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CHECK report for acde on tokay1

This page was generated on 2020-09-19 10:19:58 -0400 (Sat, 19 Sep 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE acde PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 11/1912HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
acde 1.19.0
Juan Pablo Acosta
Snapshot Date: 2020-09-18 14:43:25 -0400 (Fri, 18 Sep 2020)
URL: https://git.bioconductor.org/packages/acde
Branch: master
Last Commit: b0efcae
Last Changed Date: 2020-04-27 14:49:17 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK  OK  OK 
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: acde
Version: 1.19.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:acde.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings acde_1.19.0.tar.gz
StartedAt: 2020-09-19 02:42:51 -0400 (Sat, 19 Sep 2020)
EndedAt: 2020-09-19 02:45:18 -0400 (Sat, 19 Sep 2020)
EllapsedTime: 147.7 seconds
RetCode: 0
Status:  OK  
CheckDir: acde.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:acde.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings acde_1.19.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/acde.Rcheck'
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'acde/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'acde' version '1.19.0'
* 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 'acde' 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
* 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
bcaFDR 45.95   0.02   45.97
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
        user system elapsed
bcaFDR 43.73      0   43.74
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.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

acde.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/acde_1.19.0.tar.gz && rm -rf acde.buildbin-libdir && mkdir acde.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=acde.buildbin-libdir acde_1.19.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL acde_1.19.0.zip && rm acde_1.19.0.tar.gz acde_1.19.0.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
 79 2427k   79 1920k    0     0  3139k      0 --:--:-- --:--:-- --:--:-- 3152k
100 2427k  100 2427k    0     0  3941k      0 --:--:-- --:--:-- --:--:-- 3960k

install for i386

* installing *source* package 'acde' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'acde'
    finding HTML links ... done
    ac                                      html  
    acde-package                            html  
    bcaFDR                                  html  
    fdr                                     html  
    phytophthora                            html  
    plot.STP                                html  
    plot.TC                                 html  
    print.STP                               html  
    print.TC                                html  
    qval                                    html  
    stp                                     html  
    tc                                      html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'acde' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'acde' as acde_1.19.0.zip
* DONE (acde)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'acde' successfully unpacked and MD5 sums checked

Tests output

acde.Rcheck/tests_i386/runTests.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
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.

> BiocGenerics:::testPackage("acde")


RUNIT TEST PROTOCOL -- Sat Sep 19 02:45:11 2020 
*********************************************** 
Number of test functions: 4 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
acde RUnit Tests - 4 test functions, 0 errors, 0 failures
Number of test functions: 4 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   1.12    0.06    1.17 

acde.Rcheck/tests_x64/runTests.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
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.

> BiocGenerics:::testPackage("acde")


RUNIT TEST PROTOCOL -- Sat Sep 19 02:45:13 2020 
*********************************************** 
Number of test functions: 4 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
acde RUnit Tests - 4 test functions, 0 errors, 0 failures
Number of test functions: 4 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   1.23    0.00    1.21 

Example timings

acde.Rcheck/examples_i386/acde-Ex.timings

nameusersystemelapsed
ac0.280.050.33
acde-package2.660.032.69
bcaFDR45.95 0.0245.97
fdr0.730.010.75
phytophthora0.020.000.01
plot.STP0.530.000.53
plot.TC2.050.002.05
print.STP0.780.000.78
print.TC2.530.002.53
qval0.920.000.92
stp0.670.000.68
tc1.720.031.75

acde.Rcheck/examples_x64/acde-Ex.timings

nameusersystemelapsed
ac0.340.050.39
acde-package3.080.053.13
bcaFDR43.73 0.0043.74
fdr0.520.000.51
phytophthora0.020.000.01
plot.STP0.540.000.55
plot.TC1.940.001.94
print.STP0.550.000.54
print.TC1.860.001.86
qval0.540.000.55
stp0.710.010.72
tc1.790.031.83