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BioC 3.4: CHECK report for CountClust on morelia

This page was generated on 2017-04-15 16:27:35 -0400 (Sat, 15 Apr 2017).

Package 270/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CountClust 1.1.4
Kushal Dey
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/CountClust
Last Changed Rev: 123725 / Revision: 128728
Last Changed Date: 2016-11-05 23:41:34 -0400 (Sat, 05 Nov 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK NO, built version is LOWER than in internal repository!!!
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK NO, built version is LOWER than in internal repository!!!
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK NO, built version is LOWER than in internal repository!!!

Summary

Package: CountClust
Version: 1.1.4
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CountClust_1.1.4.tar.gz
StartedAt: 2017-04-15 00:28:57 -0700 (Sat, 15 Apr 2017)
EndedAt: 2017-04-15 00:31:46 -0700 (Sat, 15 Apr 2017)
EllapsedTime: 169.1 seconds
RetCode: 0
Status:  OK 
CheckDir: CountClust.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CountClust_1.1.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/CountClust.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.1.4’
* 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 17.9Mb
  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 sizes of PDF files under ‘inst/doc’ ... 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 21.406  0.705  22.746
compGoM                 5.858  1.192   7.569
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.4-bioc/meat/CountClust.Rcheck/00check.log’
for details.


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)

CountClust.Rcheck/CountClust-Ex.timings:

nameusersystemelapsed
BatchCorrectedCounts0.8540.0460.899
ExtractHighCorFeatures21.406 0.70522.746
ExtractTopFeatures3.2610.1193.383
FitGoM0.7580.1140.907
RemoveSparseFeatures0.0010.0000.001
StructureGGplot3.2500.3054.645
Structure_omega0.0000.0000.001
cg_topics0.3020.0610.364
compGoM5.8581.1927.569
compare_omega0.0090.0000.009
handleNA0.0020.0000.002
nullmodel_GoM2.6700.4943.196