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CHECK report for acde on tokay1

This page was generated on 2019-04-13 11:25:25 -0400 (Sat, 13 Apr 2019).

Package 11/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
acde 1.12.0
Juan Pablo Acosta
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/acde
Branch: RELEASE_3_8
Last Commit: f6ce592
Last Changed Date: 2018-10-30 11:41:58 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: acde
Version: 1.12.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:acde.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings acde_1.12.0.tar.gz
StartedAt: 2019-04-13 00:23:52 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 00:27:10 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 198.7 seconds
RetCode: 0
Status:  OK  
CheckDir: acde.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:acde.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings acde_1.12.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/acde.Rcheck'
* using R version 3.5.3 (2019-03-11)
* 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 '1.12.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 or elapsed time > 5s
        user system elapsed
bcaFDR 38.71      0   38.72
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
        user system elapsed
bcaFDR 37.69      0   37.69
* 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/3.8/bioc/src/contrib/acde_1.12.0.tar.gz && rm -rf acde.buildbin-libdir && mkdir acde.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=acde.buildbin-libdir acde_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL acde_1.12.0.zip && rm acde_1.12.0.tar.gz acde_1.12.0.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 2427k  100 2427k    0     0  14.5M      0 --:--:-- --:--:-- --:--:-- 14.9M

install for i386

* installing *source* package 'acde' ...
** 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
In R CMD INSTALL

install for x64

* installing *source* package 'acde' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'acde' as acde_1.12.0.zip
* DONE (acde)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'acde' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

acde.Rcheck/tests_i386/runTests.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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 Apr 13 00:27:05 2019 
*********************************************** 
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 
   0.87    0.06    0.95 

acde.Rcheck/tests_x64/runTests.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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 Apr 13 00:27:07 2019 
*********************************************** 
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 
   1.04    0.04    1.07 

Example timings

acde.Rcheck/examples_i386/acde-Ex.timings

nameusersystemelapsed
ac0.190.020.21
acde-package3.280.033.40
bcaFDR38.71 0.0038.72
fdr0.830.020.84
phytophthora0.030.000.03
plot.STP0.60.00.6
plot.TC1.860.001.86
print.STP0.610.000.61
print.TC2.480.012.50
qval0.580.000.57
stp0.950.000.96
tc2.610.022.62

acde.Rcheck/examples_x64/acde-Ex.timings

nameusersystemelapsed
ac0.110.010.12
acde-package2.070.022.10
bcaFDR37.69 0.0037.69
fdr0.430.010.45
phytophthora0.020.000.02
plot.STP0.450.000.45
plot.TC1.440.001.44
print.STP0.450.000.45
print.TC1.440.021.46
qval0.470.000.46
stp0.470.000.47
tc1.440.001.44