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This page was generated on 2021-10-15 15:06:55 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the synergyfinder package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/synergyfinder.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1884/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
synergyfinder 3.0.14 (landing page) Shuyu Zheng
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: synergyfinder |
Version: 3.0.14 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:synergyfinder.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings synergyfinder_3.0.14.tar.gz |
StartedAt: 2021-10-15 00:33:54 -0400 (Fri, 15 Oct 2021) |
EndedAt: 2021-10-15 00:35:41 -0400 (Fri, 15 Oct 2021) |
EllapsedTime: 107.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: synergyfinder.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:synergyfinder.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings synergyfinder_3.0.14.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/synergyfinder.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘synergyfinder/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘synergyfinder’ version ‘3.0.14’ * 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 ... NOTE Found the following hidden files and directories: .git_fetch_output.txt .git_merge_output.txt 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 ‘synergyfinder’ 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 ... NOTE Namespaces in Imports field not imported from: ‘future’ ‘gstat’ ‘nleqslv’ ‘sp’ ‘tidyverse’ All declared Imports should be used. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .Extract2DrugPlotData: no visible binding for global variable ‘input_type’ .Extract2DrugPlotData: no visible binding for global variable ‘block_id’ .Extract2DrugPlotData: no visible binding for global variable ‘value’ .Extract2DrugPlotData: no visible binding for global variable ‘left’ .Extract2DrugPlotData: no visible binding for global variable ‘right’ .Extract2DrugPlotData: no visible binding for global variable ‘conc1’ .Extract2DrugPlotData: no visible binding for global variable ‘conc2’ .Extract2DrugPlotData: no visible binding for global variable ‘text’ .ExtractMultiDrugPlotData: no visible binding for global variable ‘block_id’ Bliss: no visible binding for global variable ‘Bliss_ref’ CalculateCSS: no visible binding for global variable ‘data’ CalculateSensitivity: no visible binding for global variable ‘response_origin’ CalculateSensitivity: no visible binding for global variable ‘block_id’ CalculateSynergy: no visible binding for global variable ‘response_origin’ CalculateSynergy: no visible binding for global variable ‘block_id’ HSA: no visible binding for global variable ‘HSA_ref’ HighlightBarPlot: no visible binding for global variable ‘id’ HighlightBarPlot: no visible binding for global variable ‘value’ HighlightBarPlot: no visible binding for global variable ‘color’ Plot2DrugContour: no visible global function definition for ‘colorRampPalette’ Plot2DrugHeatmap: no visible binding for global variable ‘text’ PlotBarometer: no visible binding for global variable ‘block_id’ PlotBarometer: no visible binding for global variable ‘response_mean’ PlotBarometer: no visible binding for global variable ‘response’ PlotBarometer: no visible binding for global variable ‘r’ PlotBarometer: no visible binding for global variable ‘theta’ PlotBarometer: no visible binding for global variable ‘value’ PlotBarometer: no visible binding for global variable ‘start’ PlotBarometer: no visible binding for global variable ‘end’ PlotBarometer: no visible binding for global variable ‘label’ PlotBarometer: no visible binding for global variable ‘x’ PlotBarometer: no visible binding for global variable ‘y’ PlotBarometer: no visible binding for global variable ‘adjust’ PlotBarometer: no visible binding for global variable ‘angle’ PlotDoseResponse: no visible binding for global variable ‘grid’ PlotDoseResponseCurve: no visible binding for global variable ‘response_origin’ PlotDoseResponseCurve: no visible binding for global variable ‘block_id’ PlotMultiDrugBar: no visible binding for global variable ‘id’ PlotMultiDrugBar: no visible binding for global variable ‘value’ PlotMultiDrugBar: no visible binding for global variable ‘color’ PlotMultiDrugBar: no visible binding for global variable ‘metric’ PlotSensitivitySynergy: no visible binding for global variable ‘block_id’ PlotSensitivitySynergy: no visible binding for global variable ‘css’ PlotSensitivitySynergy: no visible binding for global variable ‘label’ PlotSensitivitySynergy: no visible binding for global variable ‘synergy’ ReshapeData: no visible binding for global variable ‘block_id’ ReshapeData: no visible binding for global variable ‘response_origin’ ReshapeData: no visible binding for global variable ‘response_sd’ ReshapeData: no visible binding for global variable ‘n’ ReshapeData: no visible binding for global variable ‘response_sem’ ReshapeData: no visible binding for global variable ‘response_mean’ ReshapeData: no visible binding for global variable ‘response_CI95’ ReshapeData: no visible binding for global variable ‘response_origin_sd’ ReshapeData: no visible binding for global variable ‘response_origin_sem’ ReshapeData: no visible binding for global variable ‘response_origin_mean’ ReshapeData: no visible binding for global variable ‘response_origin_CI95’ ZIP : <anonymous>: no visible binding for global variable ‘data’ ZIP : <anonymous>: no visible binding for global variable ‘pred’ ZIP : <anonymous>: no visible global function definition for ‘:=’ ZIP: no visible binding for global variable ‘.’ ZIP: no visible binding for global variable ‘ZIP_fit’ ZIP: no visible binding for global variable ‘ZIP_ref’ ZIP: no visible binding for global variable ‘ZIP_synergy’ Undefined global functions or variables: . := Bliss_ref HSA_ref ZIP_fit ZIP_ref ZIP_synergy adjust angle block_id color colorRampPalette conc1 conc2 css data end grid id input_type label left metric n pred r response response_CI95 response_mean response_origin response_origin_CI95 response_origin_mean response_origin_sd response_origin_sem response_sd response_sem right start synergy text theta value x y Consider adding importFrom("grDevices", "colorRampPalette") importFrom("graphics", "grid", "text") importFrom("stats", "end", "start") importFrom("utils", "data") 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 Examples with CPU (user + system) or elapsed time > 5s user system elapsed PlotMultiDrugSurface 13.257 0.268 13.547 PlotMultiDrugBar 8.995 0.047 9.048 * 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: 3 NOTEs See ‘/Users/biocbuild/bbs-3.13-bioc/meat/synergyfinder.Rcheck/00check.log’ for details.
synergyfinder.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL synergyfinder ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘synergyfinder’ ... ** using staged installation ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (synergyfinder)
synergyfinder.Rcheck/synergyfinder-Ex.timings
name | user | system | elapsed | |
Bliss | 0.269 | 0.013 | 0.282 | |
CalculateRI | 2.105 | 0.113 | 2.221 | |
CalculateSensitivity | 3.793 | 0.092 | 3.892 | |
CalculateSynergy | 2.253 | 0.013 | 2.267 | |
CorrectBaseLine | 0.186 | 0.002 | 0.188 | |
ExtractSingleDrug | 0.106 | 0.001 | 0.108 | |
FindModelType | 0.024 | 0.001 | 0.025 | |
FitDoseResponse | 0.019 | 0.000 | 0.019 | |
HSA | 0.089 | 0.001 | 0.090 | |
Loewe | 0.237 | 0.004 | 0.241 | |
Plot2DrugContour | 1.506 | 0.035 | 1.544 | |
Plot2DrugHeatmap | 0.365 | 0.002 | 0.368 | |
Plot2DrugSurface | 0.564 | 0.053 | 0.620 | |
PlotBarometer | 3.039 | 0.014 | 3.100 | |
PlotDoseResponse | 0.000 | 0.001 | 0.001 | |
PlotDoseResponseCurve | 0.172 | 0.006 | 0.177 | |
PlotMultiDrugBar | 8.995 | 0.047 | 9.048 | |
PlotMultiDrugSurface | 13.257 | 0.268 | 13.547 | |
PlotSensitivitySynergy | 4.829 | 0.071 | 4.905 | |
PlotSynergy | 2.702 | 0.009 | 2.713 | |
ReshapeData | 0.112 | 0.002 | 0.113 | |
ZIP | 0.984 | 0.004 | 0.989 | |