Shuyu Zheng
| Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022) |
| git_url: https://git.bioconductor.org/packages/synergyfinder |
| git_branch: RELEASE_3_15 |
| git_last_commit: a8b8c40 |
| git_last_commit_date: 2022-10-11 10:22:07 -0400 (Tue, 11 Oct 2022) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-10-19 13:22:23 -0400 (Wed, 19 Oct 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4386 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" | 4138 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4205 |
| 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? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1970/2140 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| synergyfinder 3.4.5 (landing page) Shuyu Zheng
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| 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: 3.4.5 |
| Command: F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:synergyfinder.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings synergyfinder_3.4.5.tar.gz |
| StartedAt: 2022-10-19 04:41:42 -0400 (Wed, 19 Oct 2022) |
| EndedAt: 2022-10-19 04:43:41 -0400 (Wed, 19 Oct 2022) |
| EllapsedTime: 119.6 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: synergyfinder.Rcheck |
| Warnings: 2 |
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###
### Running command:
###
### F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:synergyfinder.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings synergyfinder_3.4.5.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/synergyfinder.Rcheck'
* using R version 4.2.1 (2022-06-23 ucrt)
* using platform: x86_64-w64-mingw32 (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 '3.4.5'
* 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 ... WARNING
Codoc mismatches from documentation object 'PlotDoseResponse':
PlotDoseResponse
Code: function(data, block_ids = c(1), drugs = c(1, 2), adjusted =
TRUE, statistic = NULL, summary_statistic = "mean",
high_value_color = "#FF0000", low_value_color =
"#00FF00", point_color = "#C24B40", curve_color =
"black", curve_ylim = NULL, curve_grid = TRUE,
text_size_scale = 1, heatmap_text_label_size_scale =
1, heatmap_text_label_color = "#000000",
heatmap_color_range = NULL, curve_plot_title = NULL,
heatmap_plot_title = NULL, Emin = NA, Emax = NA,
save_file = FALSE, file_type = "pdf", file_name =
NULL, width = 12, height = 6)
Docs: function(data, block_ids = c(1), drugs = c(1, 2), adjusted =
TRUE, statistic = NULL, summary_statistic = "mean",
high_value_color = "#A90217", low_value_color =
"#2166AC", point_color = "#C24B40", curve_color =
"black", curve_ylim = NULL, curve_grid = TRUE,
text_size_scale = 1, heatmap_text_label_size_scale =
1, heatmap_text_label_color = "#000000",
heatmap_color_range = NULL, curve_plot_title = NULL,
heatmap_plot_title = NULL, Emin = NA, Emax = NA,
save_file = FALSE, file_type = "pdf", file_name =
NULL, width = 12, height = 6)
Mismatches in argument default values:
Name: 'high_value_color' Code: "#FF0000" Docs: "#A90217"
Name: 'low_value_color' Code: "#00FF00" Docs: "#2166AC"
Codoc mismatches from documentation object 'PlotDoseResponseCurve':
PlotDoseResponseCurve
Code: function(data, plot_block = 1, drug_index = 1, adjusted = TRUE,
Emin = NA, Emax = NA, grid = TRUE, point_color =
"#C24B40", curve_color = "black", text_size_scale = 1,
plot_title = NULL, plot_subtitle = NULL, plot_setting
= list(cex.lab = 1 * text_size_scale, mgp = c(2, 0.5,
0), font.main = 2, font.lab = 1, cex.main = 14/12 *
text_size_scale, bty = "l", lwd = 1.5), plot_new =
TRUE, record_plot = TRUE, ...)
Docs: function(data, plot_block = 1, drug_index = 1, adjusted = TRUE,
Emin = NA, Emax = NA, grid = TRUE, point_color =
"#C24B40", curve_color = "black", text_size_scale = 1,
plot_title = NULL, plot_subtitle = NULL, plot_setting
= list(cex.lab = 1 * text_size_scale, mgp = c(2, 0.5,
0), font.main = 2, font.lab = 1, cex.main = 14/12 *
text_size_scale, bty = "l", lwd = 1.5), ylim = NULL,
plot_new = TRUE, record_plot = TRUE)
Argument names in code not in docs:
...
Argument names in docs not in code:
ylim
Mismatches in argument names:
Position: 14 Code: plot_new Docs: ylim
Position: 15 Code: record_plot Docs: plot_new
Position: 16 Code: ... Docs: record_plot
Codoc mismatches from documentation object 'PlotSynergy':
PlotSynergy
Code: function(data, type = "2D", method = "ZIP", block_ids = c(1),
drugs = c(1, 2), row_range = NULL, col_range = NULL,
color_range = NULL, z_range = NULL, axis_line = FALSE,
statistic = NULL, summary_statistic = "mean",
plot_title = NULL, interpolate_len = 3,
high_value_color = "#FF0000", low_value_color =
"#00FF00", text_size_scale = 1,
heatmap_text_label_size_scale = 1,
heatmap_text_label_color = "#000000", grid = TRUE,
dynamic = FALSE, display = TRUE, save_file = FALSE,
file_type = "pdf", file_name = NULL, file_path = NULL,
height = 6, width = 6, units = "in")
Docs: function(data, type = "2D", method = "ZIP", block_ids = c(1),
drugs = c(1, 2), row_range = NULL, col_range = NULL,
color_range = NULL, z_range = NULL, axis_line = FALSE,
statistic = NULL, summary_statistic = "mean",
plot_title = NULL, interpolate_len = 3,
high_value_color = "#A90217", low_value_color =
"#2166AC", text_size_scale = 1,
heatmap_text_label_size_scale = 1,
heatmap_text_label_color = "#000000", grid = TRUE,
dynamic = FALSE, display = TRUE, save_file = FALSE,
file_type = "pdf", file_name = NULL, file_path = NULL,
height = 6, width = 6, units = "in")
Mismatches in argument default values:
Name: 'high_value_color' Code: "#FF0000" Docs: "#A90217"
Name: 'low_value_color' Code: "#00FF00" Docs: "#2166AC"
* 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 24.49 0.54 25.05
PlotMultiDrugSurface 10.64 0.24 10.89
PlotMultiDrugBar 5.11 0.12 5.23
* 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: 2 WARNINGs, 1 NOTE
See
'F:/biocbuild/bbs-3.15-bioc/meat/synergyfinder.Rcheck/00check.log'
for details.
synergyfinder.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL synergyfinder ### ############################################################################## ############################################################################## * installing to library 'F:/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 ** 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 | 0.29 | 0.02 | 0.32 | |
| CalculateRI | 1.18 | 0.11 | 1.28 | |
| CalculateSensitivity | 24.49 | 0.54 | 25.05 | |
| CalculateSynergy | 1.21 | 0.04 | 1.25 | |
| CorrectBaseLine | 0.21 | 0.00 | 0.20 | |
| ExtractSingleDrug | 0.20 | 0.00 | 0.21 | |
| FindModelType | 0.02 | 0.00 | 0.01 | |
| FitDoseResponse | 0.01 | 0.00 | 0.02 | |
| HSA | 0.22 | 0.01 | 0.23 | |
| Loewe | 0.33 | 0.00 | 0.33 | |
| Plot2DrugContour | 1.06 | 0.11 | 1.17 | |
| Plot2DrugHeatmap | 0.34 | 0.02 | 0.36 | |
| Plot2DrugSurface | 0.55 | 0.04 | 1.30 | |
| PlotBarometer | 1.74 | 0.03 | 1.76 | |
| PlotDoseResponse | 0 | 0 | 0 | |
| PlotDoseResponseCurve | 0.25 | 0.04 | 0.29 | |
| PlotMultiDrugBar | 5.11 | 0.12 | 5.23 | |
| PlotMultiDrugSurface | 10.64 | 0.24 | 10.89 | |
| PlotSensitivitySynergy | 3.09 | 0.07 | 3.17 | |
| PlotSynergy | 1.80 | 0.05 | 1.85 | |
| ReshapeData | 0.18 | 0.00 | 0.18 | |
| ZIP | 0.80 | 0.05 | 0.86 | |