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CHECK report for CountClust on veracruz1

This page was generated on 2018-04-12 13:42:35 -0400 (Thu, 12 Apr 2018).

Package 301/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CountClust 1.4.1
Kushal Dey
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/CountClust
Branch: RELEASE_3_6
Last Commit: c26642e
Last Changed Date: 2017-11-01 14:01:24 -0400 (Wed, 01 Nov 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: CountClust
Version: 1.4.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CountClust_1.4.1.tar.gz
StartedAt: 2018-04-12 02:16:19 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 02:18:52 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 153.4 seconds
RetCode: 0
Status:  OK 
CheckDir: CountClust.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CountClust_1.4.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/CountClust.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (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 18.6Mb
  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 20.377  0.359  21.675
compGoM                 5.734  0.954   6.969
StructureGGplot         5.779  0.338   6.403
* 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
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/CountClust.Rcheck/00check.log’
for details.



Installation output

CountClust.Rcheck/00install.out

* 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)

Tests output


Example timings

CountClust.Rcheck/CountClust-Ex.timings

nameusersystemelapsed
BatchCorrectedCounts0.7570.0330.803
ExtractHighCorFeatures20.377 0.35921.675
ExtractTopFeatures2.8480.1333.028
FitGoM1.1970.1051.341
FitGoMpool1.6520.2201.914
RemoveSparseFeatures0.0020.0000.002
StructureGGplot5.7790.3386.403
Structure_omega000
cg_topics0.3400.0710.422
compGoM5.7340.9546.969
compare_omega0.0390.0000.040
handleNA0.0020.0000.001
nullmodel_GoM2.6380.5713.256