BioC 2.13: CHECK report for CNVrd2 on moscato1

Package: CNVrd2

Version: 1.0.0

Command: rm -rf CNVrd2.buildbin-libdir && mkdir CNVrd2.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CNVrd2.buildbin-libdir CNVrd2_1.0.0.tar.gz >CNVrd2-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=CNVrd2.buildbin-libdir --install="check:CNVrd2-install.out" --force-multiarch --no-vignettes --timings CNVrd2_1.0.0.tar.gz && mv CNVrd2.buildbin-libdir/* CNVrd2.Rcheck/ && rmdir CNVrd2.buildbin-libdir

StartedAt: 2014-04-05 03:13:50 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 03:19:11 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 320.8 seconds

RetCode: 0

Status:  OK

CheckDir: CNVrd2.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/CNVrd2.Rcheck'
* using R version 3.0.3 (2014-03-06)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CNVrd2/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CNVrd2' version '1.0.0'
* 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 'CNVrd2' 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
Packages in Depends field not imported from:
  'DNAcopy' 'Rsamtools' 'VariantAnnotation' 'ggplot2' 'gridExtra'
  'methods' 'rjags'
  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' ... [19s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
calculateLDSNPandCNV 5.66   0.76    6.43
** running examples for arch 'x64' ... [21s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
calculateLDSNPandCNV 7.21   0.95    8.19
* 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
  'D:/biocbld/bbs-2.13-bioc/meat/CNVrd2.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'CNVrd2' ...
** 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 'CNVrd2' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CNVrd2' as CNVrd2_1.0.0.zip
* DONE (CNVrd2)

name	user	system	elapsed
CNVrd2-class	0.00	0.02	0.01
calculateLDSNPandCNV	5.66	0.76	6.43
clusteringCNVs-class	0	0	0
countReadInWindow-methods	0	0	0
countReadInWindow	0.02	0.00	0.02
emnormalCNV	0.14	0.00	0.14
groupBayesianCNVs	0.01	0.00	0.01
groupCNVs	0.13	0.00	0.13
identifyPolymorphicRegion	0	0	0
plotCNVrd2	0.06	0.00	0.06
plotPolymorphicRegion	0.02	0.00	0.02
segmentSamples	0	0	0

name	user	system	elapsed
CNVrd2-class	0	0	0
calculateLDSNPandCNV	7.21	0.95	8.19
clusteringCNVs-class	0.01	0.00	0.02
countReadInWindow-methods	0	0	0
countReadInWindow	0	0	0
emnormalCNV	0.16	0.02	0.17
groupBayesianCNVs	0.00	0.01	0.02
groupCNVs	0.14	0.00	0.14
identifyPolymorphicRegion	0	0	0
plotCNVrd2	0.07	0.00	0.06
plotPolymorphicRegion	0	0	0
segmentSamples	0	0	0