===============================
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_0.99.1.tar.gz’
===============================
BiocCheckGitClone('anglemania')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3661/f27399fb947adfa0de6134493e737658ca591af5/anglemania
→ BiocVersion: 3.22
→ Package: anglemania
→ PackageVersion: 0.99.1
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3661/f27399fb947adfa0de6134493e737658ca591af5/anglemania.BiocCheck
→ BiocCheckVersion: 1.45.6
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3661/f27399fb947adfa0de6134493e737658ca591af5/anglemania
→ installDir: NULL
→ isTarBall: FALSE
→ platform: unix
* Checking valid files...
✖ ERROR: System files found that should not be Git tracked.
• anglemania.Rproj
• ...
• src/RcppExports.o
* 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...
* Checking that provided CITATION file is correctly formatted...
! WARNING: The 'doi' argument is missing or empty in the CITATION's
'bibentry()'. Only include a CITATION file if there is a preprint or
publication associated with this Bioconductor package.
── BiocCheck v1.45.6 results ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 1 WARNINGS | i 0 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3661/f27399fb947adfa0de6134493e737658ca591af5/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 ‘0.99.1’
* package encoding: UTF-8
* checking package namespace information ... NOTE
Found export directives that require package ‘methods’:
‘exportClasses’ ‘exportMethods’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
* checking package dependencies ... INFO
Vignette dependency required without any vignettes: ‘knitr’
* 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 ... [10s/10s] OK
* checking whether the package can be loaded with stated dependencies ... [10s/10s] OK
* checking whether the package can be unloaded cleanly ... [10s/10s] OK
* checking whether the namespace can be loaded with stated dependencies ... [10s/10s] OK
* checking whether the namespace can be unloaded cleanly ... [11s/11s] OK
* checking loading without being on the library search path ... [10s/10s] 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.
package 'methods' is used but not declared
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [33s/33s] NOTE
.core_create_anglemania_object: no visible global function definition
for ‘new’
.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 new
number_angl_genes residuals setNames sn_zscore weight
Consider adding
importFrom("methods", "new")
importFrom("stats", "lm", "residuals", "setNames")
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 line endings in C/C++/Fortran sources/headers ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* 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 examples ... [40s/40s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
integrate_by_features 9.813 0.099 9.940
anglemania_object-methods 5.062 0.210 5.444
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [22s/22s]
[22s/22s] OK
* checking PDF version of manual ... [3s/3s] OK
* DONE
Status: 5 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3661/f27399fb947adfa0de6134493e737658ca591af5/anglemania.Rcheck/00check.log’
for details.
===============================
BiocCheck('anglemania_0.99.1.tar.gz')
===============================
── Installing anglemania ───────────────────────────────────────────────────────
✔ Package installed successfully
── anglemania session metadata ─────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpSYcxzM/file103ccf3b29574f/anglemania
→ BiocVersion: 3.22
→ Package: anglemania
→ PackageVersion: 0.99.1
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3661/f27399fb947adfa0de6134493e737658ca591af5/anglemania.BiocCheck
→ BiocCheckVersion: 1.45.6
→ sourceDir: /tmp/RtmpSYcxzM/file103ccf3b29574f/anglemania
→ installDir: /tmp/RtmpSYcxzM/file103ccf1b8f2b5c
→ 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...
No vignettes found.
* 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 (13%).
* 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...
✖ ERROR: No 'vignettes' directory.
* 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; 49 lines (2%) are > 80 characters long.
First few lines:
• R/anglemania.R#L40 #' @param permute_row_or_column Characte ...
• ...
• R/reexports_bigstatsr.R#L147 function(X, ind.row = bigstatsr::rows_ ...
i NOTE: Consider multiples of 4 spaces for line indents; 655 lines (24%) are
not.
First few lines:
• R/anglemania.R#L91 # Validate inputs ...
• ...
• R/reexports_bigstatsr.R#L162 } ...
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...
✖ ERROR: Subscribe to the Bioc-devel mailing list by going to
https://stat.ethz.ch/mailman/listinfo/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 ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 0 WARNINGS | i 15 NOTES
i See the anglemania.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.