Back to Multiple platform build/check report for BioC 3.18:   simplified   long
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This page was generated on 2023-11-02 11:40:25 -0400 (Thu, 02 Nov 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4729
palomino4Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4463
lconwaymacOS 12.6.5 Montereyx86_644.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" 4478
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.3.1 (2023-06-16) -- "Beagle Scouts" 4464
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

Package 115/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
bacon 1.30.0  (landing page)
Maarten van Iterson
Snapshot Date: 2023-11-01 14:05:06 -0400 (Wed, 01 Nov 2023)
git_url: https://git.bioconductor.org/packages/bacon
git_branch: RELEASE_3_18
git_last_commit: 90f4e32
git_last_commit_date: 2023-10-24 10:48:29 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.6.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for bacon on kunpeng2


To the developers/maintainers of the bacon package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/bacon.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: bacon
Version: 1.30.0
Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:bacon.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings bacon_1.30.0.tar.gz
StartedAt: 2023-11-02 08:27:32 -0000 (Thu, 02 Nov 2023)
EndedAt: 2023-11-02 08:28:47 -0000 (Thu, 02 Nov 2023)
EllapsedTime: 75.5 seconds
RetCode: 0
Status:   OK  
CheckDir: bacon.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:bacon.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings bacon_1.30.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/bacon.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘bacon/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘bacon’ version ‘1.30.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘bacon’ can be installed ... OK
* used C compiler: ‘gcc (GCC) 10.3.1’
* 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
* 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 loading without being on the library search path ... 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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
bacon            17.300  4.778   8.533
meta-methods      9.368  1.743   4.483
es-methods        9.491  0.199   3.298
topTable-methods  9.456  0.218   3.333
se-methods        9.446  0.224   3.277
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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
  ‘/home/biocbuild/bbs-3.18-bioc/meat/bacon.Rcheck/00check.log’
for details.



Installation output

bacon.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL bacon
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’
* installing *source* package ‘bacon’ ...
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 10.3.1’
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c Rinit.c -o Rinit.o
Rinit.c:9:40: warning: missing braces around initializer [-Wmissing-braces]
    9 | static const R_CMethodDef cMethods[] = {
      |                                        ^
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c bacon.c -o bacon.o
gcc -shared -L/home/biocbuild/R/R-4.3.1/lib -L/usr/local/lib -o bacon.so Rinit.o bacon.o -L/home/biocbuild/R/R-4.3.1/lib -lR
installing to /home/biocbuild/R/R-4.3.1/site-library/00LOCK-bacon/00new/bacon/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (bacon)

Tests output

bacon.Rcheck/tests/testthat.Rout


R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (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
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 8 ]
> 
> proc.time()
   user  system elapsed 
 15.825   0.323   8.672 

Example timings

bacon.Rcheck/bacon-Ex.timings

nameusersystemelapsed
bacon17.300 4.778 8.533
bias-methods0.2540.0000.254
dnormmix0.0020.0040.006
es-methods9.4910.1993.298
estimates-methods0.2510.0000.251
fit-methods0.2510.0040.255
inflation-methods0.2580.0080.266
meta-methods9.3681.7434.483
plotnormmix0.0060.0000.009
posteriors-methods0.2910.0000.292
pval-methods0.2480.0030.252
rnormmix0.0000.0000.001
se-methods9.4460.2243.277
topTable-methods9.4560.2183.333
traces-methods0.3470.0080.360
tstat-methods0.2420.0120.255