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This page was generated on 2025-10-18 12:05 -0400 (Sat, 18 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4887
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4677
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4622
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4632
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 2041/2353HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SmartPhos 0.99.30  (landing page)
Shubham Agrawal
Snapshot Date: 2025-10-17 13:45 -0400 (Fri, 17 Oct 2025)
git_url: https://git.bioconductor.org/packages/SmartPhos
git_branch: devel
git_last_commit: 38bf3de
git_last_commit_date: 2025-10-01 09:40:06 -0400 (Wed, 01 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for SmartPhos on lconway

To the developers/maintainers of the SmartPhos package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SmartPhos.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: SmartPhos
Version: 0.99.30
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SmartPhos.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SmartPhos_0.99.30.tar.gz
StartedAt: 2025-10-18 01:37:30 -0400 (Sat, 18 Oct 2025)
EndedAt: 2025-10-18 01:43:33 -0400 (Sat, 18 Oct 2025)
EllapsedTime: 363.4 seconds
RetCode: 0
Status:   OK  
CheckDir: SmartPhos.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SmartPhos.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SmartPhos_0.99.30.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/SmartPhos.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SmartPhos/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SmartPhos’ version ‘0.99.30’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 36 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 ‘SmartPhos’ can be installed ... OK
* checking installed package size ... INFO
  installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data        1.3Mb
    shiny-app   5.4Mb
* 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
Namespaces in Imports field not imported from:
  ‘DT’ ‘XML’ ‘cowplot’ ‘factoextra’ ‘ggbeeswarm’ ‘grid’ ‘plotly’
  ‘shinyBS’ ‘shinyWidgets’ ‘shinyjs’ ‘shinythemes’ ‘tools’
  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
runFisher: no visible binding for global variable ‘signature’
runGSEAforPhospho: no visible binding for global variable ‘signature’
Undefined global functions or variables:
  signature
Consider adding
  importFrom("methods", "signature")
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 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
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 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-3.22-bioc/meat/SmartPhos.Rcheck/00check.log’
for details.


Installation output

SmartPhos.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘SmartPhos’ ...
** this is package ‘SmartPhos’ version ‘0.99.30’
** 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 (SmartPhos)

Tests output

SmartPhos.Rcheck/tests/testthat.Rout


R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
> 
> library(testthat)
> library(SmartPhos)
> 
> test_check("SmartPhos")
harmonizing input:
  removing 5 sampleMap rows not in names(experiments)
harmonizing input:
  removing 5 sampleMap rows not in names(experiments)
Running gene set analysis:
Checking arguments...done!
Final gene/gene-set association: 20 genes and 22 gene sets
  Details:
  Calculating gene set statistics from 20 out of 65 gene-level statistics
  Removed 4366 genes from GSC due to lack of matching gene statistics
  Removed 28 gene sets containing no genes after gene removal
  Removed additionally 0 gene sets not matching the size limits
  Loaded additional information for 22 gene sets
Calculating gene set statistics...done!
Calculating gene set significance...done!
Adjusting for multiple testing...done!
Running gene set analysis:
Checking arguments...done!
Final gene/gene-set association: 20 genes and 22 gene sets
  Details:
  Calculating gene set statistics from 20 out of 65 gene-level statistics
  Removed 4366 genes from GSC due to lack of matching gene statistics
  Removed 28 gene sets containing no genes after gene removal
  Removed additionally 0 gene sets not matching the size limits
  Loaded additional information for 22 gene sets
Calculating gene set statistics...done!
Calculating gene set significance...done!
Adjusting for multiple testing...done!
Imputing along margin 2 (samples/columns).
Imputing along margin 2 (samples/columns).
New names:
* `` -> `...1`
* `` -> `...2`
* `` -> `...3`
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 309 ]
> 
> proc.time()
   user  system elapsed 
 72.946   5.047  79.354 

Example timings

SmartPhos.Rcheck/SmartPhos-Ex.timings

nameusersystemelapsed
Homo_sapien_kinase_substrate_network0.0870.0040.093
Mus_musculus_kinase_substrate_network0.0630.0020.065
addZeroTime0.4230.0240.454
calcKinaseScore0.9230.0500.978
clusterEnrich1.3730.0541.438
clusterTS1.2800.0451.331
dda_example0.0040.0020.005
dia_example0.0080.0020.010
enrichDifferential0.5930.0270.629
getDecouplerNetwork0.7641.1511.941
getRatioMatrix0.7770.0240.804
intensityBoxPlot1.6770.0431.730
makeSmartPhosDirectory0.0030.0400.051
medianNorm0.0000.0010.001
mscale0.0010.0010.001
normByFullProteome0.3600.0050.369
performCombinedNormalization0.1650.2260.397
performDifferentialExp0.4450.0210.473
plotHeatmap0.5530.0230.582
plotIntensity1.2760.0261.308
plotKinaseDE0.4420.0030.446
plotKinaseTimeSeries0.3800.0030.385
plotLogRatio1.2090.0101.225
plotMissing0.4690.0210.492
plotPCA0.3050.0040.309
plotTimeSeries0.6760.0220.711
plotVolcano0.7580.0210.785
preprocessPhos0.4640.0190.486
preprocessProteome0.4370.0190.457
readExperiment0.1730.0040.178
readExperimentDIA3.2930.5883.986
readPhosphoExperiment0.0270.0050.033
readPhosphoExperimentDIA1.8320.3162.147
readProteomeExperiment0.0270.0070.034
readProteomeExperimentDIA1.7690.4102.174
runFisher0.5700.0700.648
runSmartPhos000
swissProt0.2260.0230.252