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This page was generated on 2025-04-02 19:32 -0400 (Wed, 02 Apr 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.3 (2025-02-28) -- "Trophy Case" 4764
palomino8Windows Server 2022 Datacenterx644.4.3 (2025-02-28 ucrt) -- "Trophy Case" 4495
merida1macOS 12.7.5 Montereyx86_644.4.3 (2025-02-28) -- "Trophy Case" 4522
kjohnson1macOS 13.6.6 Venturaarm644.4.3 (2025-02-28) -- "Trophy Case" 4449
taishanLinux (openEuler 24.03 LTS)aarch644.4.3 (2025-02-28) -- "Trophy Case" 4426
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 1028/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
infercnv 1.22.0  (landing page)
Christophe Georgescu
Snapshot Date: 2025-03-31 13:00 -0400 (Mon, 31 Mar 2025)
git_url: https://git.bioconductor.org/packages/infercnv
git_branch: RELEASE_3_20
git_last_commit: 0d36fe0
git_last_commit_date: 2024-10-29 10:37:21 -0400 (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  ERROR    ERROR  skippedskipped
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
taishanLinux (openEuler 24.03 LTS) / aarch64  ERROR    ERROR  skipped

CHECK results for infercnv on merida1

To the developers/maintainers of the infercnv package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/infercnv.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: infercnv
Version: 1.22.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:infercnv.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings infercnv_1.22.0.tar.gz
StartedAt: 2025-04-01 04:30:27 -0400 (Tue, 01 Apr 2025)
EndedAt: 2025-04-01 04:46:52 -0400 (Tue, 01 Apr 2025)
EllapsedTime: 985.0 seconds
RetCode: 0
Status:   OK  
CheckDir: infercnv.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:infercnv.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings infercnv_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/infercnv.Rcheck’
* using R version 4.4.3 (2025-02-28)
* 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 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘infercnv/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘infercnv’ version ‘1.22.0’
* 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 ‘infercnv’ 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 ... NOTE
Unexported object imported by a ':::' call: ‘HiddenMarkov:::makedensity’
  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 ... OK
* checking Rd files ... NOTE
checkRd: (-1) run.Rd:268: Lost braces; missing escapes or markup?
   268 | \item{require_DE_all_normals}{If mask_nonDE_genes is set, those genes will be masked only if they are are found as DE according to test.use and mask_nonDE_pval in each of the comparisons to normal cells options: {"any", "most", "all"} (default: "any")
       |                                                                                                                                                                                                                     ^
* 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 LazyData ... 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
inferCNVBayesNet       361.081  6.614 342.057
run                     21.401  0.807  23.095
apply_median_filtering  13.762  0.159  15.048
plot_subclusters         1.785  3.405   5.432
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/infercnv.Rcheck/00check.log’
for details.

Installation output

infercnv.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘infercnv’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (infercnv)

Tests output

infercnv.Rcheck/tests/testthat.Rout


R version 4.4.3 (2025-02-28) -- "Trophy Case"
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.

> #!/usr/bin/env Rscript
> 
> library(testthat)
> library(infercnv)
> 
> test_check("infercnv")
INFO [2025-04-01 04:46:37] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2025-04-01 04:46:37] subtracting mean(normal) per gene per cell across all data
INFO [2025-04-01 04:46:37] -subtracting expr per gene, use_bounds=TRUE
INFO [2025-04-01 04:46:37] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2025-04-01 04:46:37] subtracting mean(normal) per gene per cell across all data
INFO [2025-04-01 04:46:37] -subtracting expr per gene, use_bounds=TRUE
INFO [2025-04-01 04:46:37] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2025-04-01 04:46:37] subtracting mean(normal) per gene per cell across all data
INFO [2025-04-01 04:46:37] -subtracting expr per gene, use_bounds=TRUE
INFO [2025-04-01 04:46:37] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2025-04-01 04:46:37] subtracting mean(normal) per gene per cell across all data
INFO [2025-04-01 04:46:37] -subtracting expr per gene, use_bounds=TRUE
INFO [2025-04-01 04:46:37] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2025-04-01 04:46:37] subtracting mean(normal) per gene per cell across all data
INFO [2025-04-01 04:46:37] -subtracting expr per gene, use_bounds=TRUE
INFO [2025-04-01 04:46:37] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2025-04-01 04:46:37] subtracting mean(normal) per gene per cell across all data
INFO [2025-04-01 04:46:37] -subtracting expr per gene, use_bounds=TRUE
WARN [2025-04-01 04:46:37] window length < 2, returning original unmodified data
WARN [2025-04-01 04:46:37] window length < 2, returning original unmodified data
INFO [2025-04-01 04:46:38] ::remove_outlier_norm:Start out_method: average_bound lower_bound: -1 upper_bound: 30
INFO [2025-04-01 04:46:38] ::remove_outlier_norm: using hard thresholds:  lower_bound: -1 upper_bound: 30
INFO [2025-04-01 04:46:38] ::remove_outlier_norm:Start out_method: average_bound lower_bound: 5 upper_bound: 15
INFO [2025-04-01 04:46:38] ::remove_outlier_norm: using hard thresholds:  lower_bound: 5 upper_bound: 15
INFO [2025-04-01 04:46:38] ::remove_outlier_norm:Start out_method: average_bound lower_bound: NA upper_bound: NA
INFO [2025-04-01 04:46:38] ::remove_outlier_norm using method: average_bound for defining outliers.
INFO [2025-04-01 04:46:38] outlier bounds defined between: -0.5 - 17.75
INFO [2025-04-01 04:46:38] ::order_reduce:Start.
INFO [2025-04-01 04:46:38] ::order_reduce:Start.
INFO [2025-04-01 04:46:38] .order_reduce(): expr and order match.
INFO [2025-04-01 04:46:38] ::process_data:order_reduce:Reduction from positional data, new dimensions (r,c) = 10,2 Total=110 Min=1 Max=10.
INFO [2025-04-01 04:46:38] ::order_reduce:Start.
INFO [2025-04-01 04:46:38] .order_reduce(): expr and order match.
INFO [2025-04-01 04:46:38] ::process_data:order_reduce:Reduction from positional data, new dimensions (r,c) = 10,2 Total=110 Min=1 Max=10.
INFO [2025-04-01 04:46:38] ::order_reduce:Start.
INFO [2025-04-01 04:46:38] ::process_data:order_reduce:The position file  and the expression file row (gene) names do not match.
[ FAIL 0 | WARN 0 | SKIP 3 | PASS 39 ]

══ Skipped tests (3) ═══════════════════════════════════════════════════════════
• empty test (3): 'test_infer_cnv.R:343:1', 'test_infer_cnv.R:349:1',
  'test_infer_cnv.R:355:1'

[ FAIL 0 | WARN 0 | SKIP 3 | PASS 39 ]
> 
> proc.time()
   user  system elapsed 
 25.848   1.773  27.907

Example timings

infercnv.Rcheck/infercnv-Ex.timings

nameusersystemelapsed
CreateInfercnvObject0.1430.0120.166
apply_median_filtering13.762 0.15915.048
color.palette0.0040.0010.004
filterHighPNormals0.0210.0030.024
inferCNVBayesNet361.081 6.614342.057
plot_cnv0.6870.1230.835
plot_per_group1.6220.2251.868
plot_subclusters1.7853.4055.432
run21.401 0.80723.095
sample_object0.0430.0050.047