BioC 2.14: CHECK report for HCsnip on morelia

Package: HCsnip

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch HCsnip_1.4.0.tar.gz

StartedAt: 2014-10-07 23:26:17 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 23:30:52 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 275.1 seconds

RetCode: 0

Status:  OK

CheckDir: HCsnip.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch HCsnip_1.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/HCsnip.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin13.1.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HCsnip/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HCsnip’ version ‘1.4.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘survival’ ‘coin’ ‘fpc’ ‘clusterRepro’ ‘impute’ ‘randomForestSRC’
  ‘sm’ ‘sigaR’ ‘Biobase’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘HCsnip’ can be installed ... [10s/11s] 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
* 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 loading without being on the library search path ... 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [170s/170s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
TwoHC_perm   99.889  2.107 102.108
TwoHC_assign 50.691  0.297  51.080
* 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
  ‘/Users/biocbuild/bbs-2.14-bioc/meat/HCsnip.Rcheck/00check.log’
for details.

* 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
* DONE (HCsnip)

name	user	system	elapsed
BullingerLeukemia	0.066	0.006	0.072
EnvioPlot	0.270	0.009	0.279
HCsnipper	1.589	0.022	1.611
RSF_eval	2.232	0.033	2.266
TcgaGBM	0.112	0.011	0.123
TwoHC_assign	50.691	0.297	51.080
TwoHC_perm	99.889	2.107	102.108
cluster_pred	1.649	0.024	1.674
measure	1.529	0.012	1.543
perm_test	2.311	0.014	2.394
surv_measure	1.679	0.018	1.727