Back to Multiple platform build/check report for BioC 3.12
A[B]CDEFGHIJKLMNOPQRSTUVWXYZ

CHECK report for bacon on riesling1

This page was generated on 2020-10-18 12:33:12 -0400 (Sun, 18 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE bacon PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 101/1874HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
bacon 1.17.0
Maarten van Iterson
Snapshot Date: 2020-10-17 14:41:49 -0400 (Sat, 17 Oct 2020)
URL: https://git.bioconductor.org/packages/bacon
Branch: master
Last Commit: 8c61588
Last Changed Date: 2020-04-27 14:55:31 -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: bacon
Version: 1.17.0
Command: D:\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:bacon.install-out.txt --library=D:\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings bacon_1.17.0.tar.gz
StartedAt: 2020-10-17 19:49:14 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 19:51:35 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 140.5 seconds
RetCode: 0
Status:  OK  
CheckDir: bacon.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:bacon.install-out.txt --library=D:\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings bacon_1.17.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.12-bioc/meat/bacon.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 'bacon/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'bacon' version '1.17.0'
* 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 'bacon' 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 ... NOTE
.hist: no visible binding for global variable '..density..'
Undefined global functions or variables:
  ..density..
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'D:/biocbuild/bbs-3.12-bioc/R/library/bacon/libs/i386/bacon.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'D:/biocbuild/bbs-3.12-bioc/R/library/bacon/libs/x64/bacon.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* 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
bacon            1.92   0.03   10.70
es-methods       0.11   0.02    7.46
meta-methods     0.11   0.01    6.56
se-methods       0.06   0.03    7.27
topTable-methods 0.09   0.00    6.45
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
bacon            2.32   0.08    9.54
es-methods       0.15   0.00    6.81
se-methods       0.13   0.00    6.64
topTable-methods 0.11   0.02    7.36
meta-methods     0.10   0.00    6.14
* 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: 2 NOTEs
See
  'D:/biocbuild/bbs-3.12-bioc/meat/bacon.Rcheck/00check.log'
for details.



Installation output

bacon.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/bacon_1.17.0.tar.gz && rm -rf bacon.buildbin-libdir && mkdir bacon.buildbin-libdir && D:\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=bacon.buildbin-libdir bacon_1.17.0.tar.gz && D:\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL bacon_1.17.0.zip && rm bacon_1.17.0.tar.gz bacon_1.17.0.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
100 16368  100 16368    0     0  1998k      0 --:--:-- --:--:-- --:--:-- 1998k

install for i386

* installing *source* package 'bacon' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Rinit.c -o Rinit.o
Rinit.c:9:40: warning: missing braces around initializer [-Wmissing-braces]
 static const R_CMethodDef cMethods[] = {
                                        ^
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c bacon.c -o bacon.o
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o bacon.dll tmp.def Rinit.o bacon.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.12-bioc/R/bin/i386 -lR
installing to D:/biocbuild/bbs-3.12-bioc/meat/bacon.buildbin-libdir/00LOCK-bacon/00new/bacon/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'bacon'
    finding HTML links ... done
    Bacon-class                             html  
    bacon                                   html  
    bias-methods                            html  
    dnormmix                                html  
    es-methods                              html  
    estimates-methods                       html  
    fit-methods                             html  
    inflation-methods                       html  
    meta-methods                            html  
    plot-Bacon-method                       html  
    plotnormmix                             html  
    posteriors-methods                      html  
    pval-methods                            html  
    rnormmix                                html  
    se-methods                              html  
    topTable-methods                        html  
    traces-methods                          html  
    tstat-methods                           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 'bacon' ...
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Rinit.c -o Rinit.o
Rinit.c:9:40: warning: missing braces around initializer [-Wmissing-braces]
 static const R_CMethodDef cMethods[] = {
                                        ^
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c bacon.c -o bacon.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o bacon.dll tmp.def Rinit.o bacon.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.12-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.12-bioc/meat/bacon.buildbin-libdir/bacon/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'bacon' as bacon_1.17.0.zip
* DONE (bacon)
* installing to library 'D:/biocbuild/bbs-3.12-bioc/R/library'
package 'bacon' successfully unpacked and MD5 sums checked

Tests output

bacon.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(bacon)
Loading required package: ggplot2
Loading required package: BiocParallel
Loading required package: ellipse

Attaching package: 'ellipse'

The following object is masked from 'package:graphics':

    pairs

> test_check("bacon")
[1]  0.914158192 -0.009646065  0.997805988
== testthat results  ===========================================================
[ OK: 8 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
   4.23    0.20   11.68 

bacon.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(bacon)
Loading required package: ggplot2
Loading required package: BiocParallel
Loading required package: ellipse

Attaching package: 'ellipse'

The following object is masked from 'package:graphics':

    pairs

> test_check("bacon")
[1]  0.914158192 -0.009646065  0.997805988
== testthat results  ===========================================================
[ OK: 8 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
   4.76    0.20   10.81 

Example timings

bacon.Rcheck/examples_i386/bacon-Ex.timings

nameusersystemelapsed
bacon 1.92 0.0310.70
bias-methods0.230.000.24
dnormmix0.000.000.01
es-methods0.110.027.46
estimates-methods0.270.000.27
fit-methods0.220.000.22
inflation-methods0.20.00.2
meta-methods0.110.016.56
plotnormmix000
posteriors-methods0.250.000.27
pval-methods0.220.000.21
rnormmix000
se-methods0.060.037.27
topTable-methods0.090.006.45
traces-methods0.330.020.36
tstat-methods0.220.000.22

bacon.Rcheck/examples_x64/bacon-Ex.timings

nameusersystemelapsed
bacon2.320.089.54
bias-methods0.250.000.25
dnormmix0.000.000.01
es-methods0.150.006.81
estimates-methods0.220.000.22
fit-methods0.210.000.20
inflation-methods0.180.000.19
meta-methods0.100.006.14
plotnormmix000
posteriors-methods0.280.000.28
pval-methods0.260.000.27
rnormmix000
se-methods0.130.006.64
topTable-methods0.110.027.36
traces-methods0.290.010.32
tstat-methods0.210.000.21