Package: Repitools

Version: 1.5.6

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Repitools_1.5.6.tar.gz

StartedAt: 2013-03-25 04:21:23 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 04:36:43 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 919.7 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: Repitools.Rcheck

Warnings: 1

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/Repitools.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'Repitools/DESCRIPTION' ... OK
* this is package 'Repitools' version '1.5.6'
* 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 ... [19s/20s] 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 sizes of PDF files under 'inst/doc' ... 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 ... [249s/484s] WARNING
Found the following significant warnings:

  Warning: '.path.package' is deprecated.
  Warning: '.path.package' is deprecated.
  Warning: '.find.package' is deprecated.
  Warning: '.find.package' is deprecated.
  Warning: '.find.package' is deprecated.
  Warning: '.path.package' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
                    user system elapsed
methylEst         34.424  7.636 193.002
sequenceCalc      21.487  3.605  25.232
empBayes          20.495  4.478 103.971
cpgDensityCalc    20.146  3.811  24.915
BayMethList-class 21.162  1.814  23.077
determineOffset   18.896  2.039  22.745
maskOut           18.784  1.966  21.356
cpgDensityPlot    13.185  3.020  16.456
gcContentCalc      6.646  0.870   7.563
findClusters       5.026  0.111   5.138
binPlots           3.942  1.044   5.039
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'tests.R' [211s/213s]
 [212s/213s] 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

WARNING: There was 1 warning.
NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/Repitools.Rcheck/00check.log'
for details.

* installing *source* package 'Repitools' ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -D R_NO_REMAP -I. -fPIC  -g -O2 -Wall -pedantic  -c const.c -o const.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -D R_NO_REMAP -I. -fPIC  -g -O2 -Wall -pedantic  -c hyp2f1.c -o hyp2f1.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -D R_NO_REMAP -I. -fPIC  -g -O2 -Wall -pedantic  -c mtherr.c -o mtherr.o
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o Repitools.so const.o hyp2f1.o mtherr.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/Repitools.Rcheck/Repitools/libs/i386
** 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
   'Repitools_vignette.Rnw' using 'UTF-8' 
** testing if installed package can be loaded
* DONE (Repitools)

name	user	system	elapsed
BAM2GRanges	1.001	0.064	1.080
BayMethList-class	21.162	1.814	23.077
GCadjustCopy	0.346	0.023	0.369
GCbiasPlots	0.006	0.010	0.016
GDL2GRL	0.473	0.036	0.510
QdnaData	0.153	0.017	0.171
abcdDNA	0.005	0.006	0.011
absoluteCN	0.006	0.009	0.014
annoDF2GR	0.053	0.007	0.060
annoGR2DF	0.252	0.021	0.273
annotationBlocksCounts	0.126	0.009	0.134
annotationBlocksLookup	0.122	0.008	0.131
annotationCounts	0.163	0.016	0.179
annotationLookup	0.156	0.009	0.166
binPlots	3.942	1.044	5.039
blocksStats	0.250	0.042	0.292
checkProbes	0.266	0.022	0.306
chromosomeCNplots	0.008	0.011	0.019
clusterPlots	2.758	0.693	3.487
cpgDensityCalc	20.146	3.811	24.915
cpgDensityPlot	13.185	3.020	16.456
determineOffset	18.896	2.039	22.745
empBayes	20.495	4.478	103.971
enrichmentCalc	3.682	1.232	4.943
enrichmentPlot	3.328	1.021	4.365
featureBlocks	0.072	0.013	0.085
featureScores	2.664	0.659	3.388
findClusters	5.026	0.111	5.138
gcContentCalc	6.646	0.870	7.563
genQC	0.009	0.007	0.016
genomeBlocks	0.133	0.009	0.142
getProbePositionsDf	0.003	0.005	0.008
getSampleOffsets	0.004	0.006	0.009
hyper	0.007	0.010	0.017
loadPairFile	0.004	0.008	0.013
loadSampleDirectory	0.004	0.009	0.013
makeWindowLookupTable	0.180	0.014	0.194
mappabilityCalc	0.004	0.008	0.013
maskOut	18.784	1.966	21.356
mergeReplicates	0.557	0.041	0.599
methylEst	34.424	7.636	193.002
multiHeatmap	0.699	0.336	1.083
plotClusters	0.149	0.009	0.157
plotQdnaByCN	0.004	0.006	0.010
processNDF	0.003	0.007	0.010
profilePlots	0.003	0.006	0.009
regionStats	0.006	0.013	0.019
relativeCN	0.196	0.032	0.228
sequenceCalc	21.487	3.605	25.232
setCNVOffsets	0.011	0.056	0.069
summarizeScores	2.282	0.746	3.040
writeWig	0.002	0.006	0.009