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CHECK report for bacon on tokay1

This page was generated on 2019-04-13 11:26:27 -0400 (Sat, 13 Apr 2019).

Package 91/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
bacon 1.10.1
Maarten van Iterson
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/bacon
Branch: RELEASE_3_8
Last Commit: f8f5cb0
Last Changed Date: 2019-01-04 13:19:23 -0400 (Fri, 04 Jan 2019)
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: bacon
Version: 1.10.1
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:bacon.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings bacon_1.10.1.tar.gz
StartedAt: 2019-04-13 00:36:19 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 00:39:41 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 201.9 seconds
RetCode: 0
Status:  OK  
CheckDir: bacon.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:bacon.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings bacon_1.10.1.tar.gz
###
##############################################################################
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/bacon.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 'bacon/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'bacon' version '1.10.1'
* 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 '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..'
.qq: no visible binding for global variable 'column'
Undefined global functions or variables:
  ..density.. column
* 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 'C:/Users/biocbuild/bbs-3.8-bioc/R/library/bacon/libs/i386/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 or elapsed time > 5s
                 user system elapsed
bacon            2.34   0.06   11.98
se-methods       0.06   0.07    7.81
es-methods       0.03   0.05    7.73
topTable-methods 0.08   0.00    8.67
meta-methods     0.03   0.01    7.81
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
bacon            2.10   0.01   11.52
es-methods       0.05   0.07    7.48
se-methods       0.05   0.05    8.64
meta-methods     0.06   0.02    8.00
topTable-methods 0.04   0.01    9.06
* 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
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/bacon.Rcheck/00check.log'
for details.



Installation output

bacon.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/bacon_1.10.1.tar.gz && rm -rf bacon.buildbin-libdir && mkdir bacon.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=bacon.buildbin-libdir bacon_1.10.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL bacon_1.10.1.zip && rm bacon_1.10.1.tar.gz bacon_1.10.1.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 15861  100 15861    0     0   417k      0 --:--:-- --:--:-- --:--:--  469k

install for i386

* installing *source* package 'bacon' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c Rinit.c -o Rinit.o
Rinit.c:12:1: warning: missing braces around initializer [-Wmissing-braces]
 };
 ^
Rinit.c:12:1: warning: (near initialization for 'cMethods[1]') [-Wmissing-braces]
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c bacon.c -o bacon.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o bacon.dll tmp.def Rinit.o bacon.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/bacon.buildbin-libdir/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
In R CMD INSTALL

install for x64

* installing *source* package 'bacon' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c Rinit.c -o Rinit.o
Rinit.c:12:1: warning: missing braces around initializer [-Wmissing-braces]
 };
 ^
Rinit.c:12:1: warning: (near initialization for 'cMethods[1]') [-Wmissing-braces]
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c bacon.c -o bacon.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o bacon.dll tmp.def Rinit.o bacon.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/bacon.buildbin-libdir/bacon/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'bacon' as bacon_1.10.1.zip
* DONE (bacon)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'bacon' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

bacon.Rcheck/tests_i386/testthat.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.

> 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]  0.914145518 -0.009654064  0.997825448
== testthat results  ===========================================================
OK: 3 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   3.06    0.07    3.12 

bacon.Rcheck/tests_x64/testthat.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.

> 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]  0.914145518 -0.009654064  0.997825448
== testthat results  ===========================================================
OK: 3 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   3.25    0.09    3.32 

Example timings

bacon.Rcheck/examples_i386/bacon-Ex.timings

nameusersystemelapsed
bacon 2.34 0.0611.98
bias-methods0.270.020.28
dnormmix0.010.000.02
es-methods0.030.057.73
estimates-methods0.280.000.29
fit-methods0.270.000.26
inflation-methods0.270.000.27
meta-methods0.030.017.81
plotnormmix000
posteriors-methods0.280.000.29
pval-methods0.290.000.28
rnormmix000
se-methods0.060.077.81
topTable-methods0.080.008.67
traces-methods0.530.000.53
tstat-methods0.310.000.32

bacon.Rcheck/examples_x64/bacon-Ex.timings

nameusersystemelapsed
bacon 2.10 0.0111.52
bias-methods0.210.000.21
dnormmix000
es-methods0.050.077.48
estimates-methods0.230.000.24
fit-methods0.220.010.23
inflation-methods0.220.000.22
meta-methods0.060.028.00
plotnormmix000
posteriors-methods0.240.000.24
pval-methods0.200.030.23
rnormmix000
se-methods0.050.058.64
topTable-methods0.040.019.06
traces-methods0.420.000.43
tstat-methods0.240.000.23