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BioC 2.14: CHECK report for GenomicRanges on zin2

This page was generated on 2014-10-08 08:48:46 -0700 (Wed, 08 Oct 2014).

Package 339/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenomicRanges 1.16.4
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/GenomicRanges
Last Changed Rev: 93112 / Revision: 95116
Last Changed Date: 2014-07-31 21:25:31 -0700 (Thu, 31 Jul 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK [ WARNINGS ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  WARNINGS  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  WARNINGS  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  WARNINGS  OK 

Summary

Package: GenomicRanges
Version: 1.16.4
Command: /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings GenomicRanges_1.16.4.tar.gz
StartedAt: 2014-10-07 23:55:14 -0700 (Tue, 07 Oct 2014)
EndedAt: 2014-10-07 23:58:31 -0700 (Tue, 07 Oct 2014)
EllapsedTime: 197.1 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: GenomicRanges.Rcheck
Warnings: 2

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings GenomicRanges_1.16.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/GenomicRanges.Rcheck’
* using R version 3.1.1 (2014-07-10)
* 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 ‘1.16.4’
* 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 ... [10s/10s] 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’
A package should be listed in only one of these fields.
Versioned 'LinkingTo' value for ‘XVector’ is only usable in R >= 3.0.2
* 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 ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic '[' and siglist 'GIntervalTree,ANY'
  generic '[' and siglist 'GenomicRanges,ANY'
  generic '[' and siglist 'List,GenomicRanges'
  generic '[' and siglist 'Seqinfo,ANY'
  generic '[' and siglist 'list,GenomicRanges'
  generic '[[<-' and siglist 'GRangesList,ANY,ANY'
  generic 'tile' and siglist 'GenomicRanges'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See the chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'inter-range-methods':
\S4method{disjoin}{GRangesList}
  Code: function(x, ...)
  Docs: function(x, ignore.strand = FALSE)
  Argument names in code not in docs:
    ...
  Argument names in docs not in code:
    ignore.strand
  Mismatches in argument names:
    Position: 2 Code: ... Docs: ignore.strand

* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [38s/47s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
tileGenome               8.901  0.116  10.102
inter-range-methods      5.825  0.032   5.892
makeGRangesFromDataFrame 5.552  0.116  12.510
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘GenomicRanges_unit_tests.R’ [46s/46s]
 [46s/46s] 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

WARNING: There were 2 warnings.
NOTE: There was 1 note.
See
  ‘/home/biocbuild/bbs-2.14-bioc/meat/GenomicRanges.Rcheck/00check.log’
for details.

GenomicRanges.Rcheck/00install.out:

* installing *source* package ‘GenomicRanges’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c IRanges_stubs.c -o IRanges_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c R_init_GenomicRanges.c -o R_init_GenomicRanges.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/XVector/include"   -fpic  -g -O2  -Wall -c XVector_stubs.c -o XVector_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/XVector/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/usr/local/lib -o GenomicRanges.so IRanges_stubs.o R_init_GenomicRanges.o XVector_stubs.o transcript_utils.o -L/home/biocbuild/bbs-2.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.14-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-class0.4040.0120.420
GRanges-class0.6200.0040.627
GRangesList-class0.8480.0040.856
GenomicRanges-comparison1.160.001.16
Seqinfo-class0.0480.0000.049
SummarizedExperiment-class0.1440.0080.149
constraint0.6160.0000.615
coverage-methods0.4800.0000.482
findOverlaps-methods2.7480.0002.762
inter-range-methods5.8250.0325.892
intra-range-methods0.5040.0000.508
makeGRangesFromDataFrame 5.552 0.11612.510
nearest-methods1.0840.0041.130
phicoef0.0040.0000.003
range-squeezers0.0000.0000.001
seqinfo2.1480.0242.175
seqlevels-utils1.5800.0401.624
setops-methods1.8360.0001.996
strand-utils0.0640.0040.142
tileGenome 8.901 0.11610.102