Package: CAMTHC

Version: 1.4.0

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_1.4.0.tar.gz

StartedAt: 2020-04-15 00:55:19 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 00:59:37 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 257.9 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_1.4.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/CAMTHC.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 ‘CAMTHC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CAMTHC’ version ‘1.4.0’
* 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-3.10-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 or elapsed time > 5s
               user system elapsed
MGsforA      25.000  4.503  29.683
redoASest    13.479  2.240  15.837
CAMASest     13.262  2.326  15.694
CAM          13.259  2.296  15.641
reselectMG   13.039  2.239  15.372
CAMMGCluster 12.957  2.312  15.367
AS-accessor  12.877  2.333  15.322
PCAmat       12.858  2.218  15.267
CAMPrep      12.815  2.207  15.148
XWProj        5.700  0.309   6.048
* 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-3.10-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/3.6/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 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(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 
  5.053   0.347   5.381 

name	user	system	elapsed
AS-accessor	12.877	2.333	15.322
AfromMarkers	0.470	0.013	0.483
CAM	13.259	2.296	15.641
CAMASest	13.262	2.326	15.694
CAMMGCluster	12.957	2.312	15.367
CAMPrep	12.815	2.207	15.148
MDL	0.001	0.000	0.001
MGsforA	25.000	4.503	29.683
MGstatistic	0.559	0.021	0.585
PCAmat	12.858	2.218	15.267
XWProj	5.700	0.309	6.048
cornerSort	0.094	0.013	0.074
redoASest	13.479	2.240	15.837
reselectMG	13.039	2.239	15.372
sffsHull	0.047	0.000	0.047
simplexplot	0.832	0.043	0.878