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This page was generated on 2024-03-28 11:36:37 -0400 (Thu, 28 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4708
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" 4446
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4471
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" 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 1023/2270HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
infercnv 1.19.1  (landing page)
Christophe Georgescu
Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024)
git_url: https://git.bioconductor.org/packages/infercnv
git_branch: devel
git_last_commit: cca1b6f
git_last_commit_date: 2023-12-01 13:33:50 -0400 (Fri, 01 Dec 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for infercnv on nebbiolo1


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: 1.19.1
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:infercnv.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings infercnv_1.19.1.tar.gz
StartedAt: 2024-03-27 23:30:28 -0400 (Wed, 27 Mar 2024)
EndedAt: 2024-03-27 23:39:11 -0400 (Wed, 27 Mar 2024)
EllapsedTime: 523.9 seconds
RetCode: 0
Status:   OK  
CheckDir: infercnv.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:infercnv.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings infercnv_1.19.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/infercnv.Rcheck’
* using R Under development (unstable) (2024-03-18 r86148)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘infercnv/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘infercnv’ version ‘1.19.1’
* 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 loading without being on the library search path ... 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 151.634  3.108 132.582
run               11.704  0.944  12.648
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/infercnv.Rcheck/00check.log’
for details.


Installation output

infercnv.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL infercnv
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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 Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences"
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.

> #!/usr/bin/env Rscript
> 
> library(testthat)
> library(infercnv)
> 
> test_check("infercnv")
INFO [2024-03-27 23:38:02] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2024-03-27 23:38:02] subtracting mean(normal) per gene per cell across all data
INFO [2024-03-27 23:38:02] -subtracting expr per gene, use_bounds=TRUE
INFO [2024-03-27 23:38:02] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2024-03-27 23:38:02] subtracting mean(normal) per gene per cell across all data
INFO [2024-03-27 23:38:02] -subtracting expr per gene, use_bounds=TRUE
INFO [2024-03-27 23:38:02] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2024-03-27 23:38:02] subtracting mean(normal) per gene per cell across all data
INFO [2024-03-27 23:38:03] -subtracting expr per gene, use_bounds=TRUE
INFO [2024-03-27 23:38:03] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2024-03-27 23:38:03] subtracting mean(normal) per gene per cell across all data
INFO [2024-03-27 23:38:03] -subtracting expr per gene, use_bounds=TRUE
INFO [2024-03-27 23:38:03] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2024-03-27 23:38:03] subtracting mean(normal) per gene per cell across all data
INFO [2024-03-27 23:38:03] -subtracting expr per gene, use_bounds=TRUE
INFO [2024-03-27 23:38:03] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2024-03-27 23:38:03] subtracting mean(normal) per gene per cell across all data
INFO [2024-03-27 23:38:03] -subtracting expr per gene, use_bounds=TRUE
WARN [2024-03-27 23:38:03] window length < 2, returning original unmodified data
WARN [2024-03-27 23:38:03] window length < 2, returning original unmodified data
INFO [2024-03-27 23:38:03] ::remove_outlier_norm:Start out_method: average_bound lower_bound: -1 upper_bound: 30
INFO [2024-03-27 23:38:03] ::remove_outlier_norm: using hard thresholds:  lower_bound: -1 upper_bound: 30
INFO [2024-03-27 23:38:03] ::remove_outlier_norm:Start out_method: average_bound lower_bound: 5 upper_bound: 15
INFO [2024-03-27 23:38:03] ::remove_outlier_norm: using hard thresholds:  lower_bound: 5 upper_bound: 15
INFO [2024-03-27 23:38:03] ::remove_outlier_norm:Start out_method: average_bound lower_bound: NA upper_bound: NA
INFO [2024-03-27 23:38:03] ::remove_outlier_norm using method: average_bound for defining outliers.
INFO [2024-03-27 23:38:03] outlier bounds defined between: -0.5 - 17.75
INFO [2024-03-27 23:38:03] ::order_reduce:Start.
INFO [2024-03-27 23:38:03] ::order_reduce:Start.
INFO [2024-03-27 23:38:03] .order_reduce(): expr and order match.
INFO [2024-03-27 23:38:03] ::process_data:order_reduce:Reduction from positional data, new dimensions (r,c) = 10,2 Total=110 Min=1 Max=10.
INFO [2024-03-27 23:38:03] ::order_reduce:Start.
INFO [2024-03-27 23:38:03] .order_reduce(): expr and order match.
INFO [2024-03-27 23:38:03] ::process_data:order_reduce:Reduction from positional data, new dimensions (r,c) = 10,2 Total=110 Min=1 Max=10.
INFO [2024-03-27 23:38:03] ::order_reduce:Start.
INFO [2024-03-27 23:38:03] ::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 
 12.229   0.649  12.866 

Example timings

infercnv.Rcheck/infercnv-Ex.timings

nameusersystemelapsed
CreateInfercnvObject0.0590.0160.075
apply_median_filtering4.1790.0324.212
color.palette0.0030.0000.003
filterHighPNormals0.0060.0080.013
inferCNVBayesNet151.634 3.108132.582
plot_cnv0.6900.0720.699
plot_per_group1.2020.0641.266
plot_subclusters0.8631.3002.161
run11.704 0.94412.648
sample_object0.0260.0000.026