Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:05 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 2105/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
synergyfinder 3.14.0 (landing page) Shuyu Zheng
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
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: 3.14.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:synergyfinder.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings synergyfinder_3.14.0.tar.gz |
StartedAt: 2024-12-20 06:37:22 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 06:39:24 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 121.9 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: synergyfinder.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:synergyfinder.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings synergyfinder_3.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/synergyfinder.Rcheck' * using R version 4.4.2 (2024-10-31 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.3.0 GNU Fortran (GCC) 13.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'synergyfinder/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'synergyfinder' version '3.14.0' * 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 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 25.02 0.33 25.36 PlotMultiDrugSurface 12.69 0.22 12.92 * 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 'F:/biocbuild/bbs-3.20-bioc/meat/synergyfinder.Rcheck/00check.log' for details.
synergyfinder.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL synergyfinder ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/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 | 0.22 | 0.00 | 0.22 | |
CalculateRI | 1.12 | 0.08 | 1.20 | |
CalculateSensitivity | 25.02 | 0.33 | 25.36 | |
CalculateSynergy | 1.61 | 0.00 | 1.61 | |
CorrectBaseLine | 0.13 | 0.01 | 0.14 | |
ExtractSingleDrug | 0.09 | 0.00 | 0.09 | |
FindModelType | 0.02 | 0.00 | 0.02 | |
FitDoseResponse | 0.01 | 0.00 | 0.01 | |
HSA | 0.11 | 0.00 | 0.11 | |
Loewe | 0.27 | 0.00 | 0.27 | |
Plot2DrugContour | 1.29 | 0.10 | 1.40 | |
Plot2DrugHeatmap | 0.49 | 0.01 | 0.50 | |
Plot2DrugSurface | 0.66 | 0.06 | 3.60 | |
PlotBarometer | 2.00 | 0.02 | 2.02 | |
PlotDoseResponse | 0 | 0 | 0 | |
PlotDoseResponseCurve | 0.19 | 0.00 | 0.18 | |
PlotMultiDrugBar | 2.78 | 0.06 | 2.85 | |
PlotMultiDrugSurface | 12.69 | 0.22 | 12.92 | |
PlotSensitivitySynergy | 2.98 | 0.11 | 3.09 | |
PlotSynergy | 1.70 | 0.01 | 1.72 | |
ReshapeData | 0.10 | 0.00 | 0.09 | |
ZIP | 0.5 | 0.0 | 0.5 | |