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This page was generated on 2020-04-15 12:41:39 -0400 (Wed, 15 Apr 2020).
| Package 1381/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| rcellminer 2.8.0 Augustin Luna
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | ERROR | |||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | |||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ ERROR ] | OK |
| Package: rcellminer |
| Version: 2.8.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:rcellminer.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings rcellminer_2.8.0.tar.gz |
| StartedAt: 2020-04-15 04:59:41 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 05:09:20 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 578.7 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: rcellminer.Rcheck |
| Warnings: NA |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:rcellminer.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings rcellminer_2.8.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/rcellminer.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rcellminer/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rcellminer’ version ‘2.8.0’
* 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 ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘rcellminer’ 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 ... NOTE
Warning: no function found corresponding to methods exports from ‘rcellminer’ for: ‘initialize’
A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.
Probably some imports need to be declared in the NAMESPACE file.
* 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 ... NOTE
getColumnQuantiles: no visible global function definition for
‘quantile’
getDrugActivityRange: no visible global function definition for ‘IQR’
getRsd: no visible binding for global variable ‘sd’
parCorPatternComparison: no visible global function definition for
‘residuals’
parCorPatternComparison: no visible global function definition for ‘lm’
parCorPatternComparison: no visible global function definition for
‘na.exclude’
plotCellMiner: no visible global function definition for ‘par’
plotCellMiner: no visible global function definition for ‘layout’
plotCellMiner: no visible global function definition for ‘lcm’
plotCellMiner: no visible global function definition for ‘axis’
plotCellMiner2D: no visible global function definition for
‘element_text’
plotCellMiner2D: no visible global function definition for ‘xlim’
plotCellMiner2D: no visible global function definition for ‘ylim’
plotDrugActivityRepeats: no visible global function definition for
‘pdf’
plotDrugActivityRepeats: no visible global function definition for
‘dev.off’
plotDrugSets: no visible binding for global variable ‘sd’
plotDrugSets: no visible global function definition for ‘pdf’
plotDrugSets: no visible global function definition for ‘par’
plotDrugSets: no visible global function definition for ‘axis’
plotDrugSets: no visible global function definition for ‘segments’
plotDrugSets: no visible global function definition for ‘dev.off’
plotStructures: no visible global function definition for ‘par’
rcdkplot: no visible global function definition for ‘par’
rcdkplot: no visible global function definition for ‘get.depictor’
rcdkplot: no visible global function definition for ‘plot’
rcdkplot: no visible global function definition for ‘rasterImage’
Undefined global functions or variables:
IQR axis dev.off element_text get.depictor layout lcm lm na.exclude
par pdf plot quantile rasterImage residuals sd segments xlim ylim
Consider adding
importFrom("grDevices", "dev.off", "pdf")
importFrom("graphics", "axis", "layout", "lcm", "par", "plot",
"rasterImage", "segments")
importFrom("stats", "IQR", "lm", "na.exclude", "quantile", "residuals",
"sd")
to your NAMESPACE file.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
Loading required package: fingerprint
Loading required package: rcellminerData
Consider citing this package: Luna A, et al. rcellminer: exploring molecular profiles and drug response of the NCI-60 cell lines in R. PMID: 26635141; citation("rcellminer")
>
> #test_package("rcellminer")
> test_check("rcellminer")
── 1. Failure: passRuleOf5 (@test_passRuleOf5.R#3) ────────────────────────────
passRuleOf5(...) isn't true.
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 236 | SKIPPED: 1 | WARNINGS: 3 | FAILED: 1 ]
1. Failure: passRuleOf5 (@test_passRuleOf5.R#3)
Error: testthat unit tests failed
Execution halted
* 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 ERROR, 3 NOTEs
See
‘/Users/biocbuild/bbs-3.10-bioc/meat/rcellminer.Rcheck/00check.log’
for details.
rcellminer.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL rcellminer ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘rcellminer’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (rcellminer)
rcellminer.Rcheck/tests/testthat.Rout.fail
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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(rcellminer)
Loading required package: Biobase
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: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, 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, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: rcdk
Loading required package: rcdklibs
Loading required package: rJava
Attaching package: 'rcdk'
The following object is masked from 'package:testthat':
matches
Loading required package: fingerprint
Loading required package: rcellminerData
Consider citing this package: Luna A, et al. rcellminer: exploring molecular profiles and drug response of the NCI-60 cell lines in R. PMID: 26635141; citation("rcellminer")
>
> #test_package("rcellminer")
> test_check("rcellminer")
── 1. Failure: passRuleOf5 (@test_passRuleOf5.R#3) ────────────────────────────
passRuleOf5(...) isn't true.
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 236 | SKIPPED: 1 | WARNINGS: 3 | FAILED: 1 ]
1. Failure: passRuleOf5 (@test_passRuleOf5.R#3)
Error: testthat unit tests failed
Execution halted
rcellminer.Rcheck/rcellminer-Ex.timings
| name | user | system | elapsed | |
| compareFingerprints | 1.808 | 0.208 | 1.345 | |
| crossCors | 0.010 | 0.002 | 0.011 | |
| crossCorsSpearman | 0.000 | 0.000 | 0.001 | |
| getActivityRangeStats | 0.041 | 0.011 | 0.052 | |
| getColumnQuantiles | 0.004 | 0.000 | 0.004 | |
| getDrugActivityData | 0.004 | 0.000 | 0.004 | |
| getDrugActivityRange | 0.003 | 0.001 | 0.004 | |
| getDrugActivityRepeatData | 0.001 | 0.000 | 0.002 | |
| getDrugMoaList | 0.080 | 0.004 | 0.086 | |
| getDrugName | 0.053 | 0.001 | 0.056 | |
| getFeatureDataFromMatList | 2.722 | 0.314 | 3.050 | |
| getFingerprintList | 0.097 | 0.010 | 0.048 | |
| getMedSenLineActivity | 0.008 | 0.001 | 0.004 | |
| getMinDrugActivityRepeatCor | 0.009 | 0.001 | 0.006 | |
| getMoaStr | 0.138 | 0.011 | 0.149 | |
| getMoaToCompounds | 0.053 | 0.004 | 0.056 | |
| getMolDataMatrices | 0.290 | 0.088 | 0.379 | |
| getNumDrugActivityRepeats | 0.004 | 0.000 | 0.004 | |
| getNumMissingLines | 0.126 | 0.017 | 0.145 | |
| getRsd | 0.008 | 0.001 | 0.009 | |
| getSmiles | 0.063 | 0.000 | 0.062 | |
| hasMoa | 0.056 | 0.003 | 0.060 | |
| isPublic | 0.002 | 0.001 | 0.003 | |
| loadCellminerPlotInfo | 0.002 | 0.000 | 0.002 | |
| loadNciColorSet | 0.003 | 0.000 | 0.003 | |
| parCorPatternComparison | 0.558 | 0.047 | 0.609 | |
| passRuleOf5 | 0.194 | 0.026 | 0.112 | |
| passRuleOf5FromNsc | 0.124 | 0.013 | 0.054 | |
| patternComparison | 0.322 | 0.062 | 0.373 | |
| plotCellMiner | 0.637 | 0.026 | 0.671 | |
| plotCellMiner2D | 0.000 | 0.000 | 0.001 | |
| plotDrugActivityRepeats | 0.433 | 0.067 | 0.506 | |
| plotDrugSets | 0.045 | 0.027 | 0.072 | |
| plotStructures | 3.486 | 0.803 | 3.569 | |
| plotStructuresFromNscs | 0.559 | 0.105 | 0.448 | |
| rcdkplot | 0.128 | 0.014 | 0.088 | |
| removeMolDataType | 0.001 | 0.000 | 0.001 | |
| rowCors | 0.002 | 0.001 | 0.002 | |
| runShinyApp | 0 | 0 | 0 | |
| runShinyComparePlots | 0.001 | 0.000 | 0.001 | |
| runShinyCompareStructures | 0 | 0 | 0 | |
| runShinyCompoundBrowser | 0.000 | 0.000 | 0.001 | |
| searchForNscs | 0.012 | 0.001 | 0.012 | |
| selectCorrelatedRows | 0.002 | 0.001 | 0.003 | |
| selectCorrelatedRowsFromMatrices | 0.006 | 0.002 | 0.008 | |