Package: CAMTHC

Version: 1.5.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CAMTHC.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CAMTHC_1.5.0.tar.gz

StartedAt: 2020-01-16 02:28:22 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 02:34:40 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 378.1 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: CAMTHC.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CAMTHC.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CAMTHC_1.5.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/CAMTHC.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CAMTHC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CAMTHC’ version ‘1.5.0’
* 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 ‘CAMTHC’ can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'CAMTHC' is deprecated and will be removed from Bioconductor
See ‘/Users/biocbuild/bbs-3.11-bioc/meat/CAMTHC.Rcheck/00install.out’ for details.
* 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 (user + system) or elapsed time > 5s
               user system elapsed
MGsforA      32.515 11.566  44.044
CAMPrep      17.734  6.398  28.656
AS-accessor  17.251  6.478  23.728
CAMMGCluster 17.359  6.115  23.946
CAM          16.776  6.158  22.908
redoASest    16.834  6.024  22.867
reselectMG   16.785  6.017  22.949
PCAmat       16.775  5.976  22.745
CAMASest     16.393  5.861  22.233
XWProj        7.498  0.922   8.442
* 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: 1 WARNING
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/CAMTHC.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL CAMTHC
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘CAMTHC’ ...
** using staged installation
** R
** data
** 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
Warning: Package 'CAMTHC' is deprecated and will be removed from Bioconductor
  version 3.12 . Package renamed to debCAM
** testing if installed package can be loaded from final location
Warning: Package 'CAMTHC' is deprecated and will be removed from Bioconductor
  version 3.12 . Package renamed to debCAM
** testing if installed package keeps a record of temporary installation path
* DONE (CAMTHC)

R Under development (unstable) (2019-12-14 r77572) -- "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(CAMTHC)
Warning message:
Package 'CAMTHC' is deprecated and will be removed from Bioconductor
  version 3.12 . Package renamed to debCAM 
> 
> test_check("CAMTHC")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 5 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  6.532   0.791   7.241 

name	user	system	elapsed
AS-accessor	17.251	6.478	23.728
AfromMarkers	0.606	0.033	0.638
CAM	16.776	6.158	22.908
CAMASest	16.393	5.861	22.233
CAMMGCluster	17.359	6.115	23.946
CAMPrep	17.734	6.398	28.656
MDL	0.001	0.000	0.001
MGsforA	32.515	11.566	44.044
MGstatistic	0.697	0.036	0.734
PCAmat	16.775	5.976	22.745
XWProj	7.498	0.922	8.442
cornerSort	0.126	0.038	0.151
redoASest	16.834	6.024	22.867
reselectMG	16.785	6.017	22.949
sffsHull	0.066	0.001	0.067
simplexplot	0.693	0.056	0.753