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This page was generated on 2024-04-27 11:40:42 -0400 (Sat, 27 Apr 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4752
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4518
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4473
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 664/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
epimutacions 1.7.1  (landing page)
Dolors Pelegri-Siso
Snapshot Date: 2024-04-26 14:00:18 -0400 (Fri, 26 Apr 2024)
git_url: https://git.bioconductor.org/packages/epimutacions
git_branch: devel
git_last_commit: deb5e62
git_last_commit_date: 2023-11-03 07:38:00 -0400 (Fri, 03 Nov 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for epimutacions on kunpeng2


To the developers/maintainers of the epimutacions package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/epimutacions.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: epimutacions
Version: 1.7.1
Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:epimutacions.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings epimutacions_1.7.1.tar.gz
StartedAt: 2024-04-27 05:35:48 -0000 (Sat, 27 Apr 2024)
EndedAt: 2024-04-27 05:44:12 -0000 (Sat, 27 Apr 2024)
EllapsedTime: 504.8 seconds
RetCode: 0
Status:   OK  
CheckDir: epimutacions.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:epimutacions.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings epimutacions_1.7.1.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/epimutacions.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* 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 ‘epimutacions/DESCRIPTION’ ... OK
* this is package ‘epimutacions’ version ‘1.7.1’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘epimutacions’ can be installed ... OK
* used C compiler: ‘gcc (GCC) 10.3.1’
* used C++ compiler: ‘g++ (GCC) 10.3.1’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code 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 ... OK
* checking Rd files ... NOTE
checkRd: (-1) add_ensemble_regulatory.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) add_ensemble_regulatory.Rd:30-31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) add_ensemble_regulatory.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) add_ensemble_regulatory.Rd:33-35: Lost braces in \itemize; \value handles \item{}{} directly
* 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 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
plot_epimutations          5.522  0.635   6.242
epimutations_one_leave_out 2.944  0.415   6.000
epimutations               2.804  0.268   5.203
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/epimutacions.Rcheck/00check.log’
for details.


Installation output

epimutacions.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL epimutacions
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library’
* installing *source* package ‘epimutacions’ ...
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 10.3.1’
using C++ compiler: ‘g++ (GCC) 10.3.1’
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c mlm_init.c -o mlm_init.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall  -c ruben.cpp -o ruben.o
g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-beta-2024-04-15_r86425/lib -L/usr/local/lib -o epimutacions.so mlm_init.o ruben.o -L/home/biocbuild/R/R-beta-2024-04-15_r86425/lib -lR
installing to /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/00LOCK-epimutacions/00new/epimutacions/libs
** R
** data
** 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 (epimutacions)

Tests output

epimutacions.Rcheck/tests/testthat.Rout


R version 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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(epimutacions)
Loading required package: epimutacionsData
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
> 
> test_check("epimutacions")
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 24 ]

[ FAIL 0 | WARN 4 | SKIP 0 | PASS 24 ]
> 
> proc.time()
   user  system elapsed 
 26.605   2.144  38.278 

Example timings

epimutacions.Rcheck/epimutacions-Ex.timings

nameusersystemelapsed
GRset0.0750.0000.075
annotate_epimutations0.0000.0010.001
epi_parameters0.0000.0000.001
epi_preprocess000
epimutations2.8040.2685.203
epimutations_one_leave_out2.9440.4156.000
norm_parameters0.0010.0000.001
plot_epimutations5.5220.6356.242
res.epi.manova0.0020.0000.001