Package: CAMTHC

Version: 1.4.0

Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:CAMTHC.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings CAMTHC_1.4.0.tar.gz

StartedAt: 2020-04-15 05:48:46 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 05:52:19 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 213.7 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: CAMTHC.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:CAMTHC.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings CAMTHC_1.4.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/CAMTHC.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (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 ‘/home/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      24.308  0.032  24.403
redoASest    13.380  0.020  13.422
reselectMG   13.048  0.052  13.127
AS-accessor  12.888  0.088  13.020
CAMASest     12.908  0.032  12.941
CAM          12.848  0.032  12.900
PCAmat       12.516  0.040  12.594
CAMPrep      11.468  0.024  11.493
CAMMGCluster 10.812  0.020  10.840
XWProj        6.560  0.020   6.639
* 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
  ‘/home/biocbuild/bbs-3.10-bioc/meat/CAMTHC.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL CAMTHC
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/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-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(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 
  4.496   0.216   4.687 

name	user	system	elapsed
AS-accessor	12.888	0.088	13.020
AfromMarkers	0.436	0.008	0.444
CAM	12.848	0.032	12.900
CAMASest	12.908	0.032	12.941
CAMMGCluster	10.812	0.020	10.840
CAMPrep	11.468	0.024	11.493
MDL	0	0	0
MGsforA	24.308	0.032	24.403
MGstatistic	0.580	0.032	0.624
PCAmat	12.516	0.040	12.594
XWProj	6.560	0.020	6.639
cornerSort	0.096	0.000	0.176
redoASest	13.380	0.020	13.422
reselectMG	13.048	0.052	13.127
sffsHull	0.048	0.004	0.050
simplexplot	0.784	0.028	0.810