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CHECK report for SEPA on veracruz1

This page was generated on 2018-04-12 13:41:09 -0400 (Thu, 12 Apr 2018).

Package 1269/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SEPA 1.8.0
Zhicheng Ji
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/SEPA
Branch: RELEASE_3_6
Last Commit: 9b312b1
Last Changed Date: 2017-10-30 12:40:52 -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: SEPA
Version: 1.8.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SEPA_1.8.0.tar.gz
StartedAt: 2018-04-12 09:24:57 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 09:33:35 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 517.8 seconds
RetCode: 0
Status:  OK 
CheckDir: SEPA.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 SEPA_1.8.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/SEPA.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 ‘SEPA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SEPA’ version ‘1.8.0’
* 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 ‘SEPA’ can be installed ... OK
* checking installed package size ... OK
* 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
patternGOanalysis: no visible global function definition for ‘new’
pseudotimepattern : <anonymous>: no visible global function definition
  for ‘lm’
pseudotimepattern: no visible global function definition for ‘p.adjust’
pseudotimepattern: no visible global function definition for ‘lm’
pseudotimepattern: no visible global function definition for ‘lines’
pseudotimepattern: no visible global function definition for ‘confint’
pseudotimepattern: no visible global function definition for ‘fitted’
pseudotimepattern : <anonymous>: no visible global function definition
  for ‘fitted’
pseudotimevisualize: no visible binding for global variable
  ‘pseudotime’
pseudotimevisualize: no visible binding for global variable ‘Var2’
pseudotimevisualize: no visible binding for global variable ‘Var1’
pseudotimevisualize: no visible binding for global variable ‘value’
pseudotimevisualize: no visible binding for global variable ‘xend’
pseudotimevisualize: no visible binding for global variable ‘yend’
truetimepattern : <anonymous> : <anonymous>: no visible global function
  definition for ‘t.test’
truetimepattern : <anonymous>: no visible global function definition
  for ‘p.adjust’
truetimevisualize : <anonymous> : <anonymous>: no visible global
  function definition for ‘median’
truetimevisualize: no visible binding for global variable ‘time’
truetimevisualize: no visible binding for global variable ‘expmean’
truetimevisualize: no visible binding for global variable ‘Gene’
windowGOanalysis: no visible global function definition for ‘new’
windowGOvisualize: no visible binding for global variable ‘Var1’
windowGOvisualize: no visible binding for global variable ‘value’
Undefined global functions or variables:
  Gene Var1 Var2 confint expmean fitted lines lm median new p.adjust
  pseudotime t.test time value xend yend
Consider adding
  importFrom("graphics", "lines")
  importFrom("methods", "new")
  importFrom("stats", "confint", "fitted", "lm", "median", "p.adjust",
             "t.test", "time")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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
windowGOvisualize   95.421  1.097  98.063
windowGOanalysis    93.314  1.129  95.985
pseudotimepattern   71.584  1.443  74.500
pseudotimevisualize 66.855  0.809  68.785
patternGOanalysis   59.842  1.064  61.869
* 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-3.6-bioc/meat/SEPA.Rcheck/00check.log’
for details.



Installation output

SEPA.Rcheck/00install.out

* installing *source* package ‘SEPA’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (SEPA)

Tests output


Example timings

SEPA.Rcheck/SEPA-Ex.timings

nameusersystemelapsed
SEPAui0.0010.0000.001
patternGOanalysis59.842 1.06461.869
patternsummary1.0730.0191.109
pseudotimepattern71.584 1.44374.500
pseudotimevisualize66.855 0.80968.785
truetimepattern1.0950.0191.140
truetimevisualize0.4810.0070.491
windowGOanalysis93.314 1.12995.985
windowGOvisualize95.421 1.09798.063