Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-23 11:46 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4372 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 2089/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
synergyfinder 3.15.0 (landing page) Shuyu Zheng
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the synergyfinder package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: synergyfinder |
Version: 3.15.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:synergyfinder.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings synergyfinder_3.15.0.tar.gz |
StartedAt: 2024-12-22 21:45:24 -0500 (Sun, 22 Dec 2024) |
EndedAt: 2024-12-22 21:45:59 -0500 (Sun, 22 Dec 2024) |
EllapsedTime: 35.4 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: synergyfinder.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:synergyfinder.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings synergyfinder_3.15.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/synergyfinder.Rcheck’ * using R Under development (unstable) (2024-11-20 r87352) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘synergyfinder/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘synergyfinder’ version ‘3.15.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 24 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally. * 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 ‘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 code 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 ... WARNING '::' or ':::' import not declared from: ‘scales’ 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’ CalculateSynergy: no visible global function definition for ‘t.test’ 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’ 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’ PlotDoseResponseCurve: no visible binding for global variable ‘response_origin’ PlotDoseResponseCurve: no visible binding for global variable ‘block_id’ PlotDoseResponseCurve: no visible global function definition for ‘dev.list’ PlotDoseResponseCurve: no visible global function definition for ‘dev.off’ 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 ‘n’ ReshapeData: no visible global function definition for ‘head’ ReshapeData: no visible binding for global variable ‘response_origin’ ReshapeData: no visible binding for global variable ‘nn’ ReshapeData: no visible binding for global variable ‘maxn’ ReshapeData: no visible binding for global variable ‘response_sd’ 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 global function definition for ‘predict’ 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 conc1 conc2 css data dev.list dev.off end head id input_type label left maxn metric n nn pred predict 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 t.test text theta value x y Consider adding importFrom("grDevices", "dev.list", "dev.off") importFrom("graphics", "text") importFrom("stats", "end", "predict", "start", "t.test") importFrom("utils", "data", "head") to your NAMESPACE file. * checking Rd files ... NOTE checkRd: (-1) FitDoseResponse.Rd:54: Lost braces 54 | href{https://onlinelibrary.wiley.com/doi/book/10.1002/0471725315}{Nonlinear | ^ checkRd: (-1) FitDoseResponse.Rd:54-55: Lost braces 54 | href{https://onlinelibrary.wiley.com/doi/book/10.1002/0471725315}{Nonlinear | ^ checkRd: (-1) FitDoseResponse.Rd:55: Escaped LaTeX specials: \& checkRd: (-1) PlotBarometer.Rd:118: Lost braces 118 | href{https://www.frontiersin.org/articles/10.3389/fphar.2015.00181/full}{What | ^ checkRd: (-1) PlotBarometer.Rd:118-119: Lost braces 118 | href{https://www.frontiersin.org/articles/10.3389/fphar.2015.00181/full}{What | ^ checkRd: (-1) PlotDoseResponseCurve.Rd:84: Lost braces 84 | link[drc]{plot.drc} function. For example, use xlim = c(0.5, 500) or | ^ * 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 CalculateSensitivity 6.056 0.095 6.16 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 2 NOTEs See ‘/Users/biocbuild/bbs-3.21-bioc/meat/synergyfinder.Rcheck/00check.log’ for details.
synergyfinder.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL synergyfinder ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/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 | 0.067 | 0.004 | 0.071 | |
CalculateRI | 0.404 | 0.019 | 0.424 | |
CalculateSensitivity | 6.056 | 0.095 | 6.160 | |
CalculateSynergy | 0.418 | 0.006 | 0.424 | |
CorrectBaseLine | 0.038 | 0.000 | 0.039 | |
ExtractSingleDrug | 0.033 | 0.000 | 0.033 | |
FindModelType | 0.004 | 0.000 | 0.005 | |
FitDoseResponse | 0.004 | 0.000 | 0.004 | |
HSA | 0.028 | 0.001 | 0.029 | |
Loewe | 0.063 | 0.001 | 0.063 | |
Plot2DrugContour | 0.388 | 0.016 | 0.405 | |
Plot2DrugHeatmap | 0.134 | 0.001 | 0.134 | |
Plot2DrugSurface | 0.175 | 0.012 | 0.187 | |
PlotBarometer | 0.625 | 0.009 | 0.636 | |
PlotDoseResponse | 0 | 0 | 0 | |
PlotDoseResponseCurve | 0.047 | 0.001 | 0.050 | |
PlotMultiDrugBar | 0.826 | 0.008 | 0.845 | |
PlotMultiDrugSurface | 4.274 | 0.055 | 4.349 | |
PlotSensitivitySynergy | 0.897 | 0.020 | 0.918 | |
PlotSynergy | 0.443 | 0.005 | 0.448 | |
ReshapeData | 0.025 | 0.001 | 0.026 | |
ZIP | 0.154 | 0.002 | 0.155 | |