Package: pathwayPCA

Version: 1.0.0

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_1.0.0.tar.gz

StartedAt: 2019-10-16 05:23:49 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 05:28:07 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 258.0 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_1.0.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/pathwayPCA.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.0.0’
* 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        14.944  1.095  16.213
LoadOntoPCs     0.400  0.336  12.504
AESPCA_pVals    0.385  0.330  12.699
ExtractAESPCs   0.362  0.281   9.094
getPathPCLs     0.322  0.045  15.070
getPathpVals    0.236  0.038  15.117
SuperPCA_pVals  0.171  0.037  12.034
* 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 3.6.1 (2019-07-05) -- "Action of the Toes"
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: 29 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 20.665   2.349  71.426 

name	user	system	elapsed
AESPCA_pVals	0.385	0.330	12.699
CheckAssay	0	0	0
CheckPwyColl	0	0	0
CheckSampleIDs	0.001	0.000	0.000
ControlFDR	0.001	0.001	0.001
CreateOmics	0.360	0.078	0.437
CreateOmicsPathway	0.004	0.004	0.007
CreatePathwayCollection	0.010	0.003	0.013
ExtractAESPCs	0.362	0.281	9.094
GumbelMixpValues	0.001	0.001	0.002
IntersectOmicsPwyCollct	0.001	0.000	0.001
JoinPhenoAssay	0.000	0.000	0.001
LoadOntoPCs	0.400	0.336	12.504
OptimGumbelMixParams	0.001	0.000	0.001
PathwaytValues	0.001	0.000	0.001
PermTestCateg	0.000	0.001	0.002
PermTestReg	0.001	0.001	0.001
PermTestSurv	0.001	0.000	0.001
SE2Tidy	14.944	1.095	16.213
SubsetPathwayCollection	0.003	0.003	0.006
SubsetPathwayData	0.621	0.242	0.888
SuperPCA_pVals	0.171	0.037	12.034
TabulatepValues	0.001	0.001	0.002
TransposeAssay	0.182	0.062	0.244
aespca	0.001	0.000	0.001
coxTrain_fun	0.000	0.001	0.001
getPathPCLs	0.322	0.045	15.070
getPathpVals	0.236	0.038	15.117
get_set_OmicsPathway	2.312	1.052	3.365
get_set_OmicsRegCateg	0.231	0.016	0.247
get_set_OmicsSurv	0.257	0.023	0.279
glmTrain_fun	0.001	0.001	0.001
lars.lsa	0.000	0.001	0.002
mysvd	0.000	0.001	0.001
normalize	0.000	0.001	0.000
olsTrain_fun	0.000	0.001	0.001
pathway_tControl	0.000	0.001	0.002
pathway_tScores	0.000	0.000	0.001
permuteSamps	0.000	0.000	0.001
print.pathwayCollection	0.006	0.002	0.009
read_gmt	0.246	0.004	0.253
show-OmicsPathway-method	0.258	0.005	0.262
superpc.st	0.001	0.001	0.002
superpc.train	0.001	0.001	0.002
write_gmt	0.005	0.001	0.005