BioC 3.5: CHECK report for RTN on oaxaca

Package: RTN

Version: 1.13.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RTN_1.13.2.tar.gz

StartedAt: 2017-03-04 08:38:02 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 08:41:40 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 218.0 seconds

RetCode: 0

Status:  OK

CheckDir: RTN.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 RTN_1.13.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/RTN.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RTN/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RTN’ version ‘1.13.2’
* 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 ‘RTN’ 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 ... OK
* 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
tpc.countedges  27.027  3.911  30.951
tni2tpc.corpcor 26.558  3.552  30.144
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* 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: OK

* installing *source* package ‘RTN’ ...
** 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 (RTN)

name	user	system	elapsed
AVS-class	0.001	0.000	0.000
RTN.data	0.613	0.016	0.629
TNA-class	0.000	0.000	0.001
TNI-class	0.433	0.012	0.446
TPC-class	0.001	0.000	0.000
avs.evse	0.001	0.000	0.001
avs.get	0	0	0
avs.plot1	0.000	0.000	0.001
avs.plot2	0	0	0
avs.preprocess	0.001	0.000	0.000
avs.vse	0.001	0.000	0.001
tna.get	0.439	0.013	0.452
tna.graph	0.436	0.010	0.446
tna.gsea1	0.400	0.008	0.408
tna.gsea2	0.357	0.010	0.367
tna.mra	0.402	0.010	0.412
tna.overlap	0.452	0.012	0.465
tna.plot.gsea1	0.387	0.010	0.396
tna.plot.gsea2	0.484	0.013	0.497
tna.shadow	0.495	0.011	0.506
tna.synergy	0.457	0.011	0.468
tni.bootstrap	0.484	0.011	0.495
tni.conditional	0.387	0.009	0.397
tni.dpi.filter	0.367	0.010	0.376
tni.get	0.465	0.011	0.477
tni.graph	0.484	0.011	0.495
tni.gsea2	0.342	0.009	0.351
tni.permutation	0.426	0.009	0.436
tni.preprocess	1.368	0.071	1.441
tni2tna.preprocess	0.483	0.014	0.499
tni2tpc.corpcor	26.558	3.552	30.144
tpc.countedges	27.027	3.911	30.951
tpc.fuseNetwork	0.429	0.016	0.445