##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:anglemania.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings anglemania_0.99.7.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/anglemania.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘anglemania/DESCRIPTION’ ... OK
* this is package ‘anglemania’ version ‘0.99.7’
* 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: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.1.sdk’
* checking installed package size ... OK
* checking package directory ... 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 ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... 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 ... 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’
select_genes: no visible binding for global variable ‘mean_zscore’
select_genes: no visible binding for global variable ‘sd_zscore’
select_genes: no visible binding for global variable ‘rank_mean_zscore’
select_genes: no visible binding for global variable ‘rank_sd_zscore’
Undefined global functions or variables:
  . anglemania_batch mean_zscore n_samples rank_mean_zscore
  rank_sd_zscore sd_zscore weight
* checking Rd files ... OK
* checking Rd metadata ... 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 compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 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 ... OK
* DONE

Status: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/anglemania.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL anglemania
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘anglemania’ ...
** this is package ‘anglemania’ version ‘0.99.7’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.1.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/rmio/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/bigstatsr/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/rmio/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/bigstatsr/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c anglemanise_cpp_utils.cpp -o anglemanise_cpp_utils.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o anglemania.so RcppExports.o anglemanise_cpp_utils.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-anglemania/00new/anglemania/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (anglemania)

R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
> 
> library(testthat)
> library(anglemania)
> 
> test_check("anglemania")
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min


Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

No dataset_key specified.
Assuming that all samples belong to the same dataset and are separated by batch_key: batch
Preparing input...
Filtering each batch to at least 1 cells per gene...

  |                                                  | 0 % elapsed=00s   
  |==================================================| 100% elapsed=00s, remaining~00s
Using the intersection of filtered genes from all batches...
Number of genes in intersected set: 300
Extracting count matrices...

  |                                                  | 0 % elapsed=00s   
  |==================================================| 100% elapsed=00s, remaining~00s
Computing angles and transforming to z-scores...

  |                                                  | 0 % elapsed=00s   Creating directory "/tmp/RtmpBJnYmu/filefbfa4fa5494e" which didn't exist..

  |=========================                         | 50% elapsed=01s, remaining~01sCreating directory "/tmp/RtmpBJnYmu/filefbfa3b2ba03" which didn't exist..

  |==================================================| 100% elapsed=02s, remaining~00s
Computing statistics...
Weighting matrix_list...
Calculating mean...
Calculating sds...
Pre-filtering features...
Extracting filtered features...
Selected 20 genes for integration.
No dataset_key specified.
Assuming that all samples belong to the same dataset and are separated by batch_key: batch
Preparing input...
Filtering each batch to at least 1 cells per gene...

  |                                                  | 0 % elapsed=00s   
  |==================================================| 100% elapsed=00s, remaining~00s
Using the intersection of filtered genes from all batches...
Number of genes in intersected set: 300
Extracting count matrices...

  |                                                  | 0 % elapsed=00s   
  |==================================================| 100% elapsed=00s, remaining~00s
Computing angles and transforming to z-scores...

  |                                                  | 0 % elapsed=00s   Creating directory "/tmp/RtmpBJnYmu/filefbfa7e089a6e" which didn't exist..

  |=========================                         | 50% elapsed=00s, remaining~00sCreating directory "/tmp/RtmpBJnYmu/filefbfa30f693e2" which didn't exist..

  |==================================================| 100% elapsed=01s, remaining~00s
Computing statistics...
Weighting matrix_list...
Calculating mean...
Calculating sds...
Pre-filtering features...
Extracting filtered features...
Selected 20 genes for integration.
Creating directory "/tmp/RtmpBJnYmu/filefbfa38d73ad8" which didn't exist..
Creating directory "/tmp/RtmpBJnYmu/filefbfa1f674f5b" which didn't exist..
Creating directory "/tmp/RtmpBJnYmu/filefbfa1a4a6d04" which didn't exist..
Creating directory "/tmp/RtmpBJnYmu/filefbfa190d6ee" which didn't exist..
Creating directory "/tmp/RtmpBJnYmu/filefbfa221a5a6b" which didn't exist..
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 23 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• On CRAN (1): 'test-anglemania.R:13:5'

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 23 ]
> 
> proc.time()
   user  system elapsed 
 14.140   1.853  15.692