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BioC 2.13: CHECK report for genoset on zin1

This page was generated on 2014-04-05 09:48:04 -0700 (Sat, 05 Apr 2014).

Package 302/750HostnameOS / ArchBUILDCHECKBUILD BIN
genoset 1.14.0
Peter M. Haverty
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/genoset
Last Changed Rev: 81642 / Revision: 88450
Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: genoset
Version: 1.14.0
Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings genoset_1.14.0.tar.gz
StartedAt: 2014-04-05 01:27:36 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 01:30:02 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 145.7 seconds
RetCode: 0
Status:  OK 
CheckDir: genoset.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/genoset.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘genoset/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘genoset’ version ‘1.14.0’
* 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 ‘genoset’ can be installed ... [19s/19s] 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:
  ‘IRanges’ ‘GenomicRanges’
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
Unexported object imported by a ‘:::’ call: ‘BiocGenerics:::testPackage’
  See the note in ?`:::` about the use of this operator.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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 ... [13s/13s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘prove.R’ [25s/21s]
  Comparing ‘prove.Rout’ to ‘prove.Rout.save’ ...7,13c7
< The following objects are masked from 'package:parallel':
< 
<     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
<     clusterExport, clusterMap, parApply, parCapply, parLapply,
<     parLapplyLB, parRapply, parSapply, parSapplyLB
< 
< The following object is masked from 'package:stats':
---
> The following object(s) are masked from 'package:stats':
17c11
< The following objects are masked from 'package:base':
---
> The following object(s) are masked from 'package:base':
19,24c13,16
<     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
<     as.data.frame, as.vector, cbind, colnames, duplicated, eval, evalq,
<     get, intersect, is.unsorted, lapply, mapply, match, mget, order,
<     paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rep.int,
<     rownames, sapply, setdiff, sort, table, tapply, union, unique,
<     unlist
---
>     Filter, Find, Map, Position, Reduce, anyDuplicated, cbind,
>     colnames, duplicated, eval, get, intersect, lapply, mapply, mget,
>     order, paste, pmax, pmax.int, pmin, pmin.int, rbind, rep.int,
>     rownames, sapply, setdiff, table, tapply, union, unique
31a24,30
> 
> Attaching package: 'Biobase'
> 
> The following object(s) are masked from 'package:BiocGenerics':
> 
>     annotation, annotation<-
> 
32a32,33
> Warning message:
> replacing previous import 'annotation' when loading 'Biobase' 
33a35
> Loading required namespace: DNAcopy
46a49
> Working on segmentation for sample number 1 : a1
65c68
< RUNIT TEST PROTOCOL -- Sat Apr  5 01:29:59 2014 
---
> RUNIT TEST PROTOCOL -- Thu Oct 25 19:26:26 2012 
67c70
< Number of test functions: 26 
---
> Number of test functions: 24 
73,74c76,77
< genoset RUnit Tests - 26 test functions, 0 errors, 0 failures
< Number of test functions: 26 
---
> genoset RUnit Tests - 24 test functions, 0 errors, 0 failures
> Number of test functions: 24 
77c80
< There were 35 warnings (use warnings() to see them)
---
> There were 37 warnings (use warnings() to see them)
 [25s/22s] 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

NOTE: There were 2 notes.
See
  ‘/home/biocbuild/bbs-2.13-bioc/meat/genoset.Rcheck/00check.log’
for details.

genoset.Rcheck/00install.out:

* installing *source* package ‘genoset’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c genoset.c -o genoset.o
gcc -std=gnu99 -shared -L/usr/local/lib -o genoset.so genoset.o -L/home/biocbuild/bbs-2.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.13-bioc/meat/genoset.Rcheck/genoset/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (genoset)

genoset.Rcheck/genoset-Ex.timings:

nameusersystemelapsed
BAFSet-class0.0000.0040.005
CNSet-class0.0040.0000.004
GenoSet-class0.1520.0000.161
GenoSet0.0480.0000.051
baf2mbaf0.0360.0040.042
boundingIndices0.0040.0000.004
boundingIndices20.0040.0000.004
calcGC0.1360.0000.136
chr-methods0.0240.0000.021
chrIndices-methods0.0160.0000.014
chrInfo0.0240.0000.024
chrNames0.0280.0000.030
chrOrder0.0040.0000.005
colMeans0.0120.0000.014
colnames0.0160.0000.014
gcCorrect0.0080.0000.006
genoPlot-methods0.0560.0040.070
genoPos-methods0.0280.0000.028
genome0.0120.0000.014
genomeAxis0.0360.0000.038
genoset-methods0.3400.0000.341
initGenoSet0.0480.0000.052
isGenomeOrder-methods0.0160.0040.016
locData-methods0.0120.0000.015
modeCenter0.0080.0000.008
pos0.0200.0000.022
rangeSampleMeans0.0640.0000.062
readGenoSet0.0040.0000.004
rownames0.0120.0000.013
runCBS1.8360.0041.844
segPairTable-methods0.0160.0000.016
segTable-methods1.4480.0001.451
segs2Rle1.4200.0041.433
segs2RleDataFrame1.5440.0001.559
subsetAssayData0.0080.0040.013
toGenomeOrder-methods0.2400.0040.245