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This page was generated on 2024-06-11 15:41 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4679
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4414
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4441
kjohnson1macOS 13.6.6 Venturaarm644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4394
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

Package 266/2239HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cardelino 1.7.0  (landing page)
Davis McCarthy
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/cardelino
git_branch: devel
git_last_commit: abf5cef
git_last_commit_date: 2024-04-30 11:45:30 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for cardelino on merida1

To the developers/maintainers of the cardelino package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/cardelino.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: cardelino
Version: 1.7.0
Command: /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_1.7.0.tar.gz
StartedAt: 2024-06-10 00:51:03 -0400 (Mon, 10 Jun 2024)
EndedAt: 2024-06-10 01:06:25 -0400 (Mon, 10 Jun 2024)
EllapsedTime: 922.1 seconds
RetCode: 0
Status:   OK  
CheckDir: cardelino.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /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_1.7.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/cardelino.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cardelino/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cardelino’ version ‘1.7.0’
* 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 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 ... 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       132.934  8.763 154.062
get_snp_matrices  34.316  1.858  40.570
clone_id          25.301  1.245  29.987
read_vcf           5.124  0.395   6.395
* 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: OK


Installation output

cardelino.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/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

cardelino.Rcheck/tests/testthat.Rout


R version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"
Copyright (C) 2024 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.

> Sys.setenv("R_TESTS" = "")
> library(testthat)
> library(cardelino)
> 
> test_check("cardelino")
[1] "Total iterations: 11"
98% converged.
98.7% converged.
98.6% converged.
98.3% converged.
[1] "Converged in 500 iterations."
DIC: 2935.37 D_mean: 2454.73 D_post: 2370.01 logLik_var: 141.34 
     [,1] [,2] [,3] [,4]
[1,]    1    2    3    4
[1] "65 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 2 | SKIP 0 | PASS 20 ]

[ FAIL 0 | WARN 2 | SKIP 0 | PASS 20 ]
> 
> # check test coverage with covr in Rstudio
> # covr::package_coverage()
> 
> proc.time()
   user  system elapsed 
 50.429   2.558  56.899 

Example timings

cardelino.Rcheck/cardelino-Ex.timings

nameusersystemelapsed
assign_cells_to_clones0.1860.0090.222
binaryPRC0.0170.0070.026
binaryROC0.0190.0050.027
clone_id25.301 1.24529.987
colMatch0.0020.0010.005
get_snp_matrices34.316 1.85840.570
get_tree0.8110.0110.926
heat_matrix1.5150.0291.780
load_GT_vcf0.4940.0530.626
load_cellSNP_vcf0.0400.0030.050
mixBinom0.0300.0010.037
mtx_to_df0.0030.0010.005
plot_config_diffs0.3460.0040.389
plot_tree0.6110.0100.696
predMixBinom0.0300.0010.036
prob_heatmap0.1940.0060.221
pub.theme0.0490.0020.056
read_vcf5.1240.3956.395
rowArgmax0.0000.0010.001
rowMax0.0010.0010.002
sample_seq_depth1.3730.0461.541
sample_tree_SNV0.0070.0020.009
sim_read_count3.5140.0263.737
vc_heatmap132.934 8.763154.062