===============================
BiocCheckGitClone('SmartPhos')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3609/2f1e4be40906ff20da58ea823bb2aaa6f48a430b/SmartPhos
→ BiocVersion: 3.22
→ Package: SmartPhos
→ PackageVersion: 0.99.29
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3609/2f1e4be40906ff20da58ea823bb2aaa6f48a430b/SmartPhos.BiocCheck
→ BiocCheckVersion: 1.45.18
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3609/2f1e4be40906ff20da58ea823bb2aaa6f48a430b/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 NAMESPACE...
* 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 v1.45.18 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/3609/2f1e4be40906ff20da58ea823bb2aaa6f48a430b/SmartPhos.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* 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 24.04.3 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 ‘0.99.29’
* 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 7.1Mb
sub-directories of 1Mb or more:
data 1.3Mb
shiny-app 5.4Mb
* checking package directory ... OK
* checking for future file timestamps ... NOTE
unable to verify current time
* 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 ... [9s/9s] OK
* checking whether the package can be loaded with stated dependencies ... [9s/9s] OK
* checking whether the package can be unloaded cleanly ... [9s/9s] OK
* checking whether the namespace can be loaded with stated dependencies ... [8s/8s] OK
* checking whether the namespace can be unloaded cleanly ... [9s/9s] OK
* checking loading without being on the library search path ... [9s/9s] 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 ... [31s/31s] 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 ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... 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 ... [7s/7s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [12s/12s] ERROR
Running examples in ‘SmartPhos-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: clusterEnrich
> ### Title: Perform Cluster Enrichment Analysis
> ### Aliases: clusterEnrich
>
> ### ** Examples
>
> library(SummarizedExperiment)
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: ‘MatrixGenerics’
The following objects are masked from ‘package:matrixStats’:
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: generics
Attaching package: ‘generics’
The following objects are masked from ‘package:base’:
as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
setequal, union
Attaching package: ‘BiocGenerics’
The following object is masked from ‘package:SmartPhos’:
plotPCA
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
unsplit, which.max, which.min
Loading required package: S4Vectors
Attaching package: ‘S4Vectors’
The following object is masked from ‘package:utils’:
findMatches
The following objects are masked from ‘package:base’:
I, expand.grid, unname
Loading required package: IRanges
Loading required package: Seqinfo
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: ‘Biobase’
The following object is masked from ‘package:MatrixGenerics’:
rowMedians
The following objects are masked from ‘package:matrixStats’:
anyMissing, rowMedians
> # Load multiAssayExperiment object
> data("dia_example")
> # Get SummarizedExperiment object
> se <- dia_example[["Phosphoproteome"]]
> colData(se) <- colData(dia_example)
> seProcess <- preprocessPhos(seData = se, normalize = TRUE, impute = "QRILC")
Loading required namespace: imputeLCMD
Failed with error: ‘there is no package called ‘imputeLCMD’’
Error in MsCoreUtils::impute_matrix(assay(ppeSub), method = impute) :
requireNamespace("imputeLCMD") is not TRUE
Calls: preprocessPhos -> <Anonymous> -> stopifnot
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [54s/54s]
[54s/54s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 20 lines of output:
* `` -> `...3`
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 307 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-preprocess_proteome_phospho.R:83:3'): preprocessProteome performs imputation ──
Error in `MsCoreUtils::impute_matrix(assay(fpeSub), method = impute)`: requireNamespace("imputeLCMD") is not TRUE
Backtrace:
▆
1. └─SmartPhos::preprocessProteome(seData, impute = "QRILC") at test-preprocess_proteome_phospho.R:83:3
2. └─MsCoreUtils::impute_matrix(assay(fpeSub), method = impute)
3. └─base::stopifnot(requireNamespace("imputeLCMD"))
── Error ('test-preprocess_proteome_phospho.R:146:3'): preprocessPhos performs imputation ──
Error in `MsCoreUtils::impute_matrix(assay(ppeSub), method = impute)`: requireNamespace("imputeLCMD") is not TRUE
Backtrace:
▆
1. └─SmartPhos::preprocessPhos(seData, impute = "QRILC") at test-preprocess_proteome_phospho.R:146:3
2. └─MsCoreUtils::impute_matrix(assay(ppeSub), method = impute)
3. └─base::stopifnot(requireNamespace("imputeLCMD"))
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 307 ]
Error: Test failures
Execution halted
* 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: 2 ERRORs, 3 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3609/2f1e4be40906ff20da58ea823bb2aaa6f48a430b/SmartPhos.Rcheck/00check.log’
for details.
===============================
BiocCheck('SmartPhos_0.99.29.tar.gz')
===============================
── Installing SmartPhos ────────────────────────────────────────────────────────
✔ Package installed successfully
── SmartPhos session metadata ──────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpqIR0eB/file20fddb425c42e7/SmartPhos
→ BiocVersion: 3.22
→ Package: SmartPhos
→ PackageVersion: 0.99.29
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3609/2f1e4be40906ff20da58ea823bb2aaa6f48a430b/SmartPhos.BiocCheck
→ BiocCheckVersion: 1.45.18
→ sourceDir: /tmp/RtmpqIR0eB/file20fddb425c42e7/SmartPhos
→ installDir: /tmp/RtmpqIR0eB/file20fddb42567b62
→ 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 4.4.0 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...
* 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 NAMESPACE...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
i NOTE: Vignette(s) found with missing chunk labels
Found in files:
• SmartPhos_Shiny.Rmd
• SmartPhos.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 788, column 23)
• ...
• R/time_series_clustering.R (line 312, column 19)
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
• enrichment.R (line 598, column 37)
• ...
• enrichment.R (line 712, column 46)
i NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
• print() in R/helper.R (line 916, column 5)
• print() in R/preprocess_proteome_phospho.R (line 206, column 7)
• print() in R/preprocess_proteome_phospho.R (line 417, column 7)
i NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
• R/enrichment.R (line 668, column 21)
• R/enrichment.R (line 786, column 16)
• R/time_series_clustering.R (line 171, column 49)
i NOTE: Avoid the use of 'paste' in condition signals
Found in files:
• R/helper.R (line 54, column 10)
• ...
• R/helper.R (line 768, column 12)
* 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 602, column 22)
• ...
• suppressWarnings() in R/enrichment.R (line 637, column 22)
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 23
functions greater than 50 lines.
The longest 5 functions are:
• runGSEAforPhospho() (R/enrichment.R): 347 lines
• ...
• preprocessProteome() (R/preprocess_proteome_phospho.R): 144 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...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
i NOTE: Consider multiples of 4 spaces for line indents; 1591 lines (24%) are
not.
First few lines:
• R/basic_visualizations.R#L39 perNA <- NULL ...
• ...
• vignettes/SmartPhos.Rmd#L325 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 v1.45.18 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 12 NOTES
i See the SmartPhos.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.