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BioC 2.12: CHECK report for Repitools on george2

This page was generated on 2013-10-09 09:37:46 -0700 (Wed, 09 Oct 2013).

Package 539/671HostnameOS / ArchBUILDCHECKBUILD BIN
Repitools 1.6.0
Mark Robinson
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/Repitools
Last Changed Rev: 75263 / Revision: 81334
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 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 Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: Repitools
Version: 1.6.0
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings Repitools_1.6.0.tar.gz
StartedAt: 2013-10-09 04:27:28 -0700 (Wed, 09 Oct 2013)
EndedAt: 2013-10-09 04:45:53 -0700 (Wed, 09 Oct 2013)
EllapsedTime: 1105.0 seconds
RetCode: 0
Status:  OK 
CheckDir: Repitools.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/Repitools.Rcheck’
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Repitools/DESCRIPTION’ ... OK
* this is package ‘Repitools’ version ‘1.6.0’
* 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 ‘Repitools’ can be installed ... [29s/29s] 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 compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... NOTE
The following files are already in R: ‘Sweave.sty’
Please remove them from your package.
* checking examples ... [4m/10m] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
methylEst         47.667  1.832 261.549
BayMethList-class 33.530  0.416  37.511
empBayes          26.174  1.236 158.424
maskOut           21.865  0.552  23.576
sequenceCalc      20.590  1.308  22.411
determineOffset   21.693  0.112  22.153
cpgDensityCalc    19.313  1.356  23.103
cpgDensityPlot    13.049  0.212  13.290
findClusters       6.592  0.016   6.630
enrichmentPlot     5.673  0.012   5.736
gcContentCalc      4.697  0.628   5.573
binPlots           4.192  0.200   6.412
clusterPlots       3.624  0.208   6.149
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘tests.R’ [174s/176s]
 [174s/177s] 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

NOTE: There was 1 note.
See
  ‘/home/biocbuild/bbs-2.12-bioc/meat/Repitools.Rcheck/00check.log’
for details.

Repitools.Rcheck/00install.out:

* installing *source* package ‘Repitools’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include   -D R_NO_REMAP -I. -fpic  -g -O2  -Wall -c const.c -o const.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include   -D R_NO_REMAP -I. -fpic  -g -O2  -Wall -c hyp2f1.c -o hyp2f1.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include   -D R_NO_REMAP -I. -fpic  -g -O2  -Wall -c mtherr.c -o mtherr.o
gcc -std=gnu99 -shared -L/usr/local/lib -o Repitools.so const.o hyp2f1.o mtherr.o -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.12-bioc/meat/Repitools.Rcheck/Repitools/libs
** R
** data
** inst
** preparing package for lazy loading
in method for ‘.featureScores’ with signature ‘"AffymetrixCelSet","GRanges"’: no definition for class “AffymetrixCelSet”
in method for ‘regionStats’ with signature ‘"AffymetrixCelSet"’: no definition for class “AffymetrixCelSet”
in method for ‘writeWig’ with signature ‘"AffymetrixCelSet"’: no definition for class “AffymetrixCelSet”
in method for ‘cpgBoxplots’ with signature ‘"AffymetrixCelSet"’: no definition for class “AffymetrixCelSet”
in method for ‘.blocksStats’ with signature ‘"AffymetrixCelSet","GRanges"’: no definition for class “AffymetrixCelSet”
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Repitools)

Repitools.Rcheck/Repitools-Ex.timings:

nameusersystemelapsed
BAM2GRanges1.4720.0281.513
BayMethList-class33.530 0.41637.511
GCadjustCopy0.0040.0040.007
GCbiasPlots0.0080.0000.007
GDL2GRL0.3200.0160.346
QdnaData0.1040.0040.106
abcdDNA0.0040.0000.005
absoluteCN0.0080.0000.007
annoDF2GR0.0520.0000.051
annoGR2DF0.0360.0000.038
annotationBlocksCounts0.1050.0000.101
annotationBlocksLookup0.1000.0000.101
annotationCounts0.1280.0000.244
annotationLookup0.1240.0000.247
binPlots4.1920.2006.412
blocksStats0.2760.0120.458
checkProbes0.2560.0080.312
chromosomeCNplots0.0160.0000.024
clusterPlots3.6240.2086.149
cpgDensityCalc19.313 1.35623.103
cpgDensityPlot13.049 0.21213.290
determineOffset21.693 0.11222.153
empBayes 26.174 1.236158.424
enrichmentCalc4.9080.0324.941
enrichmentPlot5.6730.0125.736
featureBlocks0.0600.0000.062
featureScores3.7520.0043.757
findClusters6.5920.0166.630
gcContentCalc4.6970.6285.573
genQC0.0160.0000.018
genomeBlocks0.1080.0000.125
getProbePositionsDf0.0040.0000.006
getSampleOffsets0.0080.0000.007
hyper0.0160.0000.016
loadPairFile0.0120.0000.011
loadSampleDirectory0.0120.0000.012
makeWindowLookupTable0.1760.0040.181
mappabilityCalc0.0080.0000.008
maskOut21.865 0.55223.576
mergeReplicates0.9880.0001.084
methylEst 47.667 1.832261.549
multiHeatmap0.4480.3561.254
plotClusters1.0320.0761.108
plotQdnaByCN0.0080.0000.009
processNDF0.0040.0040.010
profilePlots0.0080.0000.007
regionStats0.0160.0040.020
relativeCN0.2240.0120.264
sequenceCalc20.590 1.30822.411
setCNVOffsets0.0080.0000.008
summarizeScores3.2120.0403.253
writeWig0.0040.0000.004