Back to Multiple platform build/check report for BioC 3.16:   simplified   long
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This page was generated on 2023-04-12 11:05:37 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
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

CHECK results for infercnv on palomino4


To the developers/maintainers of the infercnv package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 971/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
infercnv 1.14.2  (landing page)
Christophe Georgescu
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/infercnv
git_branch: RELEASE_3_16
git_last_commit: 1cf5a95
git_last_commit_date: 2023-03-08 11:11:29 -0400 (Wed, 08 Mar 2023)
nebbiolo2Linux (Ubuntu 20.04.5 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
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: infercnv
Version: 1.14.2
Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:infercnv.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings infercnv_1.14.2.tar.gz
StartedAt: 2023-04-11 02:30:38 -0400 (Tue, 11 Apr 2023)
EndedAt: 2023-04-11 02:38:08 -0400 (Tue, 11 Apr 2023)
EllapsedTime: 449.7 seconds
RetCode: 0
Status:   OK  
CheckDir: infercnv.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:infercnv.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings infercnv_1.14.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/infercnv.Rcheck'
* using R version 4.2.3 (2023-03-15 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'infercnv/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'infercnv' version '1.14.2'
* 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 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 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 ... 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 ... NOTE
.whole_dataset_leiden_subclustering_per_chr: no visible binding for
  global variable 'tumor_group'
Undefined global functions or variables:
  tumor_group
* 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 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 173.54   2.27  175.73
run               12.16   0.11   12.26
* 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: 2 NOTEs
See
  'F:/biocbuild/bbs-3.16-bioc/meat/infercnv.Rcheck/00check.log'
for details.



Installation output

infercnv.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL infercnv
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/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 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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.

> #!/usr/bin/env Rscript
> 
> library(testthat)
> library(infercnv)
> 
> test_check("infercnv")
INFO [2023-04-11 02:37:55] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2023-04-11 02:37:55] subtracting mean(normal) per gene per cell across all data
INFO [2023-04-11 02:37:55] -subtracting expr per gene, use_bounds=TRUE
INFO [2023-04-11 02:37:55] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2023-04-11 02:37:55] subtracting mean(normal) per gene per cell across all data
INFO [2023-04-11 02:37:55] -subtracting expr per gene, use_bounds=TRUE
INFO [2023-04-11 02:37:55] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2023-04-11 02:37:55] subtracting mean(normal) per gene per cell across all data
INFO [2023-04-11 02:37:55] -subtracting expr per gene, use_bounds=TRUE
INFO [2023-04-11 02:37:55] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2023-04-11 02:37:55] subtracting mean(normal) per gene per cell across all data
INFO [2023-04-11 02:37:55] -subtracting expr per gene, use_bounds=TRUE
INFO [2023-04-11 02:37:55] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2023-04-11 02:37:55] subtracting mean(normal) per gene per cell across all data
INFO [2023-04-11 02:37:55] -subtracting expr per gene, use_bounds=TRUE
INFO [2023-04-11 02:37:55] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2023-04-11 02:37:55] subtracting mean(normal) per gene per cell across all data
INFO [2023-04-11 02:37:55] -subtracting expr per gene, use_bounds=TRUE
WARN [2023-04-11 02:37:55] window length < 2, returning original unmodified data
WARN [2023-04-11 02:37:55] window length < 2, returning original unmodified data
INFO [2023-04-11 02:37:55] ::remove_outlier_norm:Start out_method: average_bound lower_bound: -1 upper_bound: 30
INFO [2023-04-11 02:37:55] ::remove_outlier_norm: using hard thresholds:  lower_bound: -1 upper_bound: 30
INFO [2023-04-11 02:37:55] ::remove_outlier_norm:Start out_method: average_bound lower_bound: 5 upper_bound: 15
INFO [2023-04-11 02:37:55] ::remove_outlier_norm: using hard thresholds:  lower_bound: 5 upper_bound: 15
INFO [2023-04-11 02:37:55] ::remove_outlier_norm:Start out_method: average_bound lower_bound: NA upper_bound: NA
INFO [2023-04-11 02:37:55] ::remove_outlier_norm using method: average_bound for defining outliers.
INFO [2023-04-11 02:37:55] outlier bounds defined between: -0.5 - 17.75
INFO [2023-04-11 02:37:55] ::order_reduce:Start.
INFO [2023-04-11 02:37:55] ::order_reduce:Start.
INFO [2023-04-11 02:37:55] .order_reduce(): expr and order match.
INFO [2023-04-11 02:37:55] ::process_data:order_reduce:Reduction from positional data, new dimensions (r,c) = 10,2 Total=110 Min=1 Max=10.
INFO [2023-04-11 02:37:55] ::order_reduce:Start.
INFO [2023-04-11 02:37:55] .order_reduce(): expr and order match.
INFO [2023-04-11 02:37:55] ::process_data:order_reduce:Reduction from positional data, new dimensions (r,c) = 10,2 Total=110 Min=1 Max=10.
INFO [2023-04-11 02:37:55] ::order_reduce:Start.
INFO [2023-04-11 02:37:55] ::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 ═══════════════════════════════════════════════════════════════
• empty test (3)

[ FAIL 0 | WARN 0 | SKIP 3 | PASS 39 ]
> 
> proc.time()
   user  system elapsed 
  11.01    0.87   11.82 

Example timings

infercnv.Rcheck/infercnv-Ex.timings

nameusersystemelapsed
CreateInfercnvObject0.090.010.11
apply_median_filtering3.990.084.06
color.palette000
filterHighPNormals0.020.000.02
inferCNVBayesNet173.54 2.27175.73
plot_cnv0.470.140.63
plot_per_group1.470.201.69
run12.16 0.1112.26
sample_object0.030.000.03