===============================
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
NB: this package now depends on R (>= 4.1.0)
WARNING: Added dependency on R >= 4.1.0 because package code uses the
pipe |> or function shorthand \(...) syntax added in R 4.1.0.
File(s) using such syntax:
‘anglemania_utils.R’ ‘prepare_anglemania.R’ ‘select_genes.R’
* building ‘anglemania_0.99.4.tar.gz’
===============================
BiocCheckGitClone('anglemania')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3661/5d3fdfdcbf5f799b852a28228b00fb3f67456a0f/anglemania
→ BiocVersion: 3.22
→ Package: anglemania
→ PackageVersion: 0.99.4
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3661/5d3fdfdcbf5f799b852a28228b00fb3f67456a0f/anglemania.BiocCheck
→ BiocCheckVersion: 1.45.12
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3661/5d3fdfdcbf5f799b852a28228b00fb3f67456a0f/anglemania
→ 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 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 v1.45.12 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/3661/5d3fdfdcbf5f799b852a28228b00fb3f67456a0f/anglemania.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 ‘anglemania/DESCRIPTION’ ... OK
* this is package ‘anglemania’ version ‘0.99.4’
* 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 ‘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 ... 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 ... [7s/7s] OK
* checking whether the package can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the package can be unloaded cleanly ... [7s/7s] OK
* checking whether the namespace can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the namespace can be unloaded cleanly ... [7s/7s] OK
* checking loading without being on the library search path ... [7s/7s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘methods’
All declared Imports should be used.
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 ... [25s/25s] NOTE
.set_weights: no visible binding for global variable ‘anglemania_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’
anglemania: no visible global function definition for ‘setNames’
get_anglemania_stats_df: no visible binding for global variable
‘sn_zscore’
get_anglemania_stats_df: no visible binding for global variable ‘geneA’
get_anglemania_stats_df: no visible binding for global variable ‘geneB’
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’
Undefined global functions or variables:
. anglemania_batch geneA geneB lm mean_zscore n_samples 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 ... [20s/21s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [12s/12s]
[12s/12s] 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 ... [3s/3s] OK
* DONE
Status: 4 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3661/5d3fdfdcbf5f799b852a28228b00fb3f67456a0f/anglemania.Rcheck/00check.log’
for details.
===============================
BiocCheck('anglemania_0.99.4.tar.gz')
===============================
── Installing anglemania ───────────────────────────────────────────────────────
✔ Package installed successfully
── anglemania session metadata ─────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpEAghNw/file61452210b766/anglemania
→ BiocVersion: 3.22
→ Package: anglemania
→ PackageVersion: 0.99.4
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3661/5d3fdfdcbf5f799b852a28228b00fb3f67456a0f/anglemania.BiocCheck
→ BiocCheckVersion: 1.45.12
→ sourceDir: /tmp/RtmpEAghNw/file61452210b766/anglemania
→ installDir: /tmp/RtmpEAghNw/file614518ad4999
→ 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...
i NOTE: Update R version dependency from 4.1.0 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 (21%).
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
* 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.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...
* Checking parsed R code in R directory, examples, vignettes...
i NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1 times)
• suppressWarnings() in R/stats.R (line 35, column 14)
* 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:
• anglemania() (R/anglemania.R): 165 lines
• ...
• factorise() (R/compute_angles.R): 97 lines
* Checking man page documentation...
* 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; 19 lines (1%) are > 80 characters long.
First few lines:
• vignettes/anglemania_tutorial.Rmd#L6 - &MDC Max Delbrück Center for Molecul
...
• ...
• vignettes/anglemania_tutorial.Rmd#L457 - we can use `select_genes` to change
th ...
i NOTE: Consider multiples of 4 spaces for line indents; 4 lines (0%) are not.
First few lines:
• R/RcppExports.R#L11 BM_sn, ...
• ...
• R/RcppExports.R#L14 zscore_mean_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 v1.45.12 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 7 NOTES
i See the anglemania.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.