Package: CountClust

Version: 1.4.1

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings CountClust_1.4.1.tar.gz

StartedAt: 2018-04-11 22:35:31 -0400 (Wed, 11 Apr 2018)

EndedAt: 2018-04-11 22:37:41 -0400 (Wed, 11 Apr 2018)

EllapsedTime: 130.1 seconds

RetCode: 0

Status:  OK

CheckDir: CountClust.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings CountClust_1.4.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/CountClust.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.4.1’
* 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 18.5Mb
  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 ... NOTE
Namespace in Imports field not imported from: ‘SQUAREM’
  All declared Imports should be used.
* 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 ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
ExtractHighCorFeatures 16.496  0.136  17.004
compGoM                 5.500  0.272   6.060
StructureGGplot         4.920  0.072   5.378
* 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-3.6-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	0.760	0.004	0.784
ExtractHighCorFeatures	16.496	0.136	17.004
ExtractTopFeatures	2.092	0.076	2.167
FitGoM	1.120	0.028	1.149
FitGoMpool	1.256	0.004	1.263
RemoveSparseFeatures	0.000	0.000	0.001
StructureGGplot	4.920	0.072	5.378
Structure_omega	0	0	0
cg_topics	0.252	0.004	0.256
compGoM	5.500	0.272	6.060
compare_omega	0.028	0.000	0.030
handleNA	0.004	0.000	0.001
nullmodel_GoM	2.120	0.052	2.178