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CHECK report for infercnv on machv2

This page was generated on 2020-10-17 11:58:44 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE infercnv PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 876/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
infercnv 1.4.0
Christophe Georgescu
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/infercnv
Branch: RELEASE_3_11
Last Commit: c422114
Last Changed Date: 2020-04-27 15:26:59 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: infercnv
Version: 1.4.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:infercnv.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings infercnv_1.4.0.tar.gz
StartedAt: 2020-10-17 02:12:10 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 02:21:41 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 571.3 seconds
RetCode: 0
Status:  OK 
CheckDir: infercnv.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:infercnv.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings infercnv_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/infercnv.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.4.0’
* 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 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
.plot_cnv_references: no visible binding for global variable
  ‘infercnv_obj’
Undefined global functions or variables:
  infercnv_obj
* 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
inferCNVBayesNet       284.065  4.481 252.154
run                     15.432  0.371  15.823
apply_median_filtering  10.700  0.105  10.814
* 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
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/infercnv.Rcheck/00check.log’
for details.



Installation output

infercnv.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/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 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 [2020-10-17 02:21:32] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2020-10-17 02:21:32] subtracting mean(normal) per gene per cell across all data
INFO [2020-10-17 02:21:32] -subtracting expr per gene, use_bounds=TRUE
INFO [2020-10-17 02:21:32] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2020-10-17 02:21:32] subtracting mean(normal) per gene per cell across all data
INFO [2020-10-17 02:21:32] -subtracting expr per gene, use_bounds=TRUE
INFO [2020-10-17 02:21:32] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2020-10-17 02:21:32] subtracting mean(normal) per gene per cell across all data
INFO [2020-10-17 02:21:32] -subtracting expr per gene, use_bounds=TRUE
INFO [2020-10-17 02:21:32] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2020-10-17 02:21:32] subtracting mean(normal) per gene per cell across all data
INFO [2020-10-17 02:21:32] -subtracting expr per gene, use_bounds=TRUE
INFO [2020-10-17 02:21:32] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2020-10-17 02:21:32] subtracting mean(normal) per gene per cell across all data
INFO [2020-10-17 02:21:32] -subtracting expr per gene, use_bounds=TRUE
INFO [2020-10-17 02:21:32] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2020-10-17 02:21:32] subtracting mean(normal) per gene per cell across all data
INFO [2020-10-17 02:21:32] -subtracting expr per gene, use_bounds=TRUE
WARN [2020-10-17 02:21:32] window length < 2, returning original unmodified data
WARN [2020-10-17 02:21:32] window length < 2, returning original unmodified data
INFO [2020-10-17 02:21:32] ::remove_outlier_norm:Start out_method: average_bound lower_bound: -1 upper_bound: 30
INFO [2020-10-17 02:21:32] ::remove_outlier_norm: using hard thresholds:  lower_bound: -1 upper_bound: 30
INFO [2020-10-17 02:21:32] ::remove_outlier_norm:Start out_method: average_bound lower_bound: 5 upper_bound: 15
INFO [2020-10-17 02:21:32] ::remove_outlier_norm: using hard thresholds:  lower_bound: 5 upper_bound: 15
INFO [2020-10-17 02:21:32] ::remove_outlier_norm:Start out_method: average_bound lower_bound: NA upper_bound: NA
INFO [2020-10-17 02:21:32] ::remove_outlier_norm using method: average_bound for defining outliers.
INFO [2020-10-17 02:21:32] outlier bounds defined between: -0.5 - 17.75
INFO [2020-10-17 02:21:32] ::order_reduce:Start.
INFO [2020-10-17 02:21:32] ::order_reduce:Start.
INFO [2020-10-17 02:21:32] .order_reduce(): expr and order match.
INFO [2020-10-17 02:21:33] ::process_data:order_reduce:Reduction from positional data, new dimensions (r,c) = 10,2 Total=110 Min=1 Max=10.
INFO [2020-10-17 02:21:33] ::order_reduce:Start.
INFO [2020-10-17 02:21:33] .order_reduce(): expr and order match.
INFO [2020-10-17 02:21:33] ::process_data:order_reduce:Reduction from positional data, new dimensions (r,c) = 10,2 Total=110 Min=1 Max=10.
INFO [2020-10-17 02:21:33] ::order_reduce:Start.
INFO [2020-10-17 02:21:33] ::process_data:order_reduce:The position file  and the expression file row (gene) names do not match.
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 39 | SKIPPED: 3 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 13.491   0.642  14.124 

Example timings

infercnv.Rcheck/infercnv-Ex.timings

nameusersystemelapsed
CreateInfercnvObject0.1220.0070.129
apply_median_filtering10.700 0.10510.814
color.palette0.0050.0000.005
filterHighPNormals0.0370.0030.040
inferCNVBayesNet284.065 4.481252.154
plot_cnv1.6800.1161.953
plot_per_group2.7890.1163.212
run15.432 0.37115.823
sample_object0.0390.0020.041