===============================
BiocCheckGitClone('singIST')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3826/014f9f71b9b3075ed809f2d36c10739dc4a71e32/singIST
→ BiocVersion: 3.22
→ Package: singIST
→ PackageVersion: 0.99.61
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3826/014f9f71b9b3075ed809f2d36c10739dc4a71e32/singIST.BiocCheck
→ BiocCheckVersion: 1.47.1
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3826/014f9f71b9b3075ed809f2d36c10739dc4a71e32/singIST
→ 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 v1.47.1 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/3826/014f9f71b9b3075ed809f2d36c10739dc4a71e32/singIST.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 ‘singIST/DESCRIPTION’ ... OK
* this is package ‘singIST’ version ‘0.99.61’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 21 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 ‘singIST’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... 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 ... [18s/18s] OK
* checking whether the package can be loaded with stated dependencies ... [16s/16s] OK
* checking whether the package can be unloaded cleanly ... [17s/17s] OK
* checking whether the namespace can be loaded with stated dependencies ... [16s/16s] OK
* checking whether the namespace can be unloaded cleanly ... [18s/18s] OK
* checking loading without being on the library search path ... [17s/17s] OK
* checking whether startup messages can be suppressed ... [19s/19s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [58s/58s] OK
* 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 ... WARNING
Error: package or namespace load failed for ‘singIST’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
there is no package called ‘ScaledMatrix’
Call sequence:
6: stop(msg, call. = FALSE, domain = NA)
5: value[[3L]](cond)
4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
3: tryCatchList(expr, classes, parentenv, handlers)
2: tryCatch({
attr(package, "LibPath") <- which.lib.loc
ns <- loadNamespace(package, lib.loc)
env <- attachNamespace(ns, pos = pos, deps, exclude, include.only)
}, error = function(e) {
P <- if (!is.null(cc <- conditionCall(e)))
paste(" in", deparse(cc)[1L])
else ""
msg <- gettextf("package or namespace load failed for %s%s:\n %s",
sQuote(package), P, conditionMessage(e))
if (logical.return && !quietly)
message(paste("Error:", msg), domain = NA)
else stop(msg, call. = FALSE, domain = NA)
})
1: library(package, lib.loc = lib.lo
Execution halted
* checking Rd \usage sections ... NOTE
Error: there is no package called ‘BiocSingular’
Call sequence:
9: doWithOneRestart(return(expr), restart)
8: withOneRestart(expr, restarts[[1L]])
7: withRestarts(stop(cond), retry_loadNamespace = function() NULL)
6: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
5: asNamespace(ns)
4: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc,
.libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)
3: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
2: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()),
versionCheck = vI[[i]]), from = package)
1: loadNamespace(package, lib.loc)
Execution halted
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [338s/397s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
pullGeneSet-method 172.316 0.695 173.907
multiple_singISTrecapitulations 18.987 0.270 23.838
superpathway_recap 11.503 0.151 16.154
singIST_treat 11.308 0.127 15.295
singISTrecapitulations 11.271 0.106 14.851
celltype_recap 10.159 0.911 16.479
derive_contributions 9.406 0.295 14.149
gene_contrib 9.411 0.182 14.038
derive_scores 9.318 0.174 13.290
helpers 7.303 0.165 31.264
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ ERROR
TIMEOUT: R CMD check exceeded 15 mins
===============================
BiocCheck('singIST_0.99.61.tar.gz')
===============================
── Installing singIST ──────────────────────────────────────────────────────────
[84s/107s]
[84s/107s] 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: 1 WARNING, 1 NOTE
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3826/014f9f71b9b3075ed809f2d36c10739dc4a71e32/singIST.Rcheck/00check.log’
for details.
✔ Package installed successfully
── singIST session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpqjA3r3/file3b6f007a6ffcb3/singIST
→ BiocVersion: 3.22
→ Package: singIST
→ PackageVersion: 0.99.61
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3826/014f9f71b9b3075ed809f2d36c10739dc4a71e32/singIST.BiocCheck
→ BiocCheckVersion: 1.47.1
→ sourceDir: /tmp/RtmpqjA3r3/file3b6f007a6ffcb3/singIST
→ installDir: /tmp/RtmpqjA3r3/file3b6f004e0def3c
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on singIST ────────────────────────────────────────────────
* 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 4.2 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 (39%).
* 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:
• singISTvignette.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of singIST...
* Checking coding practice...
i NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
• R/helpers.R (line 1166, column 46)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 7
functions greater than 50 lines.
The longest 5 functions are:
• pseudobulk_log2FC() (R/helpers.R): 55 lines
• ...
• fitOptimal.superpathway.input() (R/bbb-step1-fit.R): 52 lines
* Checking man page documentation...
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
• biological_link_function.Rd
• ...
• restore_removed_columns.Rd
i NOTE: Usage of dontrun / donttest tags found in man page examples. 12% of man
pages use at least one of these tags.
Found in files:
• asmbPLSDA.cv.kcv.Rd
• ...
• setRepeatGeneSets-method.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 shorter lines; 5 lines (0%) are > 80 characters long.
First few lines:
• R/bbb-step1-fit.R#L265 #' \donttest{asmbPLSDA.cv.kcv(X.matrix, ...
• ...
• R/helpers.R#L1583 predictor_block[samples, ...
i NOTE: Consider multiples of 4 spaces for line indents; 26 lines (1%) are not.
First few lines:
• R/bbb-step1-fit.R#L27 cellt ...
• ...
• vignettes/singISTvignette.Rmd#L215 ...
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 v1.47.1 results ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 9 NOTES
i See the singIST.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.