Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-12-23 12:03 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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 272/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cardelino 1.8.0  (landing page)
Davis McCarthy
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/cardelino
git_branch: RELEASE_3_20
git_last_commit: 751cf0f
git_last_commit_date: 2024-10-29 11:15:34 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 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 nebbiolo2

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: 1.8.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:cardelino.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings cardelino_1.8.0.tar.gz
StartedAt: 2024-12-19 21:00:25 -0500 (Thu, 19 Dec 2024)
EndedAt: 2024-12-19 21:10:47 -0500 (Thu, 19 Dec 2024)
EllapsedTime: 621.6 seconds
RetCode: 0
Status:   OK  
CheckDir: cardelino.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:cardelino.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings cardelino_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/cardelino.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘cardelino/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cardelino’ version ‘1.8.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 loading without being on the library search path ... 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       53.813  0.731  54.546
get_snp_matrices 12.587  1.088  13.678
clone_id         10.854  0.211  11.065
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

cardelino.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL cardelino
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-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 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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"
95.2% converged.
96.3% converged.
97.4% converged.
95.9% converged.
[1] "Converged in 500 iterations."
DIC: 3067.87 D_mean: 2587.51 D_post: 2453.19 logLik_var: 153.67 
     [,1] [,2] [,3] [,4]
[1,]    1    2    3    4
[1] "66 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 
 21.328   1.026  22.341 

Example timings

cardelino.Rcheck/cardelino-Ex.timings

nameusersystemelapsed
assign_cells_to_clones0.0740.0000.074
binaryPRC0.0060.0000.006
binaryROC0.0060.0000.006
clone_id10.854 0.21111.065
colMatch000
get_snp_matrices12.587 1.08813.678
get_tree0.2810.0100.292
heat_matrix0.5280.0000.528
load_GT_vcf0.1870.0030.190
load_cellSNP_vcf0.0170.0000.017
mixBinom0.0080.0000.009
mtx_to_df0.0010.0000.001
plot_config_diffs0.1230.0000.123
plot_tree0.2180.0280.246
predMixBinom0.0080.0020.010
prob_heatmap0.0780.0020.079
pub.theme0.0200.0010.020
read_vcf2.9400.8013.741
rowArgmax0.0000.0000.001
rowMax000
sample_seq_depth1.0710.1001.171
sample_tree_SNV0.0040.0000.004
sim_read_count0.9590.0020.962
vc_heatmap53.813 0.73154.546