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CHECK report for HiLDA on machv2

This page was generated on 2020-10-17 11:58:41 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE HiLDA PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 822/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HiLDA 1.2.0
Zhi Yang
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/HiLDA
Branch: RELEASE_3_11
Last Commit: a23fd31
Last Changed Date: 2020-04-27 15:28:42 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: HiLDA
Version: 1.2.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:HiLDA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings HiLDA_1.2.0.tar.gz
StartedAt: 2020-10-17 02:01:28 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 02:07:14 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 346.1 seconds
RetCode: 0
Status:  OK 
CheckDir: HiLDA.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:HiLDA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings HiLDA_1.2.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/HiLDA.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HiLDA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HiLDA’ version ‘1.2.0’
* 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 ‘HiLDA’ 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 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
hildaTest         150.523  0.399 151.101
hildaGlobalResult  75.842  0.228  76.150
hildaReadMPFile    21.251  0.785  24.824
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/HiLDA.Rcheck/00check.log’
for details.



Installation output

HiLDA.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL HiLDA
###
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##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘HiLDA’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c EMalgorithm.cpp -o EMalgorithm.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c checkBoundary.cpp -o checkBoundary.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c convertFromToVector.cpp -o convertFromToVector.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o HiLDA.so EMalgorithm.o RcppExports.o checkBoundary.o convertFromToVector.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-HiLDA/00new/HiLDA/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 (HiLDA)

Tests output

HiLDA.Rcheck/tests/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-apple-darwin17.0 (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(HiLDA)
Loading required package: ggplot2
> 
> test_check("HiLDA")
#trial:  1; #iteration:   51; time(s): 0.14; convergence: TRUE; loglikelihood: -8202.3184
#trial:  2; #iteration:   63; time(s): 0.15; convergence: TRUE; loglikelihood: -8202.3184
#trial:  3; #iteration:   12; time(s): 0.03; convergence: TRUE; loglikelihood: -8202.3186
#trial:  4; #iteration:   15; time(s): 0.03; convergence: TRUE; loglikelihood: -8202.3334
#trial:  5; #iteration:   14; time(s): 0.04; convergence: TRUE; loglikelihood: -8202.3320
#trial:  6; #iteration:   19; time(s): 0.08; convergence: TRUE; loglikelihood: -8202.3202
#trial:  7; #iteration:   14; time(s): 0.04; convergence: TRUE; loglikelihood: -8202.3334
#trial:  8; #iteration:   17; time(s): 0.04; convergence: TRUE; loglikelihood: -8202.3184
#trial:  9; #iteration:   20; time(s): 0.07; convergence: TRUE; loglikelihood: -8202.3184
#trial: 10; #iteration:   19; time(s): 0.05; convergence: TRUE; loglikelihood: -8202.3186
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 4 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  3.854   0.261   4.098 

Example timings

HiLDA.Rcheck/HiLDA-Ex.timings

nameusersystemelapsed
hildaBarplot1.1750.0171.194
hildaDiffPlot0.8320.0060.838
hildaGlobalResult75.842 0.22876.150
hildaLocalResult0.0320.0040.035
hildaPlotSignature0.6610.0090.671
hildaReadMPFile21.251 0.78524.824
hildaRhat0.0490.0040.052
hildaTest150.523 0.399151.101
pmBarplot1.3210.0581.380
pmMultiBarplot1.2960.0301.327
pmPlotSignature0.9780.0211.002
pmgetSignature0.4130.0150.430
visPMS0.6500.0540.705