Shuyu Zheng
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/synergyfinder |
| git_branch: master |
| git_last_commit: f5b5ab3 |
| git_last_commit_date: 2022-03-04 04:17:39 -0400 (Fri, 04 Mar 2022) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:08:49 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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 | ||||
|
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 1925/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| synergyfinder 3.3.8 (landing page) Shuyu Zheng
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: synergyfinder |
| Version: 3.3.8 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:synergyfinder.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings synergyfinder_3.3.8.tar.gz |
| StartedAt: 2022-03-17 20:26:39 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 20:28:14 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 94.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: synergyfinder.Rcheck |
| Warnings: 1 |
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:synergyfinder.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings synergyfinder_3.3.8.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/synergyfinder.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'synergyfinder/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'synergyfinder' version '3.3.8'
* 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 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 ... 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'
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'
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 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 end head id input_type label left
maxn metric n nn 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("graphics", "text")
importFrom("stats", "end", "start")
importFrom("utils", "data", "head")
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
CalculateSensitivity 16.67 0.36 17.03
PlotMultiDrugSurface 8.78 0.47 9.26
* 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 WARNING, 1 NOTE
See
'D:/biocbuild/bbs-3.15-bioc/meat/synergyfinder.Rcheck/00check.log'
for details.
synergyfinder.Rcheck/00install.out
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL synergyfinder
###
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* installing to library 'D:/biocbuild/bbs-3.15-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
converting help for package 'synergyfinder'
finding HTML links ... done
Bliss html
CalculateCSS html
CalculateIC50 html
CalculateRI html
CalculateSensitivity html
CalculateSynergy html
CorrectBaseLine html
DimensionReduction html
ExtractSingleDrug html
FindModelPar html
FindModelType html
FitDoseResponse html
GenerateSurface html
HSA html
HighlightBarPlot html
ImputeIC50 html
Loewe html
NCATS_screening_data html
ONEIL_screening_data html
Plot2DrugContour html
Plot2DrugHeatmap html
Plot2DrugSurface html
PlotBarometer html
PlotDoseResponse html
PlotDoseResponseCurve html
PlotMultiDrugBar html
PlotMultiDrugSurface html
PlotSensitivitySynergy html
PlotSynergy html
PredictResponse html
ReshapeData html
ZIP html
dot-AdjustColumnName html
dot-Bootstrapping html
dot-Distance html
dot-ExtendedScores html
dot-Extract2DrugPlotData html
dot-ExtractMultiDrugPlotData html
dot-Own_log html
dot-Own_log2 html
dot-PredictResponseFromModel html
dot-Pt2mm html
dot-RoundValues html
dot-ScoreCurve html
dot-ScoreCurve_L4 html
dot-SolveExpDoesL4 html
dot-SolveExpDoesLL4 html
dot-SolveExpDose html
dot-SolveLoewe html
mathews_screening_data html
** 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)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'nanotatoR' is missing or broken
done
synergyfinder.Rcheck/synergyfinder-Ex.timings
| name | user | system | elapsed | |
| Bliss | 0.31 | 0.02 | 0.33 | |
| CalculateRI | 0.97 | 0.12 | 1.09 | |
| CalculateSensitivity | 16.67 | 0.36 | 17.03 | |
| CalculateSynergy | 1.53 | 0.00 | 1.53 | |
| CorrectBaseLine | 0.19 | 0.00 | 0.19 | |
| ExtractSingleDrug | 0.14 | 0.00 | 0.14 | |
| FindModelType | 0.01 | 0.00 | 0.02 | |
| FitDoseResponse | 0 | 0 | 0 | |
| HSA | 0.18 | 0.00 | 0.17 | |
| Loewe | 0.22 | 0.00 | 0.22 | |
| Plot2DrugContour | 0.93 | 0.04 | 0.98 | |
| Plot2DrugHeatmap | 0.5 | 0.0 | 0.5 | |
| Plot2DrugSurface | 0.58 | 0.05 | 0.72 | |
| PlotBarometer | 1.36 | 0.00 | 1.36 | |
| PlotDoseResponse | 0 | 0 | 0 | |
| PlotDoseResponseCurve | 0.22 | 0.00 | 0.22 | |
| PlotMultiDrugBar | 4.11 | 0.06 | 4.17 | |
| PlotMultiDrugSurface | 8.78 | 0.47 | 9.26 | |
| PlotSensitivitySynergy | 2.25 | 0.08 | 2.33 | |
| PlotSynergy | 1.11 | 0.00 | 1.11 | |
| ReshapeData | 0.16 | 0.00 | 0.16 | |
| ZIP | 0.40 | 0.02 | 0.42 | |