BioC 2.13: CHECK report for supraHex on zin1

Package: supraHex

Version: 1.0.0

Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings supraHex_1.0.0.tar.gz

StartedAt: 2014-04-05 04:16:10 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 04:16:45 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 35.0 seconds

RetCode: 0

Status:  OK

CheckDir: supraHex.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/supraHex.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (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 ‘1.0.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘supraHex’ can be installed ... [2s/2s] 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 dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘Biobase’
  All declared Imports should be used.
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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [12s/12s] 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
  ‘/home/biocbuild/bbs-2.13-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	1.596	0.012	1.609
sCompReorder	1.336	0.004	1.344
sDistance	0.120	0.000	0.118
sDmat	0.136	0.000	0.139
sDmatCluster	0.192	0.004	0.197
sDmatMinima	0.132	0.000	0.131
sHexDist	0.008	0.000	0.010
sHexGrid	0.008	0.000	0.008
sInitial	0.008	0.000	0.008
sNeighAny	0.048	0.000	0.047
sNeighDirect	0.012	0.000	0.010
sPipeline	0.368	0.004	0.373
sTopology	0.032	0.000	0.030
sTrainBatch	0.048	0.000	0.050
sTrainSeq	1.356	0.016	1.374
sTrainology	0.008	0.000	0.008
sWriteData	0.176	0.000	0.175
visColorbar	0.052	0.000	0.051
visColormap	0.008	0.000	0.010
visCompReorder	1.256	0.008	1.268
visDmatCluster	0.22	0.00	0.22
visHexComp	0.108	0.000	0.108
visHexGrid	0.100	0.000	0.103
visHexMapping	1.596	0.004	1.603
visHexMulComp	0.740	0.000	0.739
visHexPattern	1.236	0.016	1.255
visKernels	0.008	0.004	0.014
visVp	0.028	0.000	0.031