Zhi Yang
| Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020) |
| URL: https://git.bioconductor.org/packages/HiLDA |
| Branch: master |
| Last Commit: 5851756 |
| Last Changed Date: 2019-10-29 13:43:37 -0500 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-01-16 13:54:52 -0500 (Thu, 16 Jan 2020).
| Package 789/1818 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| HiLDA 1.1.0 Zhi Yang
| malbec2 | Linux (Ubuntu 18.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: HiLDA |
| Version: 1.1.0 |
| 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_1.1.0.tar.gz |
| StartedAt: 2020-01-16 05:24:27 -0500 (Thu, 16 Jan 2020) |
| EndedAt: 2020-01-16 05:29:42 -0500 (Thu, 16 Jan 2020) |
| EllapsedTime: 314.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: HiLDA.Rcheck |
| Warnings: 0 |
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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_1.1.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/HiLDA.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.1.0’
* 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 107.138 0.615 109.809
hildaGlobalResult 55.098 0.330 58.540
hildaReadMPFile 26.340 3.520 36.293
* 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.
HiLDA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL HiLDA ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’ * installing *source* package ‘HiLDA’ ... ** using staged installation ** libs clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c EMalgorithm.cpp -o EMalgorithm.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c checkBoundary.cpp -o checkBoundary.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c convertFromToVector.cpp -o convertFromToVector.o clang++ -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)
HiLDA.Rcheck/tests/testthat.Rout
R Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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: 48; time(s): 0.23; convergence: TRUE; loglikelihood: -8202.3184
#trial: 2; #iteration: 12; time(s): 0.06; convergence: TRUE; loglikelihood: -8202.3185
#trial: 3; #iteration: 18; time(s): 0.05; convergence: TRUE; loglikelihood: -8202.3184
#trial: 4; #iteration: 48; time(s): 0.16; convergence: TRUE; loglikelihood: -8202.3199
#trial: 5; #iteration: 51; time(s): 0.12; convergence: TRUE; loglikelihood: -8202.3188
#trial: 6; #iteration: 14; time(s): 0.08; convergence: TRUE; loglikelihood: -8202.3333
#trial: 7; #iteration: 63; time(s): 0.15; convergence: TRUE; loglikelihood: -8202.3184
#trial: 8; #iteration: 29; time(s): 0.15; convergence: TRUE; loglikelihood: -8202.3188
#trial: 9; #iteration: 12; time(s): 0.04; convergence: TRUE; loglikelihood: -8202.3184
#trial: 10; #iteration: 39; time(s): 0.11; convergence: TRUE; loglikelihood: -8202.3199
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 4 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
4.855 0.598 5.402
HiLDA.Rcheck/HiLDA-Ex.timings
| name | user | system | elapsed | |
| hildaBarplot | 1.693 | 0.052 | 1.831 | |
| hildaDiffPlot | 1.359 | 0.018 | 1.459 | |
| hildaGlobalResult | 55.098 | 0.330 | 58.540 | |
| hildaLocalResult | 0.025 | 0.004 | 0.028 | |
| hildaPlotSignature | 1.168 | 0.011 | 1.294 | |
| hildaReadMPFile | 26.340 | 3.520 | 36.293 | |
| hildaRhat | 0.024 | 0.004 | 0.034 | |
| hildaTest | 107.138 | 0.615 | 109.809 | |
| pmBarplot | 1.697 | 0.103 | 1.853 | |
| pmMultiBarplot | 1.934 | 0.130 | 2.143 | |
| pmPlotSignature | 1.270 | 0.073 | 1.344 | |
| pmgetSignature | 0.589 | 0.095 | 0.683 | |
| visPMS | 0.672 | 0.070 | 0.742 | |