Chengyang Ji
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/sitePath |
| Branch: RELEASE_3_11 |
| Last Commit: 6c69dfc |
| Last Changed Date: 2020-06-11 02:59:43 -0400 (Thu, 11 Jun 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:55:46 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE sitePath PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1677/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| sitePath 1.4.2 Chengyang Ji
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | NA | |||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |
| Package: sitePath |
| Version: 1.4.2 |
| Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:sitePath.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings sitePath_1.4.2.tar.gz |
| StartedAt: 2020-10-17 05:35:19 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 05:39:38 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 259.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: sitePath.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:sitePath.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings sitePath_1.4.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/sitePath.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 ‘sitePath/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sitePath’ version ‘1.4.2’
* 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 ‘sitePath’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 6.9Mb
sub-directories of 1Mb or more:
extdata 1.2Mb
libs 5.3Mb
* 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 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
pre-assessment 5.052 0 5.052
* 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: 2 NOTEs
See
‘/home/biocbuild/bbs-3.11-bioc/meat/sitePath.Rcheck/00check.log’
for details.
sitePath.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL sitePath ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’ * installing *source* package ‘sitePath’ ... ** 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 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 exportFunc.cpp -o exportFunc.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 fixationSite.cpp -o fixationSite.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 minEntropy.cpp -o minEntropy.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 searchNode.cpp -o searchNode.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 searchTree.cpp -o searchTree.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 treemer.cpp -o treemer.o g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.11-bioc/R/lib -L/usr/local/lib -o sitePath.so RcppExports.o exportFunc.o fixationSite.o minEntropy.o searchNode.o searchTree.o treemer.o -L/home/biocbuild/bbs-3.11-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.11-bioc/R/library/00LOCK-sitePath/00new/sitePath/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 (sitePath)
sitePath.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(sitePath)
>
> test_check("sitePath")
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══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 4347 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
213.572 0.202 213.801
sitePath.Rcheck/sitePath-Ex.timings
| name | user | system | elapsed | |
| addMSA | 0.205 | 0.004 | 0.220 | |
| extractTips | 0.273 | 0.004 | 0.277 | |
| findSites | 1.663 | 0.000 | 1.662 | |
| plot.lineagePath | 1.031 | 0.032 | 1.063 | |
| plot.sitePath | 0.491 | 0.004 | 0.495 | |
| plotSingleSite | 2.333 | 0.012 | 2.345 | |
| pre-assessment | 5.052 | 0.000 | 5.052 | |
| setSiteNumbering | 0.136 | 0.000 | 0.136 | |
| treemer | 0.879 | 0.004 | 0.883 | |