Mac ARM64 build report for BioC 3.18 - CHECK results for cardelino on kjohnson1

Hostname	OS	Arch (*)	R version	Installed pkgs
kjohnson1	macOS 13.6.1 Ventura	arm64	4.3.3 (2024-02-29) -- "Angel Food Cake"	4376
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:cardelino.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings cardelino_1.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/cardelino.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cardelino/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cardelino’ version ‘1.4.0’
* 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 ‘cardelino’ can be installed ... OK
* 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 R 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
vc_heatmap       69.273 15.898  86.243
get_snp_matrices 15.125  1.138  17.194
clone_id         13.004  1.635  14.880
read_vcf          4.703  0.779   5.999
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK

Installation output

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL cardelino
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘cardelino’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (cardelino)

Tests output


R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (64-bit)

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.

> Sys.setenv("R_TESTS" = "")
> library(testthat)
> library(cardelino)
> 
> test_check("cardelino")
[1] "Total iterations: 11"
95% converged.
91.3% converged.
90.4% converged.
90.1% converged.
DIC: 2862.6 D_mean: 2419.93 D_post: 2319.17 logLik_var: 135.86 
     [,1] [,2] [,3] [,4]
[1,]    1    2    3    4
[1] "74 samples have multiple labels."
Scanning file to determine attributes.
File attributes:
  meta lines: 37
  header_line: 38
  variant count: 112
  column count: 86

Meta line 37 read in.
All meta lines processed.
gt matrix initialized.
Character matrix gt created.
  Character matrix gt rows: 112
  Character matrix gt cols: 86
  skip: 0
  nrows: 112
  row_num: 0

Processed variant: 112
All variants processed
[1] "112 out of 112 SNPs passed."
Scanning file to determine attributes.
File attributes:
  meta lines: 37
  header_line: 38
  variant count: 112
  column count: 86

Meta line 37 read in.
All meta lines processed.
gt matrix initialized.
Character matrix gt created.
  Character matrix gt rows: 112
  Character matrix gt cols: 86
  skip: 0
  nrows: 112
  row_num: 0

Processed variant: 112
All variants processed
[ FAIL 0 | WARN 3 | SKIP 0 | PASS 20 ]

[ FAIL 0 | WARN 3 | SKIP 0 | PASS 20 ]
> 
> # check test coverage with covr in Rstudio
> # covr::package_coverage()
> 
> proc.time()
   user  system elapsed 
 31.491   2.737  34.604

Example timings

name	user	system	elapsed
assign_cells_to_clones	0.061	0.006	0.068
binaryPRC	0.007	0.002	0.009
binaryROC	0.007	0.001	0.009
clone_id	13.004	1.635	14.880
colMatch	0.002	0.000	0.002
get_snp_matrices	15.125	1.138	17.194
get_tree	0.370	0.009	0.418
heat_matrix	0.628	0.010	0.803
load_GT_vcf	0.357	0.050	0.496
load_cellSNP_vcf	0.036	0.002	0.055
mixBinom	0.012	0.001	0.029
mtx_to_df	0.002	0.001	0.002
plot_config_diffs	0.173	0.003	0.239
plot_tree	0.256	0.005	0.319
predMixBinom	0.010	0.000	0.016
prob_heatmap	0.059	0.003	0.090
pub.theme	0.031	0.001	0.042
read_vcf	4.703	0.779	5.999
rowArgmax	0.000	0.000	0.001
rowMax	0.001	0.000	0.001
sample_seq_depth	0.014	0.002	0.016
sample_tree_SNV	0.005	0.002	0.007
sim_read_count	1.753	0.068	1.860
vc_heatmap	69.273	15.898	86.243

CHECK results for cardelino on kjohnson1

Summary

Command output

Installation output

Tests output

Example timings