Back to Multiple platform build/check report for BioC 3.11
ABCDEFG[H]IJKLMNOPQRSTUVWXYZ

CHECK report for HiLDA on malbec2

This page was generated on 2020-10-17 11:54:56 -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: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:HiLDA.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings HiLDA_1.2.0.tar.gz
StartedAt: 2020-10-17 02:11:36 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 02:15:32 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 236.4 seconds
RetCode: 0
Status:  OK 
CheckDir: HiLDA.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:HiLDA.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings HiLDA_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/HiLDA.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (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         84.848  0.052  84.916
hildaGlobalResult 42.075  0.024  42.144
hildaReadMPFile   16.218  0.661  43.943
* 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
  ‘/home/biocbuild/bbs-3.11-bioc/meat/HiLDA.Rcheck/00check.log’
for details.



Installation output

HiLDA.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL HiLDA
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘HiLDA’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c EMalgorithm.cpp -o EMalgorithm.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-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-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c checkBoundary.cpp -o checkBoundary.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c convertFromToVector.cpp -o convertFromToVector.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.11-bioc/R/lib -L/usr/local/lib -o HiLDA.so EMalgorithm.o RcppExports.o checkBoundary.o convertFromToVector.o -L/home/biocbuild/bbs-3.11-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.11-bioc/R/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-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(HiLDA)
Loading required package: ggplot2
> 
> test_check("HiLDA")
#trial:  1; #iteration:   19; time(s): 0.04; convergence: TRUE; loglikelihood: -8202.3189
#trial:  2; #iteration:   14; time(s): 0.03; convergence: TRUE; loglikelihood: -8202.3332
#trial:  3; #iteration:   25; time(s): 0.05; convergence: TRUE; loglikelihood: -8202.3184
#trial:  4; #iteration:   19; time(s): 0.03; convergence: TRUE; loglikelihood: -8202.3184
#trial:  5; #iteration:   37; time(s): 0.05; convergence: TRUE; loglikelihood: -8202.3184
#trial:  6; #iteration:   15; time(s): 0.02; convergence: TRUE; loglikelihood: -8202.3186
#trial:  7; #iteration:   25; time(s): 0.03; convergence: TRUE; loglikelihood: -8202.3184
#trial:  8; #iteration:   18; time(s): 0.03; convergence: TRUE; loglikelihood: -8202.3183
#trial:  9; #iteration:   21; time(s): 0.03; convergence: TRUE; loglikelihood: -8202.3185
#trial: 10; #iteration:   18; time(s): 0.03; convergence: TRUE; loglikelihood: -8202.3186
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 4 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  2.924   0.092   3.002 

Example timings

HiLDA.Rcheck/HiLDA-Ex.timings

nameusersystemelapsed
hildaBarplot0.7420.0040.765
hildaDiffPlot0.5540.0000.555
hildaGlobalResult42.075 0.02442.144
hildaLocalResult0.0230.0000.023
hildaPlotSignature0.3830.0000.382
hildaReadMPFile16.218 0.66143.943
hildaRhat0.0470.0000.047
hildaTest84.848 0.05284.916
pmBarplot0.8480.0000.849
pmMultiBarplot0.9140.0040.918
pmPlotSignature0.6620.0040.666
pmgetSignature0.2650.0000.265
visPMS0.4260.0000.425