===============================
R CMD BUILD
===============================
* checking for file ‘anglemania/DESCRIPTION’ ... OK
* preparing ‘anglemania’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... OK
* cleaning src
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘anglemania_0.99.2.tar.gz’
===============================
BiocCheckGitClone('anglemania')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3661/a2b9d34df9f1a01f5dcaffd968293f1ac06fb672/anglemania
→ BiocVersion: 3.22
→ Package: anglemania
→ PackageVersion: 0.99.2
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3661/a2b9d34df9f1a01f5dcaffd968293f1ac06fb672/anglemania.BiocCheck
→ BiocCheckVersion: 1.45.6
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3661/a2b9d34df9f1a01f5dcaffd968293f1ac06fb672/anglemania
→ installDir: NULL
→ isTarBall: FALSE
→ platform: unix
* Checking valid files...
Warning in grep(filter_expr, ignore.case = TRUE, flist[["FALSE"]], value = TRUE) :
TRE pattern compilation error 'Invalid use of repetition operators'
Error in grep(filter_expr, ignore.case = TRUE, flist[["FALSE"]], value = TRUE) :
invalid regular expression '^# Temporary and output folders$|^/data$|^/playground$|^/archive$|^/guix$|^/inst/CITATION$|^# RStudio project files$|^.*\.Rproj$|^\.Rproj\.user$|^anglemania\.Rproj$|^$|^# R-related system files$|^\.Rhistory$|^\.Rprofile$|^$|^# Documentation and vignette output$|^/docs$|^/doc/$|^/inst/doc$|^vignettes/.*\.html$|^vignettes/.*_files$|^$|^# Compiled objects \(C/C++/Fortran)$|^.*\.o$|^.*\.so$|^.*\.dll$|^.*\.a$|^$|^# macOS system files$|^\.DS_Store$', reason 'Invalid use of repetition operators'
Calls: BiocCheckGitClone -> checkBadFiles -> grep
Execution halted
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3661/a2b9d34df9f1a01f5dcaffd968293f1ac06fb672/anglemania.Rcheck’
* using R version 4.5.0 (2025-04-11)
* 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 ‘anglemania/DESCRIPTION’ ... OK
* this is package ‘anglemania’ version ‘0.99.2’
* 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 serialization versions ... OK
* checking whether package ‘anglemania’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... OK
* 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 ... [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 use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: ‘bigstatsr:::check_args’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [41s/41s] NOTE
.set_weights: no visible binding for global variable ‘batch’
.set_weights: no visible binding for global variable ‘n_samples’
.set_weights: no visible binding for global variable ‘.’
.set_weights: no visible binding for global variable ‘weight’
get_dstat: no visible global function definition for ‘setNames’
normalize_matrix : <anonymous> : <anonymous>: no visible global
function definition for ‘residuals’
normalize_matrix : <anonymous> : <anonymous>: no visible global
function definition for ‘lm’
select_genes: no visible binding for global variable ‘sn_zscore’
select_genes: no visible binding for global variable ‘mean_zscore’
variable_genes_overlap: no visible binding for global variable
‘intersecting_genes’
variable_genes_overlap: no visible binding for global variable
‘number_angl_genes’
Undefined global functions or variables:
. batch intersecting_genes lm mean_zscore n_samples number_angl_genes
residuals setNames sn_zscore weight
Consider adding
importFrom("stats", "lm", "residuals", "setNames")
to your NAMESPACE file.
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... NOTE
Compilation used the following non-portable flag(s):
‘-Werror=format-security’
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/home/pkgbuild/packagebuilder/workers/jobs/3661/R-libs/anglemania/libs/anglemania.so’:
Found ‘abort’, possibly from ‘abort’ (C)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... [51s/51s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
integrate_by_features 11.335 0.051 11.412
anglemania_object-methods 6.729 0.394 7.294
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [27s/27s]
[27s/27s] 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: 5 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3661/a2b9d34df9f1a01f5dcaffd968293f1ac06fb672/anglemania.Rcheck/00check.log’
for details.
===============================
BiocCheck('anglemania_0.99.2.tar.gz')
===============================
── Installing anglemania ───────────────────────────────────────────────────────
✔ Package installed successfully
── anglemania session metadata ─────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp4Nezr0/file11098862e78a17/anglemania
→ BiocVersion: 3.22
→ Package: anglemania
→ PackageVersion: 0.99.2
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3661/a2b9d34df9f1a01f5dcaffd968293f1ac06fb672/anglemania.BiocCheck
→ BiocCheckVersion: 1.45.6
→ sourceDir: /tmp/Rtmp4Nezr0/file11098862e78a17/anglemania
→ installDir: /tmp/Rtmp4Nezr0/file11098813d48f7b
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on anglemania ─────────────────────────────────────────────
* 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...
* 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 (12%).
* 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: Vignette(s) found with missing chunk labels
Found in files:
• anglemania_tutorial_Seurat.Rmd
• anglemania_tutorial.Rmd
• Functions_Showcasing.Rmd
i NOTE: 'sessionInfo' not found in vignette(s)
Missing from file(s):
• vignettes/Functions_Showcasing.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of anglemania...
* Checking coding practice...
i NOTE: Avoid sapply(); use vapply()
Found in files:
• R/anglemanise_utils.R (line 124, column 10)
• ...
• R/integrate_by_features.R (line 229, column 22)
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
• anglemanise_utils.R (line 318, column 32)
• ...
• objects.R (line 127, column 36)
i NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
• print() in R/anglemanise_utils.R (line 516, column 3)
i NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
• R/anglemanise_utils.R (line 76, column 18)
• ...
• R/factorise.R (line 173, column 10)
i NOTE: Avoid the use of 'paste' in condition signals
Found in files:
• R/anglemanise_utils.R (line 485, column 7)
* Checking parsed R code in R directory, examples, vignettes...
i NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1 times)
• suppressWarnings() in R/anglemanise_utils.R (line 66, column 12)
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 8
functions greater than 50 lines.
The longest 5 functions are:
• .core_create_anglemania_object() (R/objects.R): 126 lines
• ...
• factorise() (R/factorise.R): 82 lines
* Checking man page documentation...
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
• integrate_seurat_list.Rd
• pipe.Rd
i NOTE: Usage of dontrun / donttest tags found in man page examples. 8% of man
pages use at least one of these tags.
Found in files:
• integrate_seurat_list.Rd
i NOTE: Use donttest instead of dontrun.
Found in files:
• integrate_seurat_list.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; 103 lines (3%) are > 80 characters long.
First few lines:
• R/anglemania.R#L40 #' @param permute_row_or_column Characte ...
• ...
• vignettes/Functions_Showcasing.Rmd#L85 * we can use select_genes to change
the ...
i NOTE: Consider multiples of 4 spaces for line indents; 754 lines (23%) are
not.
First few lines:
• R/anglemania.R#L91 # Validate inputs ...
• ...
• vignettes/Functions_Showcasing.Rmd#L90 zscore_sn_threshold ...
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 v1.45.6 results ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 17 NOTES
i See the anglemania.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.