BioC 3.3: CHECK report for SEPA on morelia

Package: SEPA

Version: 1.1.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SEPA_1.1.0.tar.gz

StartedAt: 2015-10-22 11:07:36 -0400 (Thu, 22 Oct 2015)

EndedAt: 2015-10-22 11:15:59 -0400 (Thu, 22 Oct 2015)

EllapsedTime: 503.1 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_1.1.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/SEPA.Rcheck’
* using R Under development (unstable) (2015-10-08 r69496)
* 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 ‘1.1.0’
* 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 ... [8s/9s] 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’
Undefined global functions or variables:
  Gene Var1 Var2 expmean pseudotime value xend yend
* 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 ... [405s/411s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
windowGOanalysis    98.218  1.987 101.830
windowGOvisualize   91.457  2.023  94.522
pseudotimepattern   73.051  2.335  76.415
pseudotimevisualize 71.568  1.710  74.701
patternGOanalysis   55.169  0.951  56.950
* 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-3.3-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	0.000	0.000	0.001
patternGOanalysis	55.169	0.951	56.950
patternsummary	1.280	0.020	1.301
pseudotimepattern	73.051	2.335	76.415
pseudotimevisualize	71.568	1.710	74.701
truetimepattern	1.024	0.017	1.042
truetimevisualize	0.236	0.006	0.243
windowGOanalysis	98.218	1.987	101.830
windowGOvisualize	91.457	2.023	94.522