===============================
BiocCheckGitClone('SmartPhos')
===============================
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3609/8c717a4c3938d36ec1da439bc5dfc81f05fd4f98/SmartPhos
BiocVersion: 3.21
Package: SmartPhos
PackageVersion: 0.99.5
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3609/8c717a4c3938d36ec1da439bc5dfc81f05fd4f98/SmartPhos.BiocCheck
BiocCheckVersion: 1.43.12
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3609/8c717a4c3938d36ec1da439bc5dfc81f05fd4f98/SmartPhos
installDir: NULL
isTarBall: FALSE
platform: unix
* Checking valid files...
* Checking individual file sizes...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
i NOTE: (Optional) CITATION file not found. Only include a CITATION file if
there is a preprint or publication for this Bioconductor package. Note that
Bioconductor packages are not required to have a CITATION file but it is useful
both for users and for tracking Bioconductor project-wide metrics. When
including a CITATION file, add the publication using the 'doi' argument of
'bibentry()'.
BiocCheck v1.43.12 results
0 ERRORS | 0 WARNINGS | i 1 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory /home/pkgbuild/packagebuilder/workers/jobs/3609/8c717a4c3938d36ec1da439bc5dfc81f05fd4f98/SmartPhos.Rcheck
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* using option --no-vignettes
* checking for file SmartPhos/DESCRIPTION ... OK
* checking extension type ... Package
* this is package SmartPhos version 0.99.5
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 35 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 5.9Mb
sub-directories of 1Mb or more:
data 1.3Mb
shiny-app 4.1Mb
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking build directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
LICENSE
is not mentioned in the DESCRIPTION file.
* 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 ... [11s/11s] OK
* checking whether the package can be loaded with stated dependencies ... [11s/11s] OK
* checking whether the package can be unloaded cleanly ... [11s/11s] OK
* checking whether the namespace can be loaded with stated dependencies ... [11s/11s] OK
* checking whether the namespace can be unloaded cleanly ... [11s/11s] OK
* checking loading without being on the library search path ... [11s/11s] OK
* checking use of S3 registration ... 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 ... [37s/37s] NOTE
calcKinaseScore: no visible binding for global variable site
calcKinaseScore: no visible binding for global variable stat
calcKinaseScore: no visible binding for global variable log2FC
calcKinaseScore: no visible binding for global variable target
calcKinaseScore: no visible binding for global variable correlation
calcKinaseScore: no visible binding for global variable statistic
calcKinaseScore: no visible binding for global variable condition
calcKinaseScore: no visible binding for global variable score
calcKinaseScore: no visible binding for global variable p_value
clusterEnrich : <anonymous>: no visible binding for global variable
cluster
clusterEnrich: no visible binding for global variable padj
clusterEnrich: no visible binding for global variable Name
clusterEnrich: no visible binding for global variable ifSig
clusterEnrich: no visible binding for global variable atLeast1
clusterEnrich: no visible binding for global variable pval
clusterEnrich: no visible binding for global variable cluster
clusterTS: no visible binding for global variable prob
clusterTS: no visible binding for global variable feature
clusterTS: no visible binding for global variable cluster
clusterTS: no visible binding for global variable cNum
clusterTS: no visible binding for global variable time
clusterTS: no visible binding for global variable value
clusterTS: no visible binding for global variable timeTreat
clusterTS: no visible binding for global variable treatment
clusterTS: no visible binding for global variable geneGroup
enrichDifferential: no visible binding for global variable pvalue
enrichDifferential: no visible binding for global variable Gene
enrichDifferential: no visible binding for global variable stat
enrichDifferential: no visible binding for global variable gseMethod
enrichDifferential: no visible binding for global variable p.up.adj
enrichDifferential: no visible binding for global variable p.down.adj
enrichDifferential: no visible global function definition for desc
enrichDifferential: no visible binding for global variable Stat
enrichDifferential: no visible binding for global variable p.up
enrichDifferential: no visible binding for global variable p.down
enrichDifferential: no visible binding for global variable site
enrichDifferential: no visible binding for global variable Name
enrichDifferential: no visible binding for global variable
Site.number
enrichDifferential: no visible binding for global variable Number.up
enrichDifferential: no visible binding for global variable
Number.down
enrichDifferential: no visible binding for global variable
Number.pSite.Db
enrichDifferential: no visible binding for global variable
Number.PTM.site.Db
enrichDifferential: no visible binding for global variable padj
getDecouplerNetwork: no visible binding for global variable
Homo_sapien_kinase_substrate_network
getDecouplerNetwork: no visible binding for global variable
Mus_musculus_kinase_substrate_network
intensityBoxPlot: no visible binding for global variable group
intensityBoxPlot: no visible binding for global variable value
intensityBoxPlot: no visible binding for global variable subjectID
mscale : <anonymous>: no visible global function definition for
meanAD
performDifferentialExp: no visible binding for global variable logFC
performDifferentialExp: no visible binding for global variable
P.Value
performDifferentialExp: no visible binding for global variable
adj.P.Val
performDifferentialExp: no visible binding for global variable
Row.names
performDifferentialExp: no visible binding for global variable B
performDifferentialExp: no visible binding for global variable
AveExpr
performDifferentialExp: no visible binding for global variable padj
performDifferentialExp: no visible binding for global variable pvalue
performDifferentialExp: no visible binding for global variable
t_statistic
performDifferentialExp: no visible binding for global variable pval
performDifferentialExp: no visible binding for global variable
adj_pval
performDifferentialExp: no visible binding for global variable df
performDifferentialExp: no visible binding for global variable
avg_abundance
performDifferentialExp: no visible binding for global variable
n_approx
performDifferentialExp: no visible binding for global variable n_obs
plotAdjustmentResults: no visible binding for global variable id
plotAdjustmentResults: no visible binding for global variable
adjustment
plotAdjustmentResults: no visible binding for global variable ratio
plotAdjustmentResults: no visible binding for global variable medVal
plotHeatmap: no visible binding for global variable stat
plotIntensity: no visible binding for global variable id
plotIntensity: no visible binding for global variable value
plotIntensity: no visible binding for global variable name
plotKinaseDE: no visible binding for global variable p_value
plotKinaseDE: no visible binding for global variable score
plotKinaseDE: no visible binding for global variable score_sign
plotKinaseDE: no visible binding for global variable significance
plotKinaseTimeSeries: no visible binding for global variable p_value
plotKinaseTimeSeries: no visible binding for global variable
timepoint
plotKinaseTimeSeries: no visible binding for global variable
Activity_score
plotKinaseTimeSeries: no visible binding for global variable sig
plotLogRatio: no visible binding for global variable feature
plotLogRatio: no visible binding for global variable value
plotLogRatio: no visible binding for global variable name
plotMissing: no visible binding for global variable perNA
plotTimeSeries: no visible binding for global variable time
plotTimeSeries: no visible binding for global variable value
plotTimeSeries: no visible binding for global variable subjectID
plotVolcano: no visible binding for global variable log2FC
plotVolcano: no visible binding for global variable pvalue
plotVolcano: no visible binding for global variable Gene
plotVolcano: no visible binding for global variable ID
readPhosphoExperimentDIA : <anonymous>: no visible binding for global
variable swissProt
runFisher: no visible binding for global variable category
runFisher: no visible binding for global variable site.ptm
runFisher: no visible binding for global variable site.direction
runFisher: no visible binding for global variable site.annotation
runFisher: no visible binding for global variable Set.size
runFisher: no visible binding for global variable pval
runGSEAforPhospho: no visible binding for global variable category
runGSEAforPhospho: no visible binding for global variable site.ptm
runGSEAforPhospho: no visible binding for global variable
site.annotation
runGSEAforPhospho: no visible binding for global variable nSite
runGSEAforPhospho: no visible binding for global variable enrichScore
runGSEAforPhospho: no visible binding for global variable pvalue
runMatrixQCvis: no visible global function definition for shinyQC
splineFilter: no visible binding for global variable p
splineFilter: no visible global function definition for relevel
Undefined global functions or variables:
Activity_score AveExpr B Gene Homo_sapien_kinase_substrate_network ID
Mus_musculus_kinase_substrate_network Name Number.PTM.site.Db
Number.down Number.pSite.Db Number.up P.Value Row.names Set.size
Site.number Stat adj.P.Val adj_pval adjustment atLeast1 avg_abundance
cNum category cluster condition correlation desc df enrichScore
feature geneGroup group gseMethod id ifSig log2FC logFC meanAD medVal
nSite n_approx n_obs name p p.down p.down.adj p.up p.up.adj p_value
padj perNA prob pval pvalue ratio relevel score score_sign shinyQC
sig significance site site.annotation site.direction site.ptm stat
statistic subjectID swissProt t_statistic target time timeTreat
timepoint treatment value
Consider adding
importFrom("stats", "df", "relevel", "time")
to your NAMESPACE file.
Found the following calls to data() loading into the global environment:
File SmartPhos/R/helper.R:
data("swissProt")
File SmartPhos/R/kinase_activity.R:
data("Homo_sapien_kinase_substrate_network")
data("Mus_musculus_kinase_substrate_network")
See section Good practice in ?data.
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'addZeroTime.Rd':
\examples lines wider than 100 characters:
addZeroTime(se, condition = "treatment", treat = "EGF", zeroTreat = "1stCrtl", timeRange = c("20min","40min", "6h"))
Rd file 'calcKinaseScore.Rd':
\examples lines wider than 100 characters:
site = c("EGFR_Y1172", "EGFR_Y1197", "EGFR_S1166", "ROCK2_S1374", "WASL_Y256", "GAB1_Y259", "ADD1_S586", "EPHA2_Y772", "PRKDC_T2638", " ... [TRUNCATED]
stat = c(-10.038770, -5.945562, 5.773384, -7.303834, 5.585326, 5.971104, 5.199119, -5.169500, 5.130228, 5.407387, 4.493933),
log2FC = c(-2.6113343, -2.4858615, 1.0056629, -1.1561780, 1.6421145, 2.0296634, 1.3766283, -0.8531656, 1.0742881, 1.0042942, 1.0608129)
target = c("EGFR_Y1172", "EGFR_Y1197", "EGFR_S1166", "ROCK2_S1374", "WASL_Y256", "GAB1_Y259", "ADD1_S586", "EPHA2_Y772", "PRKDC_T2638", ... [TRUNCATED]
Rd file 'clusterEnrich.Rd':
\examples lines wider than 100 characters:
result <- addZeroTime(seProcess, condition = "treatment", treat = "EGF", zeroTreat = "1stCrtl", timeRange = c("20min","40min", "6h"))
Rd file 'clusterTS.Rd':
\examples lines wider than 100 characters:
result <- addZeroTime(seProcess, condition = "treatment", treat = "EGF", zeroTreat = "1stCrtl", timeRange = c("20min","40min", "6h"))
Rd file 'enrichDifferential.Rd':
\examples lines wider than 100 characters:
dea <- performDifferentialExp(se = result, assay = "Intensity", method = "limma", reference = "1stCrtl", target = "EGF", condition = "t ... [TRUNCATED]
resTab <- enrichDifferential(dea = dea$resDE, type = "Pathway enrichment", gsaMethod = "PAGE", geneSet = inGMT, statType = "stat", nPer ... [TRUNCATED]
Rd file 'intensityBoxPlot.Rd':
\examples lines wider than 100 characters:
de <- performDifferentialExp(se = result, assay = "Intensity", method = "limma", reference = "1stCrtl", target = "EGF", condition = "tr ... [TRUNCATED]
Rd file 'performDifferentialExp.Rd':
\examples lines wider than 100 characters:
performDifferentialExp(se = result, assay = "Intensity", method = "limma", reference = "1stCrtl", target = "EGF", condition = "treatmen ... [TRUNCATED]
Rd file 'plotPCA.Rd':
\examples lines wider than 100 characters:
pcaResult <- stats::prcomp(t(SummarizedExperiment::assays(result)[["imputed"]]), center = TRUE, scale.=TRUE)
Rd file 'plotTimeSeries.Rd':
\examples lines wider than 100 characters:
plotTimeSeries(result, type = "expression", geneID = "p18", symbol = "TMEM238", condition = "treatment", treatment = "EGF", timerange = ... [TRUNCATED]
Rd file 'plotVolcano.Rd':
\examples lines wider than 100 characters:
de <- performDifferentialExp(se = result, assay = "Intensity", method = "limma", reference = "1stCrtl", target = "EGF", condition = "tr ... [TRUNCATED]
Rd file 'readExperiment.Rd':
\examples lines wider than 100 characters:
readExperiment(fileTable, localProbCut = 0.75, scoreDiffCut = 5, fdrCut = 0.1, scoreCut = 10, pepNumCut = 1, ifLFQ = TRUE, annotation_c ... [TRUNCATED]
Rd file 'readExperimentDIA.Rd':
\examples lines wider than 100 characters:
readExperimentDIA(fileTable, localProbCut = 0.75, annotation_col = c("id"), onlyReviewed = FALSE, normalizeByProtein = FALSE)
Rd file 'readPhosphoExperimentDIA.Rd':
\examples lines wider than 100 characters:
readPhosphoExperimentDIA(fileTable, localProbCut = 0.75, onlyReviewed = FALSE, showProgressBar = FALSE)
Rd file 'runFisher.Rd':
\examples lines wider than 100 characters:
de <- performDifferentialExp(se = result, assay = "Intensity", method = "limma", reference = "1stCrtl", target = "EGF", condition = "tr ... [TRUNCATED]
These lines will be truncated in the PDF manual.
* 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 ... [6s/6s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in vignettes ... OK
* checking examples ... [54s/54s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [56s/56s]
[57s/56s] 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 ... [4s/4s] OK
* DONE
Status: 4 NOTEs
See
/home/pkgbuild/packagebuilder/workers/jobs/3609/8c717a4c3938d36ec1da439bc5dfc81f05fd4f98/SmartPhos.Rcheck/00check.log
for details.
===============================
BiocCheck('SmartPhos_0.99.5.tar.gz')
===============================
Installing SmartPhos
Package installed successfully
SmartPhos session metadata
sourceDir: /tmp/RtmpDVMZ1E/file3441a75a77908/SmartPhos
BiocVersion: 3.21
Package: SmartPhos
PackageVersion: 0.99.5
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3609/8c717a4c3938d36ec1da439bc5dfc81f05fd4f98/SmartPhos.BiocCheck
BiocCheckVersion: 1.43.12
sourceDir: /tmp/RtmpDVMZ1E/file3441a75a77908/SmartPhos
installDir: /tmp/RtmpDVMZ1E/file3441a75db257d0
isTarBall: TRUE
platform: unix
Running BiocCheck on SmartPhos
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R version dependency...
i NOTE: Update R version dependency from 3.5.0 to 4.5.0.
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
* Checking build system compatibility...
* Checking for proper Description: field...
* Checking if DESCRIPTION is well formatted...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
i NOTE: Provide 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (26%).
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
i NOTE: No 'fnd' role found in Authors@R. If the work is supported by a grant,
consider adding the 'fnd' role to the list of authors.
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
i NOTE: 'sessionInfo' not found in vignette(s)
Missing from file(s):
vignettes/SmartPhos_Shiny.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of SmartPhos...
* Checking coding practice...
i NOTE: Avoid sapply(); use vapply()
Found in files:
R/enrichment.R (line 665, column 24)
...
R/time_series_clustering.R (line 270, column 19)
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
enrichment.R (line 46, column 16)
...
enrichment.R (line 597, column 46)
i NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
print() in R/basic_visualizations.R (line 256, column 7)
...
print() in R/preprocess_proteome_phospho.R (line 349, column 7)
i NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
R/basic_visualizations.R (line 276, column 29)
...
R/time_series_clustering.R (line 534, column 19)
* Checking parsed R code in R directory, examples, vignettes...
i NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 4 times)
suppressWarnings() in R/enrichment.R (line 495, column 22)
...
suppressWarnings() in R/enrichment.R (line 529, column 22)
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 21
functions greater than 50 lines.
The longest 5 functions are:
runGSEAforPhospho() (R/enrichment.R): 312 lines
...
preprocessProteome() (R/preprocess_proteome_phospho.R): 126 lines
* Checking man page documentation...
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
checkRatioMat.Rd
...
runSmartPhos.Rd
* Checking package NEWS...
i NOTE: Consider adding a NEWS file, so your package news will be included in
Bioconductor release announcements.
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
i NOTE: Consider shorter lines; 822 lines (16%) are > 80 characters long.
First few lines:
R/basic_visualizations.R#L6 #' \code{plotMissing} generates a bar pl ...
...
vignettes/SmartPhos.Rmd#L250 By combining prior knowledge about known ...
i NOTE: Consider multiples of 4 spaces for line indents; 1237 lines (23%) are
not.
First few lines:
R/basic_visualizations.R#L33 # Extract the assay data from the Summ ...
...
vignettes/SmartPhos.Rmd#L240 ifFDR = FALSE) ...
i See https://contributions.bioconductor.org/r-code.html
i See styler package: https://cran.r-project.org/package=styler as described in
the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
i Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
i Maintainer is registered at support site.
i Package is in the Support Site Watched Tags.
BiocCheck v1.43.12 results
0 ERRORS | 0 WARNINGS | i 14 NOTES
i See the SmartPhos.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.