===============================
BiocCheckGitClone('MutSeqR')
===============================
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3856/b35ccc56ae591b15a57872653505b7003afe96aa/MutSeqR
BiocVersion: 3.23
Package: MutSeqR
PackageVersion: 0.99.6
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3856/b35ccc56ae591b15a57872653505b7003afe96aa/MutSeqR.BiocCheck
BiocCheckVersion: 1.47.7
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3856/b35ccc56ae591b15a57872653505b7003afe96aa/MutSeqR
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...
* Checking that provided CITATION file is correctly formatted...
BiocCheck v1.47.7 results
0 ERRORS | 0 WARNINGS | i 0 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory /home/pkgbuild/packagebuilder/workers/jobs/3856/b35ccc56ae591b15a57872653505b7003afe96aa/MutSeqR.Rcheck
* using R Under development (unstable) (2025-10-20 r88955)
* 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 MutSeqR/DESCRIPTION ... OK
* this is package MutSeqR version 0.99.6
* 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 MutSeqR 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 ... [12s/12s] 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 ... [12s/12s] OK
* checking whether the namespace can be unloaded cleanly ... [12s/12s] OK
* checking loading without being on the library search path ... [12s/12s] OK
* checking whether startup messages can be suppressed ... [12s/12s] 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 ... [62s/62s] 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
Codoc mismatches from Rd file 'spectra_comparison.Rd':
spectra_comparison
Code: function(mf_data, exp_variable, mf_type = "min", contrasts,
cont_sep = "\t")
Docs: function(mf_data, exp_variable, mf_type = "min", contrasts,
cont_sep = "\t", seed = 1234)
Argument names in docs not in code:
seed
Error: package or namespace load failed for MutSeqR in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
there is no package called BiocParallel
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({
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.loc, character.only = TRUE, verbose = FALSE)
Execution halted
Error: package or namespace load failed for MutSeqR in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
there is no package called BiocParallel
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({
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.loc, character.only = TRUE, verbose = FALSE)
Execution halted
* checking Rd \usage sections ... NOTE
Error: there is no package called BiocParallel
Call sequence:
16: doWithOneRestart(return(expr), restart)
15: withOneRestart(expr, restarts[[1L]])
14: withRestarts(stop(cond), retry_loadNamespace = function() NULL)
13: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
12: asNamespace(ns)
11: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc,
.libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)
10: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
9: asNamespace(ns)
8: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc,
.libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)
7: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
6: asNamespace(ns)
5: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc,
.libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)
4: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), version
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 ... ERROR
TIMEOUT: R CMD check exceeded 15 mins
===============================
BiocCheck('MutSeqR_0.99.6.tar.gz')
===============================
Installing MutSeqR
ERROR: /tmp/Rtmpa9Jbw3/file1d923b1a70d539/MutSeqR must be installable and
loadable.
Package installed successfully
MutSeqR session metadata
sourceDir: /tmp/Rtmpa9Jbw3/file1d923b1a70d539/MutSeqR
BiocVersion: 3.23
Package: MutSeqR
PackageVersion: 0.99.6
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3856/b35ccc56ae591b15a57872653505b7003afe96aa/MutSeqR.BiocCheck
BiocCheckVersion: 1.47.7
sourceDir: /tmp/Rtmpa9Jbw3/file1d923b1a70d539/MutSeqR
installDir: /tmp/Rtmpa9Jbw3/file1d923b127e3389
isTarBall: TRUE
platform: unix
Running BiocCheck on MutSeqR
* 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 4.5.0 to 4.6.0
* 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...
Warning in readLines(con) :
URL 'http://bioconductor.org/js/versions.js': Timeout of 60 seconds was reached
* 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 (50%).
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
* Checking NAMESPACE...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of MutSeqR...
* Checking coding practice...
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
proast.min.R (line 262, column 24)
...
write_nice_excel.R (line 128, column 16)
i NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
cat() in R/proast.min.R (line 81, column 13)
...
print() in R/proast.min.R (line 14931, column 9)
i NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
R/proast.min.R (line 4103, column 26)
...
R/proast.min.R (line 13038, column 30)
i NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
R/plot_mean_mf.R (line 188, column 10)
...
R/proast.min.R (line 14206, column 38)
! WARNING: Remove set.seed usage (found 1 times)
set.seed() in R/proast.min.R (line 8826, column 5)
* 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 81
functions greater than 50 lines.
The longest 5 functions are:
f.select.m5.con() (R/proast.min.R): 1436 lines
...
f.nlminb() (R/proast.min.R): 721 lines
* Checking man page documentation...
Error in loadNamespace(pkgname, lib.loc = lib.loc) :
there is no package called MutSeqR
Calls: BiocCheck ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted