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CHECK report for SEPA on malbec1

This page was generated on 2019-04-16 11:51:25 -0400 (Tue, 16 Apr 2019).

Package 1413/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SEPA 1.12.0
Zhicheng Ji
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/SEPA
Branch: RELEASE_3_8
Last Commit: 0b21a28
Last Changed Date: 2018-10-30 11:41:58 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: SEPA
Version: 1.12.0
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:SEPA.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings SEPA_1.12.0.tar.gz
StartedAt: 2019-04-16 02:57:41 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 03:06:07 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 506.0 seconds
RetCode: 0
Status:  OK 
CheckDir: SEPA.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:SEPA.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings SEPA_1.12.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/SEPA.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (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 ‘1.12.0’
* 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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
windowGOvisualize   104.292  0.172 104.726
windowGOanalysis     94.036  0.204  94.405
pseudotimepattern    71.648  0.436  72.191
pseudotimevisualize  67.580  0.004  67.759
patternGOanalysis    66.704  0.512  67.342
* 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
  ‘/home/biocbuild/bbs-3.8-bioc/meat/SEPA.Rcheck/00check.log’
for details.



Installation output

SEPA.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL SEPA
###
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘SEPA’ ...
** R
** data
** inst
** byte-compile and prepare 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
SEPAui000
patternGOanalysis66.704 0.51267.342
patternsummary1.4640.0041.476
pseudotimepattern71.648 0.43672.191
pseudotimevisualize67.580 0.00467.759
truetimepattern0.9920.0040.999
truetimevisualize0.4120.0000.412
windowGOanalysis94.036 0.20494.405
windowGOvisualize104.292 0.172104.726