BioC 3.2: CHECK report for SEPA on oaxaca

Package: SEPA

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SEPA_1.0.0.tar.gz

StartedAt: 2016-04-23 04:15:28 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 04:26:47 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 679.6 seconds

RetCode: 0

Status:  OK

CheckDir: SEPA.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SEPA_1.0.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/SEPA.Rcheck’
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.0.0’
* 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 ... [11s/11s] 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
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’
truetimevisualize: no visible binding for global variable ‘expmean’
truetimevisualize: no visible binding for global variable ‘Gene’
windowGOvisualize: no visible binding for global variable ‘Var1’
windowGOvisualize: no visible binding for global variable ‘value’
* 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 ... [550s/571s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
windowGOvisualize   130.771  2.466 141.003
windowGOanalysis    127.537  2.647 133.537
pseudotimepattern    94.024  2.616  96.781
pseudotimevisualize  92.893  2.093  95.081
patternGOanalysis    84.119  1.698  95.069
* 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-3.2-bioc/meat/SEPA.Rcheck/00check.log’
for details.

* 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)

name	user	system	elapsed
SEPAui	0.001	0.000	0.000
patternGOanalysis	84.119	1.698	95.069
patternsummary	1.933	0.022	1.957
pseudotimepattern	94.024	2.616	96.781
pseudotimevisualize	92.893	2.093	95.081
truetimepattern	1.736	0.024	1.789
truetimevisualize	0.298	0.006	0.303
windowGOanalysis	127.537	2.647	133.537
windowGOvisualize	130.771	2.466	141.003