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This page was generated on 2021-10-15 15:05:47 -0400 (Fri, 15 Oct 2021).

CHECK results for normr on nebbiolo1

To the developers/maintainers of the normr package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/normr.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1280/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
normr 1.18.1  (landing page)
Johannes Helmuth
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/normr
git_branch: RELEASE_3_13
git_last_commit: f1d3f26
git_last_commit_date: 2021-09-20 10:47:57 -0400 (Mon, 20 Sep 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: normr
Version: 1.18.1
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:normr.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings normr_1.18.1.tar.gz
StartedAt: 2021-10-14 10:50:11 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 10:53:55 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 224.1 seconds
RetCode: 0
Status:   OK  
CheckDir: normr.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:normr.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings normr_1.18.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/normr.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘normr/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘normr’ version ‘1.18.1’
* 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 ‘normr’ 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
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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: OK


Installation output

normr.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL normr
###
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* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘normr’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -fopenmp -D_GLIBCXX_USE_C99 -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -fopenmp -D_GLIBCXX_USE_C99 -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c em.cpp -o em.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -fopenmp -D_GLIBCXX_USE_C99 -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c normr_init.c -o normr_init.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.13-bioc/R/lib -L/usr/local/lib -o normr.so RcppExports.o em.o normr_init.o -fopenmp -D_GLIBCXX_USE_C99 -L/home/biocbuild/bbs-3.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.13-bioc/R/library/00LOCK-normr/00new/normr/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘getClasses’ in package ‘normr’
** 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 (normr)

Tests output

normr.Rcheck/tests/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-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(normr)

Attaching package: 'normr'

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

    getClasses

> 
> test_check("normr")
══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (2)

[ FAIL 0 | WARN 3 | SKIP 2 | PASS 439 ]
> 
> proc.time()
   user  system elapsed 
 42.010   1.311  43.313 

Example timings

normr.Rcheck/normr-Ex.timings

nameusersystemelapsed
NormRCountConfig-class0.0060.0010.006
NormRFit-class0.2120.0100.222
normR-diffR0.8680.0640.941
normR-enrichR1.3470.0161.363
normR-regimeR0.5590.0340.594
normR0.5410.0240.565