Shuyu Zheng
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/synergyfinder |
| Branch: RELEASE_3_12 |
| Last Commit: 5d572fb |
| Last Changed Date: 2021-04-21 10:12:08 -0400 (Wed, 21 Apr 2021) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:33:53 -0400 (Thu, 06 May 2021).
|
To the developers/maintainers of the synergyfinder package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1828/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| synergyfinder 2.4.16 (landing page) Shuyu Zheng
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: synergyfinder |
| Version: 2.4.16 |
| Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:synergyfinder.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings synergyfinder_2.4.16.tar.gz |
| StartedAt: 2021-05-06 07:26:08 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 07:29:52 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 223.9 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: synergyfinder.Rcheck |
| Warnings: 1 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:synergyfinder.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings synergyfinder_2.4.16.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/synergyfinder.Rcheck'
* using R version 4.0.5 (2021-03-31)
* 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 '2.4.16'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'drc', 'reshape2', 'tidyverse', 'dplyr', 'tidyr', 'purrr', 'furrr',
'ggplot2', 'ggforce', 'grid', 'vegan', 'gstat', 'sp',
'SpatialExtremes', 'ggrepel', 'kriging', 'plotly', 'stringr',
'future', 'mice', 'lattice', 'nleqslv', 'magrittr', 'pbapply', 'metR'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpMJlvGL/R.INSTALL284fd866a9/synergyfinder/man/Plot2DrugContour.Rd:73: file link 'wireframe' in package 'lattice' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpMJlvGL/R.INSTALL284fd866a9/synergyfinder/man/Plot2DrugHeatmap.Rd:79: file link 'wireframe' in package 'lattice' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpMJlvGL/R.INSTALL284fd866a9/synergyfinder/man/Plot2DrugSurface.Rd:87: file link 'wireframe' in package 'lattice' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpMJlvGL/R.INSTALL284fd866a9/synergyfinder/man/PlotDoseResponseCurve.Rd:73: file link 'plot.new' in package 'graphics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpMJlvGL/R.INSTALL284fd866a9/synergyfinder/man/PlotSensitiveSynergy.Rd:43: file link 'wireframe' in package 'lattice' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpMJlvGL/R.INSTALL284fd866a9/synergyfinder/man/dot-ScoreCurve_L4.Rd:10: file link 'L.4' in package 'drc' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpMJlvGL/R.INSTALL284fd866a9/synergyfinder/man/dot-ScoreCurve_L4.Rd:13: file link 'L.4' in package 'drc' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpMJlvGL/R.INSTALL284fd866a9/synergyfinder/man/dot-ScoreCurve_L4.Rd:16: file link 'L.4' in package 'drc' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpMJlvGL/R.INSTALL284fd866a9/synergyfinder/man/dot-ScoreCurve_L4.Rd:19: file link 'L.4' in package 'drc' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpMJlvGL/R.INSTALL284fd866a9/synergyfinder/man/dot-own_log.Rd:11: file link 'L.4' in package 'drc' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpMJlvGL/R.INSTALL284fd866a9/synergyfinder/man/dot-own_log.Rd:14: file link 'L.4' in package 'drc' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpMJlvGL/R.INSTALL284fd866a9/synergyfinder/man/dot-own_log.Rd:17: file link 'L.4' in package 'drc' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpMJlvGL/R.INSTALL284fd866a9/synergyfinder/man/dot-own_log2.Rd:11: file link 'L.4' in package 'drc' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.12-bioc/meat/synergyfinder.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
'drc' 'reshape2' 'tidyverse' 'dplyr' 'tidyr' 'purrr' 'furrr' 'ggplot2' 'ggforce' 'grid' 'vegan' 'gstat' 'sp' 'methods' 'SpatialExtremes' 'ggrepel' 'kriging' 'plotly' 'stringr' 'future' 'mice' 'lattice' 'nleqslv' 'stats' 'graphics' 'grDevices' 'magrittr' 'pbapply' 'metR'
A package should be listed in only one of these fields.
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... NOTE
Namespaces in Imports field not imported from:
'future' 'gstat' 'nleqslv' 'sp' 'tidyverse'
All declared Imports should be used.
Packages in Depends field not imported from:
'SpatialExtremes' 'dplyr' 'drc' 'furrr' 'future' 'ggforce' 'ggrepel'
'grid' 'gstat' 'kriging' 'lattice' 'metR' 'methods' 'mice' 'nleqslv'
'pbapply' 'plotly' 'purrr' 'reshape2' 'sp' 'stringr' 'tidyr'
'tidyverse' 'vegan'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* 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'
PlotDoseResponse: no visible binding for global variable 'grid'
PlotDoseResponseCurve: no visible binding for global variable 'respone'
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'
PlotSensitiveSynergy: no visible binding for global variable 'block_id'
PlotSensitiveSynergy: no visible binding for global variable 'css'
PlotSensitiveSynergy: no visible binding for global variable 'label'
PlotSensitiveSynergy: no visible binding for global variable 'synergy'
ReshapeData: no visible binding for global variable 'block_id'
ReshapeData: no visible binding for global variable 'response_origin'
ReshapeData: no visible binding for global variable 'n'
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 grid id input_type label left
metric n pred r respone 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", "grid", "text")
importFrom("stats", "end", "start")
importFrom("utils", "data")
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 examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
PlotMultiDrugSurface 9.75 0.3 10.05
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
PlotMultiDrugSurface 8.69 0.30 8.98
PlotMultiDrugBar 5.06 0.03 5.10
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 4 NOTEs
See
'C:/Users/biocbuild/bbs-3.12-bioc/meat/synergyfinder.Rcheck/00check.log'
for details.
synergyfinder.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/synergyfinder_2.4.16.tar.gz && rm -rf synergyfinder.buildbin-libdir && mkdir synergyfinder.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=synergyfinder.buildbin-libdir synergyfinder_2.4.16.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL synergyfinder_2.4.16.zip && rm synergyfinder_2.4.16.tar.gz synergyfinder_2.4.16.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 106k 100 106k 0 0 2324k 0 --:--:-- --:--:-- --:--:-- 2368k
install for i386
* 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
CalculateSens 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
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpMJlvGL/R.INSTALL284fd866a9/synergyfinder/man/Plot2DrugContour.Rd:73: file link 'wireframe' in package 'lattice' does not exist and so has been treated as a topic
Plot2DrugHeatmap html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpMJlvGL/R.INSTALL284fd866a9/synergyfinder/man/Plot2DrugHeatmap.Rd:79: file link 'wireframe' in package 'lattice' does not exist and so has been treated as a topic
Plot2DrugSurface html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpMJlvGL/R.INSTALL284fd866a9/synergyfinder/man/Plot2DrugSurface.Rd:87: file link 'wireframe' in package 'lattice' does not exist and so has been treated as a topic
PlotBarometer html
PlotDoseResponse html
PlotDoseResponseCurve html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpMJlvGL/R.INSTALL284fd866a9/synergyfinder/man/PlotDoseResponseCurve.Rd:73: file link 'plot.new' in package 'graphics' does not exist and so has been treated as a topic
PlotMultiDrugBar html
PlotMultiDrugSurface html
PlotSensitiveSynergy html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpMJlvGL/R.INSTALL284fd866a9/synergyfinder/man/PlotSensitiveSynergy.Rd:43: file link 'wireframe' in package 'lattice' does not exist and so has been treated as a topic
PlotSynergy html
PredictModelSpecify 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-Pt2mm html
dot-RoundValues html
dot-ScoreCurve html
dot-ScoreCurve_L4 html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpMJlvGL/R.INSTALL284fd866a9/synergyfinder/man/dot-ScoreCurve_L4.Rd:10: file link 'L.4' in package 'drc' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpMJlvGL/R.INSTALL284fd866a9/synergyfinder/man/dot-ScoreCurve_L4.Rd:13: file link 'L.4' in package 'drc' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpMJlvGL/R.INSTALL284fd866a9/synergyfinder/man/dot-ScoreCurve_L4.Rd:16: file link 'L.4' in package 'drc' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpMJlvGL/R.INSTALL284fd866a9/synergyfinder/man/dot-ScoreCurve_L4.Rd:19: file link 'L.4' in package 'drc' does not exist and so has been treated as a topic
dot-SolveExpDoesL4 html
dot-SolveExpDoesLL4 html
dot-SolveExpDose html
dot-SolveLoewe html
dot-own_log html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpMJlvGL/R.INSTALL284fd866a9/synergyfinder/man/dot-own_log.Rd:11: file link 'L.4' in package 'drc' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpMJlvGL/R.INSTALL284fd866a9/synergyfinder/man/dot-own_log.Rd:14: file link 'L.4' in package 'drc' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpMJlvGL/R.INSTALL284fd866a9/synergyfinder/man/dot-own_log.Rd:17: file link 'L.4' in package 'drc' does not exist and so has been treated as a topic
dot-own_log2 html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpMJlvGL/R.INSTALL284fd866a9/synergyfinder/man/dot-own_log2.Rd:11: file link 'L.4' in package 'drc' does not exist and so has been treated as a topic
mathews_screening_data html
** building package indices
** 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
install for x64
* installing *source* package 'synergyfinder' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'synergyfinder' as synergyfinder_2.4.16.zip
* DONE (synergyfinder)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'synergyfinder' successfully unpacked and MD5 sums checked
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synergyfinder.Rcheck/examples_i386/synergyfinder-Ex.timings
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synergyfinder.Rcheck/examples_x64/synergyfinder-Ex.timings
|