Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-21 13:05:55 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4079
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4140
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for acde on tokay2


To the developers/maintainers of the acde package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/acde.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 11/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
acde 1.24.0  (landing page)
Juan Pablo Acosta
Snapshot Date: 2022-01-20 01:55:04 -0500 (Thu, 20 Jan 2022)
git_url: https://git.bioconductor.org/packages/acde
git_branch: RELEASE_3_14
git_last_commit: 0c3c4d4
git_last_commit_date: 2021-10-26 12:20:51 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: acde
Version: 1.24.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:acde.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings acde_1.24.0.tar.gz
StartedAt: 2022-01-20 15:37:49 -0500 (Thu, 20 Jan 2022)
EndedAt: 2022-01-20 15:40:34 -0500 (Thu, 20 Jan 2022)
EllapsedTime: 164.5 seconds
RetCode: 0
Status:   OK  
CheckDir: acde.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:acde.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings acde_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/acde.Rcheck'
* using R version 4.1.2 (2021-11-01)
* 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 '1.24.0'
* 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 LazyData ... 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 35.06      0   35.11
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
        user system elapsed
bcaFDR 38.17   0.02   38.19
* 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

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/acde_1.24.0.tar.gz && rm -rf acde.buildbin-libdir && mkdir acde.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=acde.buildbin-libdir acde_1.24.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL acde_1.24.0.zip && rm acde_1.24.0.tar.gz acde_1.24.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  1 2428k    1 45687    0     0   295k      0  0:00:08 --:--:--  0:00:08  295k
100 2428k  100 2428k    0     0  5808k      0 --:--:-- --:--:-- --:--:-- 5808k

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_1.24.0.zip
* DONE (acde)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'acde' successfully unpacked and MD5 sums checked

Tests output

acde.Rcheck/tests_i386/runTests.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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 -- Thu Jan 20 15:40:23 2022 
*********************************************** 
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 
   1.15    0.07    1.21 

acde.Rcheck/tests_x64/runTests.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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 -- Thu Jan 20 15:40:25 2022 
*********************************************** 
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 
   1.40    0.06    1.46 

Example timings

acde.Rcheck/examples_i386/acde-Ex.timings

nameusersystemelapsed
ac0.50.00.5
acde-package3.260.033.56
bcaFDR35.06 0.0035.11
fdr0.510.000.52
phytophthora0.020.000.01
plot.STP0.50.00.5
plot.TC1.730.001.74
print.STP0.580.000.57
print.TC1.760.021.78
qval0.550.000.55
stp0.560.000.56
tc1.820.011.83

acde.Rcheck/examples_x64/acde-Ex.timings

nameusersystemelapsed
ac0.400.030.44
acde-package2.970.033.00
bcaFDR38.17 0.0238.19
fdr0.590.000.59
phytophthora0.000.010.02
plot.STP0.570.000.56
plot.TC1.900.001.91
print.STP0.560.000.56
print.TC1.790.021.80
qval0.530.000.53
stp0.540.000.59
tc2.110.002.11