Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-07-24 11:41 -0400 (Wed, 24 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4688
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4284
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4455
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4404
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 243/2248HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
broadSeq 0.99.3  (landing page)
Rishi Das Roy
Snapshot Date: 2024-07-23 14:00 -0400 (Tue, 23 Jul 2024)
git_url: https://git.bioconductor.org/packages/broadSeq
git_branch: devel
git_last_commit: 788035b
git_last_commit_date: 2024-06-05 05:25:26 -0400 (Wed, 05 Jun 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  ERROR    ERROR  skippedskipped
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for broadSeq on kjohnson3

To the developers/maintainers of the broadSeq package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/broadSeq.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: broadSeq
Version: 0.99.3
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:broadSeq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings broadSeq_0.99.3.tar.gz
StartedAt: 2024-07-23 20:22:02 -0400 (Tue, 23 Jul 2024)
EndedAt: 2024-07-23 20:23:42 -0400 (Tue, 23 Jul 2024)
EllapsedTime: 100.0 seconds
RetCode: 0
Status:   OK  
CheckDir: broadSeq.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:broadSeq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings broadSeq_0.99.3.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/broadSeq.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 13.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘broadSeq/DESCRIPTION’ ... OK
* this is package ‘broadSeq’ version ‘0.99.3’
* 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 ‘broadSeq’ 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 ... NOTE
Namespace in Imports field not imported from: ‘BiocStyle’
  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
genes_plot: warning in facet(facet.by, scale = "free"): partial
  argument match of 'scale' to 'scales'
volcanoPlot: warning in ggscatter(x = lFCName, y = "padj", color =
  "Significant", palette = palette, title = "Volcano plot", label =
  labelName, repel = TRUE, label.rectangle = TRUE, show.legend = FALSE,
  label.select = selectedLabel): partial argument match of
  'show.legend' to 'show.legend.text'
assay_plot: no visible global function definition for ‘ggarrange’
assay_plot: no visible global function definition for ‘text_grob’
biplotAnyPC: no visible binding for global variable ‘PC’
biplotAnyPC: no visible binding for global variable ‘var_pct’
biplotAnyPC: no visible global function definition for ‘pull’
biplotAnyPC: no visible binding for global variable ‘gene’
biplotAnyPC: no visible global function definition for ‘aes’
biplotAnyPC: no visible global function definition for ‘arrow’
biplotAnyPC: no visible global function definition for ‘unit’
combinedEnrichment: no visible global function definition for
  ‘keytypes’
extract_topGeneLoadings: no visible global function definition for
  ‘desc’
extract_topGeneLoadings: no visible global function definition for
  ‘all_of’
genes_plot: no visible global function definition for ‘rowData’
normalizeEdgerCPM: no visible global function definition for ‘is’
plotAnyPC: no visible binding for global variable ‘PC’
plotAnyPC: no visible binding for global variable ‘var_pct’
plotHeatmapCluster: no visible global function definition for ‘is’
plotHeatmapCluster: no visible global function definition for ‘colData’
plotHeatmapCluster: no visible global function definition for ‘rowData’
plotHeatmapCluster: no visible global function definition for ‘all_of’
plot_MDS: no visible global function definition for ‘is’
plot_MDS: no visible global function definition for ‘dist’
plot_MDS: no visible global function definition for ‘cmdscale’
plot_MDS: no visible global function definition for ‘colData’
prcompTidy: no visible global function definition for ‘is’
prcompTidy: no visible global function definition for ‘prcomp’
prcompTidy: no visible binding for global variable ‘stdev’
prcompTidy: no visible binding for global variable ‘var’
prcompTidy: no visible binding for global variable ‘var_pct’
prcompTidy: no visible binding for global variable ‘PC’
prcompTidy: no visible binding for global variable ‘.’
prcompTidy: no visible binding for global variable ‘gene’
transformDESeq2: no visible global function definition for ‘is’
transformDESeq2: no visible global function definition for ‘assays<-’
transformDESeq2: no visible global function definition for ‘assay’
use_DELocal: no visible global function definition for ‘desc’
use_DELocal: no visible binding for global variable ‘relative.logFC’
use_EBSeq: no visible global function definition for ‘desc’
use_EBSeq: no visible binding for global variable ‘PPDE’
use_NOIseq: no visible global function definition for ‘desc’
use_NOIseq: no visible binding for global variable ‘prob’
use_SAMseq: no visible binding for global variable ‘q-value(%)’
use_deseq2: no visible binding for global variable ‘padj’
use_edgeR: no visible binding for global variable ‘logFC’
use_edgeR: no visible binding for global variable ‘FDR’
use_edgeR: no visible global function definition for ‘:=’
use_limma: no visible global function definition for ‘par’
use_limma: no visible binding for global variable ‘logFC’
use_limma: no visible binding for global variable ‘B’
use_limma: no visible global function definition for ‘:=’
volcanoPlot: no visible global function definition for ‘labs’
volcanoPlot: no visible global function definition for ‘geom_abline’
Undefined global functions or variables:
  . := B FDR PC PPDE aes all_of arrow assay assays<- cmdscale colData
  desc dist gene geom_abline ggarrange is keytypes labs logFC padj par
  prcomp prob pull q-value(%) relative.logFC rowData stdev text_grob
  unit var var_pct
Consider adding
  importFrom("graphics", "par")
  importFrom("methods", "is")
  importFrom("stats", "cmdscale", "dist", "prcomp", "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/broadSeq.Rcheck/00check.log’
for details.


Installation output

broadSeq.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘broadSeq’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (broadSeq)

Tests output


Example timings

broadSeq.Rcheck/broadSeq-Ex.timings

nameusersystemelapsed
genes_plot1.0200.0311.054
normalizeEdgerCPM0.5650.0220.587
plotHeatmapCluster0.1390.0040.145
plot_MDS2.1990.0332.233
prcompTidy0.6210.0130.635
round_df0.0020.0020.007
sampleAssay_plot2.6630.1412.806
transformDESeq22.0490.0272.077
use_DELocal0.8360.0190.856
use_EBSeq0.2260.0080.235
use_NOIseq0.1590.0020.161
use_deseq21.1530.0031.156
use_edgeR0.1100.0020.112
use_limma0.0580.0020.060
use_multDE2.2730.0182.291