BioC 3.2: CHECK report for SEPA on linux1.bioconductor.org

Package: SEPA

Version: 1.0.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings SEPA_1.0.0.tar.gz

StartedAt: 2015-10-27 07:59:01 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 08:07:45 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 523.3 seconds

RetCode: 0

Status:  OK

CheckDir: SEPA.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings SEPA_1.0.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/SEPA.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.0.0’
* 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 ... [8s/8s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [439s/439s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
windowGOanalysis    108.600  0.100 108.865
windowGOvisualize   100.669  0.056 100.800
pseudotimepattern    79.135  0.236  79.514
pseudotimevisualize  74.900  0.004  75.010
patternGOanalysis    68.553  0.212  68.816
* 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-3.2-bioc/meat/SEPA.Rcheck/00check.log’
for details.

* installing *source* package ‘SEPA’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import by ‘graph::.__C__dist’ when loading ‘topGO’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import by ‘graph::.__C__dist’ when loading ‘topGO’
* DONE (SEPA)

name	user	system	elapsed
SEPAui	0.001	0.000	0.000
patternGOanalysis	68.553	0.212	68.816
patternsummary	1.596	0.000	1.596
pseudotimepattern	79.135	0.236	79.514
pseudotimevisualize	74.900	0.004	75.010
truetimepattern	1.031	0.004	1.036
truetimevisualize	0.203	0.000	0.203
windowGOanalysis	108.600	0.100	108.865
windowGOvisualize	100.669	0.056	100.800