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CHECK report for M3C on malbec1

This page was generated on 2018-04-12 13:16:33 -0400 (Thu, 12 Apr 2018).

Package 766/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
M3C 1.0.0
Christopher John
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/M3C
Branch: RELEASE_3_6
Last Commit: 86ddd10
Last Changed Date: 2017-10-30 12:41:35 -0400 (Mon, 30 Oct 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: M3C
Version: 1.0.0
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings M3C_1.0.0.tar.gz
StartedAt: 2018-04-12 00:41:16 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 00:43:56 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 160.0 seconds
RetCode: 0
Status:  OK 
CheckDir: M3C.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings M3C_1.0.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/M3C.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 ‘M3C/DESCRIPTION’ ... OK
* this is package ‘M3C’ version ‘1.0.0’
* 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 ‘M3C’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
* 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 ... NOTE
CDF: no visible binding for global variable ‘consensusindex’
CDF: no visible binding for global variable ‘k’
CDF: no visible global function definition for ‘png’
CDF: no visible global function definition for ‘dev.off’
CDF: no visible binding for global variable ‘K’
CDF: no visible binding for global variable ‘PAC_SCORE’
M3C: no visible binding for global variable ‘i’
M3C: no visible binding for global variable ‘K’
M3C: no visible binding for global variable ‘RCSI’
M3C: no visible binding for global variable ‘P_SCORE’
M3C: no visible global function definition for ‘png’
M3C: no visible global function definition for ‘dev.off’
M3Creal: no visible global function definition for ‘colorRampPalette’
M3Creal: no visible global function definition for ‘png’
M3Creal: no visible global function definition for ‘dev.off’
clustersim: no visible binding for global variable ‘X3’
clustersim: no visible binding for global variable ‘PC1’
clustersim: no visible binding for global variable ‘PC2’
clustersim: no visible global function definition for ‘png’
clustersim: no visible global function definition for ‘dev.off’
myPal: no visible global function definition for ‘rgb’
Undefined global functions or variables:
  K PAC_SCORE PC1 PC2 P_SCORE RCSI X3 colorRampPalette consensusindex
  dev.off i k png rgb
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.off", "png", "rgb")
to your NAMESPACE file.
* 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
M3C 3.668   0.06   94.03
* checking for unstated dependencies in vignettes ... NOTE
'::' or ':::' imports not declared from:
  ‘ggsci’ ‘gplots’
'library' or 'require' calls not declared from:
  ‘ggsci’ ‘gplots’
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.6-bioc/meat/M3C.Rcheck/00check.log’
for details.



Installation output

M3C.Rcheck/00install.out

* installing *source* package ‘M3C’ ...
** 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 (M3C)

Tests output


Example timings

M3C.Rcheck/M3C-Ex.timings

nameusersystemelapsed
M3C 3.668 0.06094.030
clustersim3.7000.0723.778