BioC 2.13: CHECK report for HCsnip on moscato1

Package: HCsnip

Version: 1.2.0

Command: rm -rf HCsnip.buildbin-libdir && mkdir HCsnip.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=HCsnip.buildbin-libdir HCsnip_1.2.0.tar.gz >HCsnip-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=HCsnip.buildbin-libdir --install="check:HCsnip-install.out" --force-multiarch --no-vignettes --timings HCsnip_1.2.0.tar.gz && mv HCsnip.buildbin-libdir/* HCsnip.Rcheck/ && rmdir HCsnip.buildbin-libdir

StartedAt: 2014-04-05 04:31:52 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 04:41:59 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 607.8 seconds

RetCode: 0

Status:  OK

CheckDir: HCsnip.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/HCsnip.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 'HCsnip/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'HCsnip' version '1.2.0'
* 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 'HCsnip' 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:
  'Biobase' 'clusterRepro' 'coin' 'fpc' 'impute' 'randomForestSRC'
  'sigaR' 'sm' 'survival'
  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 for old-style vignette sources ... NOTE
Vignette sources only in 'inst/doc':
  'HCsnip.Rnw'
A 'vignettes' directory will be required as from R 3.1.0
* checking examples ...
** running examples for arch 'i386' ... [247s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
TwoHC_perm   141.63   0.27  141.96
TwoHC_assign  83.96   0.00   84.01
** running examples for arch 'x64' ... [241s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
TwoHC_perm   135.54   0.44  136.01
TwoHC_assign  80.98   0.01   81.06
* 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 were 2 notes.
See
  'D:/biocbld/bbs-2.13-bioc/meat/HCsnip.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'HCsnip' ...
** 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 'HCsnip' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'HCsnip' as HCsnip_1.2.0.zip
* DONE (HCsnip)

name	user	system	elapsed
BullingerLeukemia	0.08	0.00	0.08
EnvioPlot	0.49	0.00	0.49
HCsnipper	1.99	0.02	2.01
RSF_eval	3.26	0.01	3.46
TcgaGBM	0.27	0.00	0.26
TwoHC_assign	83.96	0.00	84.01
TwoHC_perm	141.63	0.27	141.96
cluster_pred	2.06	0.02	2.08
measure	2.18	0.00	2.18
perm_test	2.87	0.00	2.87
surv_measure	2.13	0.01	2.14

name	user	system	elapsed
BullingerLeukemia	0.23	0.02	0.25
EnvioPlot	0.60	0.00	0.59
HCsnipper	2.08	0.01	2.09
RSF_eval	3.62	0.02	3.96
TcgaGBM	0.18	0.00	0.19
TwoHC_assign	80.98	0.01	81.06
TwoHC_perm	135.54	0.44	136.01
cluster_pred	2.96	0.02	2.98
measure	3.14	0.00	3.14
perm_test	2.93	0.04	2.98
surv_measure	1.9	0.0	1.9