BioC 2.14: CHECK report for supraHex on petty

Package: supraHex

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch supraHex_1.2.0.tar.gz

StartedAt: 2014-10-08 00:20:11 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 00:21:48 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 96.2 seconds

RetCode: 0

Status:  OK

CheckDir: supraHex.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 supraHex_1.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/supraHex.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘supraHex/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘supraHex’ 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 for sufficient/correct file permissions ... OK
* checking whether package ‘supraHex’ can be installed ... [4s/6s] 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
Package in Depends field not imported from: ‘hexbin’
  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 ... [25s/25s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  ‘/Users/biocbuild/bbs-2.14-bioc/meat/supraHex.Rcheck/00check.log’
for details.

* installing *source* package ‘supraHex’ ...
** 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 (supraHex)

name	user	system	elapsed
sBMH	0.160	0.007	0.167
sCompReorder	3.862	0.060	3.937
sDistance	0.214	0.005	0.219
sDmat	0.257	0.003	0.261
sDmatCluster	0.424	0.013	0.439
sDmatMinima	0.328	0.003	0.331
sHexDist	0.009	0.000	0.009
sHexGrid	0.006	0.000	0.007
sInitial	0.007	0.001	0.008
sMapOverlay	0.414	0.013	0.430
sNeighAny	0.016	0.001	0.018
sNeighDirect	0.012	0.000	0.012
sPipeline	0.674	0.017	0.696
sTopology	0.041	0.011	0.052
sTrainBatch	0.103	0.002	0.109
sTrainSeq	1.685	0.002	1.689
sTrainology	0.011	0.001	0.011
sWriteData	0.412	0.007	0.420
visColoralpha	0.014	0.001	0.015
visColorbar	0.171	0.000	0.171
visColormap	0.013	0.000	0.013
visCompReorder	2.717	0.039	2.760
visDmatCluster	0.490	0.033	0.524
visDmatHeatmap	0.425	0.006	0.431
visHeatmap	0.236	0.003	0.239
visHeatmapAdv	1.198	0.012	1.224
visHexComp	0.222	0.007	0.230
visHexGrid	0.210	0.005	0.216
visHexMapping	3.577	0.095	3.691
visHexMulComp	1.512	0.038	1.553
visHexPattern	2.344	0.123	2.473
visKernels	0.022	0.011	0.034
visTreeBootstrap	0.402	0.006	0.410
visVp	0.066	0.011	0.078