BioC 3.5: CHECK report for CountClust on malbec2

Package: CountClust

Version: 1.2.0

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings CountClust_1.2.0.tar.gz

StartedAt: 2017-08-15 22:14:30 -0400 (Tue, 15 Aug 2017)

EndedAt: 2017-08-15 22:16:45 -0400 (Tue, 15 Aug 2017)

EllapsedTime: 135.2 seconds

RetCode: 0

Status:  OK

CheckDir: CountClust.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings CountClust_1.2.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/CountClust.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CountClust/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CountClust’ version ‘1.2.0’
* package encoding: UTF-8
* 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 ‘CountClust’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 18.0Mb
  sub-directories of 1Mb or more:
    data  17.5Mb
* 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 ... OK
* 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’ ... NOTE
The following directory looks like a leftover from 'knitr':
  ‘figure’
Please remove from your package.
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
ExtractHighCorFeatures 14.672  0.420  17.340
compGoM                 5.892  1.600   9.801
StructureGGplot         4.612  0.248   5.338
* 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
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.5-bioc/meat/CountClust.Rcheck/00check.log’
for details.

* installing *source* package ‘CountClust’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (CountClust)

name	user	system	elapsed
BatchCorrectedCounts	0.616	0.008	0.639
ExtractHighCorFeatures	14.672	0.420	17.340
ExtractTopFeatures	2.036	0.316	2.357
FitGoM	0.924	0.032	0.956
FitGoMpool	1.724	0.008	1.734
RemoveSparseFeatures	0.004	0.000	0.001
StructureGGplot	4.612	0.248	5.338
Structure_omega	0.000	0.000	0.001
cg_topics	0.560	0.164	0.728
compGoM	5.892	1.600	9.801
compare_omega	0.028	0.000	0.028
handleNA	0.004	0.000	0.002
nullmodel_GoM	1.864	0.008	1.872