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Package 268/658HostnameOS / ArchBUILDCHECKBUILD BIN
genoset 1.11.26
Peter M. Haverty
Snapshot Date: 2013-03-24 17:01:43 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/genoset
Last Changed Rev: 73833 / Revision: 74774
Last Changed Date: 2013-02-28 12:44:05 -0800 (Thu, 28 Feb 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK [ OK ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: genoset
Version: 1.11.26
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings genoset_1.11.26.tar.gz
StartedAt: 2013-03-25 01:54:56 -0700 (Mon, 25 Mar 2013)
EndedAt: 2013-03-25 02:00:09 -0700 (Mon, 25 Mar 2013)
EllapsedTime: 312.9 seconds
RetCode: 0
Status:  OK 
CheckDir: genoset.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/genoset.Rcheck’
* using R version 3.0.0 beta (2013-03-19 r62328)
* 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 ‘1.11.26’
* 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 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 for unstated 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 ... 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 examples ... [28s/29s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘prove.R’ [62s/60s]
  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':
19,23c13,16
<     Filter, Find, Map, Position, Reduce, anyDuplicated, as.data.frame,
<     cbind, colnames, duplicated, eval, get, intersect, 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
30a24,30
> 
> Attaching package: 'Biobase'
> 
> The following object(s) are masked from 'package:BiocGenerics':
> 
>     annotation, annotation<-
> 
31a32,33
> Warning message:
> replacing previous import 'annotation' when loading 'Biobase' 
66c68
< RUNIT TEST PROTOCOL -- Mon Mar 25 02:00:04 2013 
---
> RUNIT TEST PROTOCOL -- Thu Oct 25 19:26:26 2012 
78c80
< There were 50 or more warnings (use warnings() to see the first 50)
---
> There were 37 warnings (use warnings() to see them)
 [63s/61s] 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

genoset.Rcheck/00install.out:

* installing *source* package ‘genoset’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-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-2.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.12-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
   ‘genoset.Rnw’ 
** testing if installed package can be loaded
* DONE (genoset)

genoset.Rcheck/genoset-Ex.timings:

nameusersystemelapsed
BAFSet-class0.3640.0160.380
BAFSet0.6000.0160.625
BAFSet.to.ExpressionSets0.2040.0200.224
CNSet-class0.1600.0040.162
CNSet0.4160.0000.424
GenoSet-class0.1360.0000.135
GenoSet0.3880.0000.389
baf0.0400.0200.063
baf2mbaf0.0560.0080.065
boundingIndices0.0280.0000.028
boundingIndices20.0160.0000.014
chr-methods0.4640.0000.463
chrIndices-methods0.0400.0000.038
chrInfo0.0760.0000.076
chrNames0.9320.0000.933
chrOrder0.0120.0000.013
cn0.0520.0240.077
colMeans0.0360.0000.037
featureNames0.0960.0000.097
gcCorrect0.0240.0000.025
genoPlot-methods0.1680.0040.180
genoPos-methods0.0880.0000.090
genomeAxis0.1200.0040.130
genoset-methods0.5410.0280.572
initGenoSet0.3080.0040.310
isGenomeOrder-methods0.0280.0040.030
locData-methods0.0360.0000.035
lrr0.0520.0040.053
modeCenter0.0160.0000.016
pos0.5360.0000.536
rangeSampleMeans0.1000.0040.109
readGenoSet0.0120.0000.027
runCBS2.7280.0042.890
sampleNames0.0440.0000.045
segPairTable-methods0.0840.0000.085
segTable-methods2.0360.0122.137
segs2Rle1.9920.0002.260
segs2RleDataFrame2.0120.0522.427
subsetAssayData0.0320.0080.038
toGenomeOrder-methods0.2360.0240.439