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BioC 2.14: CHECK report for genoset on petty

This page was generated on 2014-10-08 08:59:30 -0700 (Wed, 08 Oct 2014).

Package 341/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
genoset 1.16.2
Peter M. Haverty
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/genoset
Last Changed Rev: 89646 / Revision: 95116
Last Changed Date: 2014-04-29 11:27:54 -0700 (Tue, 29 Apr 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK [ OK ] OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK 

Summary

Package: genoset
Version: 1.16.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch genoset_1.16.2.tar.gz
StartedAt: 2014-10-07 22:12:39 -0700 (Tue, 07 Oct 2014)
EndedAt: 2014-10-07 22:17:26 -0700 (Tue, 07 Oct 2014)
EllapsedTime: 287.0 seconds
RetCode: 0
Status:  OK 
CheckDir: genoset.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch genoset_1.16.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/genoset.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.16.2’
* 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 ... [35s/35s] 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 ... 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [21s/22s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘prove.R’ [29s/27s]
  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
<     anyDuplicated, append, as.data.frame, as.vector, cbind, colnames,
<     do.call, duplicated, eval, evalq, Filter, Find, get, intersect,
<     is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax,
<     pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, 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' 
33a35,38
> Loading required namespace: DNAcopy
> Using mclapply for segmentation ...
> Working on segmentation for sample number 1 : a1
> Working on segmentation for sample number 2 : a2
37a43
> Working on segmentation for sample number 1 : a1
39c45,46
< 
---
> Using mclapply for segmentation ...
> Working on segmentation for sample number 1 : a1
41c48,60
< 
---
> Using mclapply for segmentation ...
> Working on segmentation for sample number 1 : a1
> Working on segmentation for sample number 2 : a2
> Using mclapply for segmentation ...
> Working on segmentation for sample number 1 : a1
> Working on segmentation for sample number 2 : a2
> Using mclapply for segmentation ...
> Working on segmentation for sample number 1 : a1
> Working on segmentation for sample number 2 : a2
> Using mclapply for segmentation ...
> Working on segmentation for sample number 1 : a1
> Working on segmentation for sample number 2 : a2
> Using mclapply for segmentation ...
49c68
< RUNIT TEST PROTOCOL -- Tue Oct  7 22:17:17 2014 
---
> RUNIT TEST PROTOCOL -- Thu Oct 25 19:26:26 2012 
51c70
< Number of test functions: 27 
---
> Number of test functions: 24 
57,58c76,77
< genoset RUnit Tests - 27 test functions, 0 errors, 0 failures
< Number of test functions: 27 
---
> genoset RUnit Tests - 24 test functions, 0 errors, 0 failures
> Number of test functions: 24 
60a80
> There were 37 warnings (use warnings() to see them)
Warning messages:
1: In readLines(from) : line 61 appears to contain an embedded nul
2: In readLines(from) : line 63 appears to contain an embedded nul
 [30s/28s] 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 was 1 note.
See
  ‘/Users/biocbuild/bbs-2.14-bioc/meat/genoset.Rcheck/00check.log’
for details.

genoset.Rcheck/00install.out:

* installing *source* package ‘genoset’ ...
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c genoset.c -o genoset.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/usr/local/lib -L/usr/local/lib -o genoset.so genoset.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.14-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
GenoSet-class0.5330.0010.535
GenoSet0.0940.0040.098
baf2mbaf0.0890.0180.107
boundingIndices0.0020.0000.003
boundingIndices20.0010.0000.002
calcGC0.0010.0000.001
chr-methods0.0390.0230.061
chrIndices-methods0.0240.0120.035
chrInfo-methods0.0490.0130.063
chrNames-methods0.0440.0110.055
chrOrder0.0020.0000.002
colMeans0.0180.0000.019
colnames0.0190.0110.030
gcCorrect0.0080.0010.008
genoPlot-methods0.1160.0140.131
genoPos-methods0.0510.0120.063
genome-GenoSet-method0.0230.0130.036
genome0.0190.0120.032
genomeAxis0.0780.0140.093
genoset-subset0.8290.0200.850
initGenoSet0.0960.0000.096
isGenomeOrder-methods0.0250.0120.037
locData-methods0.0210.0120.032
modeCenter0.0110.0020.013
pos-methods0.0280.0210.049
rangeSampleMeans0.1550.0110.166
readGenoSet0.0010.0000.001
rownames-methods0.0180.0120.030
runCBS2.4760.0092.485
segPairTable-methods0.0310.0000.032
segTable-methods1.9360.0151.971
segs2Rle1.8370.0151.859
segs2RleDataFrame1.9420.0161.968
subsetAssayData0.0170.0110.029
toGenomeOrder-methods0.3260.0140.340