062
tileGenome9.1690.1689.424