Package: pathwayPCA

Version: 0.99.5

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:pathwayPCA.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings pathwayPCA_0.99.5.tar.gz

StartedAt: 2019-04-09 02:35:30 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 02:38:38 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 187.7 seconds

RetCode: 0

Status:  OK

CheckDir: pathwayPCA.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:pathwayPCA.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings pathwayPCA_0.99.5.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/pathwayPCA.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (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        9.611  0.363   9.972
SuperPCA_pVals 0.632  0.066   8.944
AESPCA_pVals   0.225  0.116   7.606
LoadOntoPCs    0.182  0.127   7.851
ExtractAESPCs  0.175  0.081   5.347
getPathpVals   0.142  0.109  10.942
getPathPCLs    0.136  0.106  10.308
* 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

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL pathwayPCA
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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-pc-linux-gnu (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 
  3.779   0.585  70.192 

name	user	system	elapsed
AESPCA_pVals	0.225	0.116	7.606
CheckAssay	0	0	0
CheckPwyColl	0.000	0.000	0.001
CheckSampleIDs	0.000	0.000	0.001
ControlFDR	0.001	0.000	0.001
CreateOmics	0.245	0.024	0.269
CreateOmicsPathway	0.003	0.000	0.002
CreatePathwayCollection	0.008	0.000	0.009
ExtractAESPCs	0.175	0.081	5.347
GumbelMixpValues	0.001	0.000	0.001
IntersectOmicsPwyCollct	0.000	0.000	0.001
JoinPhenoAssay	0	0	0
LoadOntoPCs	0.182	0.127	7.851
OptimGumbelMixParams	0.000	0.000	0.001
PathwaytValues	0	0	0
PermTestCateg	0	0	0
PermTestReg	0	0	0
PermTestSurv	0	0	0
SE2Tidy	9.611	0.363	9.972
SubsetPathwayCollection	0.002	0.000	0.001
SubsetPathwayData	0.169	0.044	0.213
SuperPCA_pVals	0.632	0.066	8.944
TabulatepValues	0.001	0.000	0.000
TransposeAssay	0.081	0.028	0.110
aespca	0	0	0
coxTrain_fun	0	0	0
getPathPCLs	0.136	0.106	10.308
getPathpVals	0.142	0.109	10.942
get_set_OmicsPathway	1.024	0.212	1.236
get_set_OmicsRegCateg	0.070	0.012	0.082
get_set_OmicsSurv	0.117	0.004	0.121
glmTrain_fun	0.001	0.000	0.001
lars.lsa	0.001	0.000	0.000
mysvd	0.001	0.000	0.000
normalize	0.001	0.000	0.000
olsTrain_fun	0.001	0.000	0.001
pathway_tControl	0.001	0.000	0.001
pathway_tScores	0.001	0.000	0.000
permuteSamps	0	0	0
print.pathwayCollection	0.001	0.003	0.004
read_gmt	0.179	0.008	0.257
show-OmicsPathway-method	0.078	0.000	0.079
superpc.st	0	0	0
superpc.train	0	0	0
write_gmt	0.002	0.002	0.004