Package: pathwayPCA

Version: 1.2.0

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_1.2.0.tar.gz

StartedAt: 2020-04-15 04:28:16 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 04:31:36 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 200.4 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_1.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/pathwayPCA.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.2.0’
* 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        11.541  0.515  12.168
AESPCA_pVals    0.268  0.156   9.359
LoadOntoPCs     0.263  0.143   8.948
ExtractAESPCs   0.245  0.127   6.738
getPathpVals    0.192  0.022  11.753
getPathPCLs     0.179  0.024  11.543
SuperPCA_pVals  0.143  0.019   9.424
* 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 version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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: 47 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 17.614   1.108  58.002 

name	user	system	elapsed
AESPCA_pVals	0.268	0.156	9.359
CheckAssay	0	0	0
CheckPwyColl	0.001	0.001	0.000
CheckSampleIDs	0	0	0
Contains	0.001	0.001	0.002
ControlFDR	0.001	0.000	0.001
CreateOmics	0.281	0.047	0.330
CreateOmicsPathway	0.002	0.002	0.003
CreatePathwayCollection	0.007	0.001	0.008
ExtractAESPCs	0.245	0.127	6.738
GumbelMixpValues	0.001	0.001	0.001
IntersectOmicsPwyCollct	0	0	0
JoinPhenoAssay	0	0	0
LoadOntoPCs	0.263	0.143	8.948
OptimGumbelMixParams	0.000	0.000	0.001
PathwaytValues	0.000	0.001	0.001
PermTestCateg	0	0	0
PermTestReg	0.001	0.000	0.000
PermTestSurv	0.001	0.001	0.000
SE2Tidy	11.541	0.515	12.168
SubsetPathwayCollection	0.001	0.001	0.003
SubsetPathwayData	0.447	0.109	0.556
SuperPCA_pVals	0.143	0.019	9.424
TabulatepValues	0.000	0.000	0.001
TransposeAssay	0.157	0.026	0.182
WhichPathways	0.005	0.001	0.006
aespca	0.000	0.000	0.001
coxTrain_fun	0.001	0.000	0.001
getPathPCLs	0.179	0.024	11.543
getPathpVals	0.192	0.022	11.753
get_set_OmicsPathway	1.890	0.443	2.358
get_set_OmicsRegCateg	0.173	0.009	0.182
get_set_OmicsSurv	0.168	0.007	0.175
glmTrain_fun	0.000	0.001	0.001
lars.lsa	0	0	0
mysvd	0.001	0.001	0.001
normalize	0	0	0
olsTrain_fun	0.000	0.000	0.001
pathway_tControl	0.000	0.000	0.001
pathway_tScores	0.000	0.001	0.001
permuteSamps	0.001	0.000	0.001
print.pathwayCollection	0.005	0.002	0.006
read_gmt	0.230	0.003	0.254
show-OmicsPathway-method	0.191	0.008	0.201
superpc.st	0.000	0.000	0.001
superpc.train	0.000	0.000	0.001
write_gmt	0.005	0.001	0.005