BioC 2.14: CHECK report for Genominator on moscato2

Package: Genominator

Version: 1.18.0

Command: rm -rf Genominator.buildbin-libdir && mkdir Genominator.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Genominator.buildbin-libdir Genominator_1.18.0.tar.gz >Genominator-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=Genominator.buildbin-libdir --install="check:Genominator-install.out" --force-multiarch --no-vignettes --timings Genominator_1.18.0.tar.gz

StartedAt: 2014-10-08 01:31:31 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 01:35:31 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 239.3 seconds

RetCode: 0

Status:  OK

CheckDir: Genominator.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf Genominator.buildbin-libdir && mkdir Genominator.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Genominator.buildbin-libdir Genominator_1.18.0.tar.gz >Genominator-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=Genominator.buildbin-libdir --install="check:Genominator-install.out" --force-multiarch --no-vignettes --timings Genominator_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-2.14-bioc/meat/Genominator.Rcheck'
* using R version 3.1.1 (2014-07-10)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Genominator/DESCRIPTION' ... OK
* this is package 'Genominator' version '1.18.0'
* 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 whether package 'Genominator' can be installed ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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
'library' or 'require' calls to packages already attached by Depends:
  'GenomeGraphs' 'IRanges'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'GenomeGraphs' 'RSQLite'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [31s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
addPrimingWeights 6.45   0.55    7.11
** running examples for arch 'x64' ... [38s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
addPrimingWeights 8.27   0.39    8.66
joinExpData       5.74   0.01    5.79
* 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
  'E:/biocbld/bbs-2.14-bioc/meat/Genominator.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'Genominator' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'Genominator' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Genominator' as Genominator_1.18.0.zip
* DONE (Genominator)

name	user	system	elapsed
ExpData	0	0	0
addPrimingWeights	6.45	0.55	7.11
aggregateExpData	1.49	0.00	1.48
applyMapped	1.26	0.00	1.28
collapseExpData	2.39	0.01	2.40
computeCoverage	0.89	0.03	0.92
computePrimingWeights	0.65	0.24	0.89
getRegion	0.28	0.00	0.28
importFromAlignedReads	0	0	0
importToExpData	0.47	0.00	0.47
joinExpData	4.09	0.00	4.09
makeGeneRepresentation	0.23	0.00	0.23
mergeWithAnnotation	0.45	0.00	0.46
plot.genominator.coverage	2.73	0.01	2.76
plot.genominator.goodness.of.fit	0.72	0.02	0.74
regionGoodnessOfFit-methods	0.87	0.00	0.87
splitByAnnotation	0.86	0.00	0.86
summarizeByAnnotation	0.47	0.00	0.46
summarizeExpData	0.54	0.00	0.55
validAnnotation	0.03	0.00	0.03
yeastAnno	0.21	0.00	0.20

name	user	system	elapsed
ExpData	0	0	0
addPrimingWeights	8.27	0.39	8.66
aggregateExpData	2.31	0.00	2.42
applyMapped	1.69	0.00	1.70
collapseExpData	2.65	0.03	2.69
computeCoverage	1.19	0.00	1.19
computePrimingWeights	0.71	0.21	0.92
getRegion	0.31	0.00	0.31
importFromAlignedReads	0	0	0
importToExpData	0.64	0.00	0.64
joinExpData	5.74	0.01	5.79
makeGeneRepresentation	0.27	0.00	0.26
mergeWithAnnotation	0.61	0.00	0.61
plot.genominator.coverage	3.48	0.05	3.53
plot.genominator.goodness.of.fit	0.87	0.00	0.87
regionGoodnessOfFit-methods	0.76	0.02	0.78
splitByAnnotation	1.14	0.01	1.15
summarizeByAnnotation	0.59	0.03	0.63
summarizeExpData	0.72	0.00	0.72
validAnnotation	0.03	0.00	0.03
yeastAnno	0.14	0.03	0.17