Tyler Backman
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/bioassayR |
| Branch: master |
| Last Commit: 8d59dff |
| Last Changed Date: 2019-01-04 13:20:36 -0400 (Fri, 04 Jan 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 11:36:27 -0400 (Tue, 09 Apr 2019).
| Package 135/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| bioassayR 1.21.1 Tyler Backman
| malbec2 | Linux (Ubuntu 18.04.2 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 | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
| Package: bioassayR |
| Version: 1.21.1 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:bioassayR.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings bioassayR_1.21.1.tar.gz |
| StartedAt: 2019-04-08 22:59:01 -0400 (Mon, 08 Apr 2019) |
| EndedAt: 2019-04-08 23:00:34 -0400 (Mon, 08 Apr 2019) |
| EllapsedTime: 92.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: bioassayR.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:bioassayR.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings bioassayR_1.21.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/bioassayR.Rcheck’ * using R Under development (unstable) (2019-03-18 r76245) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘bioassayR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘bioassayR’ version ‘1.21.1’ * 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 ‘bioassayR’ 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in Makefiles ... OK * checking for GNU extensions in Makefiles ... OK * checking include directives in Makefiles ... 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
bioassayR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL bioassayR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’ * installing *source* package ‘bioassayR’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘organism’ in package ‘bioassayR’ Creating a new generic function for ‘organism<-’ in package ‘bioassayR’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (bioassayR)
bioassayR.Rcheck/tests/testthat.Rout
R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
Copyright (C) 2019 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(bioassayR)
Loading required package: DBI
Loading required package: RSQLite
Loading required package: Matrix
Loading required package: rjson
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:Matrix':
colMeans, colSums, rowMeans, rowSums, which
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, mapply, match, mget, order, paste,
pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums,
rownames, sapply, setdiff, sort, table, tapply, union, unique,
unsplit, which, which.max, which.min
Attaching package: 'bioassayR'
The following objects are masked from 'package:BiocGenerics':
organism, organism<-
>
> test_check("bioassayR")
══ testthat results ═══════════════════════════════════════════════════════════
OK: 24 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
4.873 0.188 5.054
bioassayR.Rcheck/bioassayR-Ex.timings
| name | user | system | elapsed | |
| BioAssayDB-class | 0.001 | 0.000 | 0.002 | |
| activeAgainst | 0.031 | 0.004 | 0.163 | |
| activeTargets | 0.047 | 0.000 | 0.047 | |
| addBioassayIndex | 0.015 | 0.004 | 0.020 | |
| addDataSource | 0.023 | 0.000 | 0.023 | |
| allCids | 0.021 | 0.000 | 0.021 | |
| allTargets | 0.006 | 0.000 | 0.006 | |
| assaySetTargets | 0.054 | 0.000 | 0.055 | |
| bioactivityFingerprint | 0.255 | 0.004 | 0.258 | |
| bioassay-class | 0.021 | 0.000 | 0.022 | |
| bioassaySet-class | 0.001 | 0.000 | 0.000 | |
| connectBioassayDB | 0.015 | 0.000 | 0.016 | |
| crossReactivityProbability | 0.191 | 0.000 | 0.190 | |
| disconnectBioassayDB | 0.009 | 0.000 | 0.009 | |
| dropBioassay | 0.037 | 0.000 | 0.055 | |
| dropBioassayIndex | 0.019 | 0.000 | 0.019 | |
| getAssay | 0.001 | 0.004 | 0.005 | |
| getAssays | 0.011 | 0.004 | 0.015 | |
| getBioassaySetByCids | 0.136 | 0.000 | 0.136 | |
| inactiveTargets | 0.008 | 0.000 | 0.008 | |
| loadBioassay | 0.028 | 0.000 | 0.028 | |
| loadIdMapping | 0.009 | 0.000 | 0.010 | |
| newBioassayDB | 0.009 | 0.000 | 0.009 | |
| parsePubChemBioassay | 0.009 | 0.000 | 0.009 | |
| perTargetMatrix | 0.253 | 0.000 | 0.253 | |
| queryBioassayDB | 0.029 | 0.004 | 0.033 | |
| samplebioassay | 0.002 | 0.000 | 0.003 | |
| scaleBioassaySet | 0.038 | 0.000 | 0.038 | |
| screenedAtLeast | 0.013 | 0.000 | 0.012 | |
| selectiveAgainst | 0.112 | 0.004 | 0.116 | |
| targetSelectivity | 0.024 | 0.000 | 0.025 | |
| translateTargetId | 0.028 | 0.000 | 0.028 | |
| trinarySimilarity | 0.243 | 0.000 | 0.243 | |