Package: pathwayPCA

Version: 0.99.5

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:pathwayPCA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings pathwayPCA_0.99.5.tar.gz

StartedAt: 2019-04-09 04:14:50 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 04:19:32 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 282.3 seconds

RetCode: 0

Status:  OK

CheckDir: pathwayPCA.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:pathwayPCA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings pathwayPCA_0.99.5.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/pathwayPCA.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pathwayPCA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pathwayPCA’ version ‘0.99.5’
* package encoding: UTF-8
* 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 ‘pathwayPCA’ 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
SE2Tidy        14.402  0.750  15.182
SuperPCA_pVals  0.889  0.073  11.870
LoadOntoPCs     0.415  0.371  12.419
ExtractAESPCs   0.380  0.267   8.768
AESPCA_pVals    0.325  0.312  11.992
getPathPCLs     0.211  0.071  14.585
getPathpVals    0.173  0.060  14.554
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL pathwayPCA
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘pathwayPCA’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (pathwayPCA)

R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(pathwayPCA)
> 
> test_check("pathwayPCA")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 27 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  4.670   1.440 101.052 

name	user	system	elapsed
AESPCA_pVals	0.325	0.312	11.992
CheckAssay	0.001	0.000	0.001
CheckPwyColl	0.001	0.000	0.001
CheckSampleIDs	0	0	0
ControlFDR	0.000	0.000	0.002
CreateOmics	0.382	0.083	0.466
CreateOmicsPathway	0.005	0.004	0.008
CreatePathwayCollection	0.011	0.003	0.014
ExtractAESPCs	0.380	0.267	8.768
GumbelMixpValues	0.001	0.001	0.001
IntersectOmicsPwyCollct	0.001	0.001	0.001
JoinPhenoAssay	0.000	0.000	0.001
LoadOntoPCs	0.415	0.371	12.419
OptimGumbelMixParams	0.001	0.001	0.001
PathwaytValues	0.001	0.000	0.002
PermTestCateg	0.001	0.001	0.002
PermTestReg	0.001	0.001	0.001
PermTestSurv	0.001	0.001	0.002
SE2Tidy	14.402	0.750	15.182
SubsetPathwayCollection	0.004	0.003	0.007
SubsetPathwayData	0.366	0.161	0.527
SuperPCA_pVals	0.889	0.073	11.870
TabulatepValues	0.000	0.001	0.001
TransposeAssay	0.139	0.037	0.177
aespca	0.000	0.000	0.001
coxTrain_fun	0.000	0.001	0.001
getPathPCLs	0.211	0.071	14.585
getPathpVals	0.173	0.060	14.554
get_set_OmicsPathway	1.780	0.850	2.631
get_set_OmicsRegCateg	0.104	0.033	0.137
get_set_OmicsSurv	0.150	0.036	0.186
glmTrain_fun	0.000	0.001	0.001
lars.lsa	0.001	0.001	0.001
mysvd	0.000	0.001	0.001
normalize	0	0	0
olsTrain_fun	0.001	0.000	0.001
pathway_tControl	0.000	0.000	0.002
pathway_tScores	0.000	0.000	0.001
permuteSamps	0.000	0.000	0.001
print.pathwayCollection	0.005	0.001	0.007
read_gmt	0.182	0.005	0.189
show-OmicsPathway-method	0.094	0.018	0.112
superpc.st	0.001	0.001	0.002
superpc.train	0.001	0.000	0.001
write_gmt	0.005	0.000	0.006