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CHECK report for CAMTHC on merida2

This page was generated on 2019-04-09 13:37:04 -0400 (Tue, 09 Apr 2019).

Package 201/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CAMTHC 1.1.3
Lulu Chen
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/CAMTHC
Branch: master
Last Commit: 8564b7a
Last Changed Date: 2019-02-05 17:25:26 -0400 (Tue, 05 Feb 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK 

Summary

Package: CAMTHC
Version: 1.1.3
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_1.1.3.tar.gz
StartedAt: 2019-04-08 23:38:50 -0400 (Mon, 08 Apr 2019)
EndedAt: 2019-04-08 23:42:55 -0400 (Mon, 08 Apr 2019)
EllapsedTime: 244.4 seconds
RetCode: 0
Status:  OK 
CheckDir: CAMTHC.Rcheck
Warnings: 0

Command output

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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_1.1.3.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/CAMTHC.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* 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 ‘1.1.3’
* 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 ... 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
MGsforA      25.824  4.484  30.520
redoASest    14.608  2.448  17.335
PCAmat       13.386  2.329  15.828
reselectMG   13.403  2.289  15.814
CAMPrep      12.901  2.255  15.232
AS-accessor  12.817  2.294  15.203
CAMMGCluster 12.425  2.208  14.705
CAMASest     12.000  2.235  14.280
CAM          11.694  2.099  13.869
XWProj        5.608  0.353   5.994
* 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


Installation output

CAMTHC.Rcheck/00install.out

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###
### Running command:
###
###   /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’ ...
** 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
* DONE (CAMTHC)

Tests output

CAMTHC.Rcheck/tests/testthat.Rout


R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 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)
> 
> test_check("CAMTHC")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 5 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  3.838   0.315   4.098 

Example timings

CAMTHC.Rcheck/CAMTHC-Ex.timings

nameusersystemelapsed
AS-accessor12.817 2.29415.203
AfromMarkers0.4410.0120.454
CAM11.694 2.09913.869
CAMASest12.000 2.23514.280
CAMMGCluster12.425 2.20814.705
CAMPrep12.901 2.25515.232
MDL0.0000.0000.001
MGsforA25.824 4.48430.520
MGstatistic0.5110.0170.532
PCAmat13.386 2.32915.828
XWProj5.6080.3535.994
cornerSort0.1390.0140.119
redoASest14.608 2.44817.335
reselectMG13.403 2.28915.814
sffsHull0.0450.0000.046
simplexplot0.6830.0450.750