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CHECK report for CAMTHC on tokay2

This page was generated on 2020-10-17 11:56:12 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE CAMTHC PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 223/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CAMTHC 1.6.0
Lulu Chen
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/CAMTHC
Branch: RELEASE_3_11
Last Commit: c81a87e
Last Changed Date: 2020-04-27 15:17:16 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: CAMTHC
Version: 1.6.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CAMTHC.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings CAMTHC_1.6.0.tar.gz
StartedAt: 2020-10-17 02:11:23 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 02:19:39 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 496.7 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: CAMTHC.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CAMTHC.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings CAMTHC_1.6.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/CAMTHC.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CAMTHC/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CAMTHC' version '1.6.0'
* 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 whether package 'CAMTHC' can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'CAMTHC' is deprecated and will be removed from Bioconductor
See 'C:/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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
MGsforA      21.08   0.05   21.13
AS-accessor  15.39   0.12   15.78
CAM          14.74   0.34   15.13
reselectMG   12.83   0.05   13.70
redoASest    12.76   0.03   12.80
CAMASest     11.34   0.06   11.42
CAMMGCluster 11.05   0.05   11.10
PCAmat       10.02   0.05   10.06
CAMPrep       9.97   0.03   10.00
cornerSort    0.05   0.03   14.00
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
MGsforA      24.03   0.09   29.94
PCAmat       13.66   0.08   13.73
CAM          12.40   0.13   12.53
CAMPrep      12.02   0.03   19.12
redoASest    11.75   0.10   14.72
reselectMG   11.25   0.06   34.05
CAMASest     10.99   0.01   11.01
CAMMGCluster 10.65   0.11   10.77
AS-accessor  10.46   0.14   53.06
XWProj        5.53   0.02    5.55
simplexplot   2.63   0.08    6.69
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/CAMTHC.Rcheck/00check.log'
for details.

Installation output

CAMTHC.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/CAMTHC_1.6.0.tar.gz && rm -rf CAMTHC.buildbin-libdir && mkdir CAMTHC.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CAMTHC.buildbin-libdir CAMTHC_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL CAMTHC_1.6.0.zip && rm CAMTHC_1.6.0.tar.gz CAMTHC_1.6.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 2503k  100 2503k    0     0  16.8M      0 --:--:-- --:--:-- --:--:-- 17.5M

install for i386

* installing *source* package 'CAMTHC' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'CAMTHC'
    finding HTML links ... done
    AS-accessor                             html  
    AfromMarkers                            html  
    CAM                                     html  
    CAMASObj-class                          html  
    CAMASest                                html  
    CAMMGCluster                            html  
    CAMMGObj-class                          html  
    CAMObj-class                            html  
    CAMPrep                                 html  
    CAMPrepObj-class                        html  
    CAMTHC-package                          html  
    MDL                                     html  
    MDLObj-class                            html  
    MGsforA                                 html  
    MGstatistic                             html  
    PCAmat                                  html  
    XWProj                                  html  
    cornerSort                              html  
    ratMix3                                 html  
    redoASest                               html  
    reselectMG                              html  
    sffsHull                                html  
    simplexplot                             html  
** 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

install for x64

* installing *source* package 'CAMTHC' ...
** testing if installed package can be loaded
Warning: Package 'CAMTHC' is deprecated and will be removed from Bioconductor
  version 3.12 . Package renamed to debCAM
* MD5 sums
packaged installation of 'CAMTHC' as CAMTHC_1.6.0.zip
* DONE (CAMTHC)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'CAMTHC' successfully unpacked and MD5 sums checked

Tests output

CAMTHC.Rcheck/tests_i386/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 
   3.95    0.31    4.34

CAMTHC.Rcheck/tests_x64/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 
   4.06    0.21    4.28

Example timings

CAMTHC.Rcheck/examples_i386/CAMTHC-Ex.timings

nameusersystemelapsed
AS-accessor15.39 0.1215.78
AfromMarkers0.570.050.63
CAM14.74 0.3415.13
CAMASest11.34 0.0611.42
CAMMGCluster11.05 0.0511.10
CAMPrep 9.97 0.0310.00
MDL000
MGsforA21.08 0.0521.13
MGstatistic0.330.030.36
PCAmat10.02 0.0510.06
XWProj4.700.034.73
cornerSort 0.05 0.0314.00
redoASest12.76 0.0312.80
reselectMG12.83 0.0513.70
sffsHull0.040.000.03
simplexplot3.060.043.50

CAMTHC.Rcheck/examples_x64/CAMTHC-Ex.timings

nameusersystemelapsed
AS-accessor10.46 0.1453.06
AfromMarkers0.440.060.50
CAM12.40 0.1312.53
CAMASest10.99 0.0111.01
CAMMGCluster10.65 0.1110.77
CAMPrep12.02 0.0319.12
MDL000
MGsforA24.03 0.0929.94
MGstatistic0.890.031.06
PCAmat13.66 0.0813.73
XWProj5.530.025.55
cornerSort0.050.010.05
redoASest11.75 0.1014.72
reselectMG11.25 0.0634.05
sffsHull0.060.000.06
simplexplot2.630.086.69