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This page was generated on 2024-06-11 15:43 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4679
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4414
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4441
kjohnson1macOS 13.6.6 Venturaarm644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4394
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 2060/2239HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
synergyfinder 3.13.0  (landing page)
Shuyu Zheng
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/synergyfinder
git_branch: devel
git_last_commit: 98b3790
git_last_commit_date: 2024-04-30 10:53:39 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published


CHECK results for synergyfinder on kjohnson1

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.

raw results


Summary

Package: synergyfinder
Version: 3.13.0
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_3.13.0.tar.gz
StartedAt: 2024-06-11 10:24:41 -0400 (Tue, 11 Jun 2024)
EndedAt: 2024-06-11 10:26:25 -0400 (Tue, 11 Jun 2024)
EllapsedTime: 104.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: synergyfinder.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### 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_3.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/synergyfinder.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* 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 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘synergyfinder/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘synergyfinder’ version ‘3.13.0’
* 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 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 20.702  0.294  21.117
PlotMultiDrugSurface 13.025  0.190  13.288
* 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-3.20-bioc/meat/synergyfinder.Rcheck/00check.log’
for details.


Installation output

synergyfinder.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL synergyfinder
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-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)

Tests output


Example timings

synergyfinder.Rcheck/synergyfinder-Ex.timings

nameusersystemelapsed
Bliss0.2340.0140.250
CalculateRI1.2420.0621.307
CalculateSensitivity20.702 0.29421.117
CalculateSynergy1.3480.0131.366
CorrectBaseLine0.1460.0020.149
ExtractSingleDrug0.1020.0020.104
FindModelType0.0130.0010.014
FitDoseResponse0.0150.0000.016
HSA0.1190.0030.122
Loewe0.2100.0020.213
Plot2DrugContour1.2880.0491.358
Plot2DrugHeatmap0.4340.0060.459
Plot2DrugSurface0.5980.0390.657
PlotBarometer1.9660.0242.006
PlotDoseResponse000
PlotDoseResponseCurve0.1710.0060.183
PlotMultiDrugBar2.1250.0322.220
PlotMultiDrugSurface13.025 0.19013.288
PlotSensitivitySynergy2.9640.0523.030
PlotSynergy1.4870.0161.514
ReshapeData0.0980.0020.100
ZIP0.5260.0080.539