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This page was generated on 2021-11-27 14:05:42 -0500 (Sat, 27 Nov 2021).

CHECK results for infercnv on merida1

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? here 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 924/2068HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
infercnv 1.11.1  (landing page)
Christophe Georgescu
Snapshot Date: 2021-11-26 14:50:14 -0500 (Fri, 26 Nov 2021)
git_url: https://git.bioconductor.org/packages/infercnv
git_branch: master
git_last_commit: bc68968
git_last_commit_date: 2021-11-08 13:30:08 -0500 (Mon, 08 Nov 2021)
nebbiolo1Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    ERROR  skippedskipped
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: infercnv
Version: 1.11.1
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_1.11.1.tar.gz
StartedAt: 2021-11-27 04:07:16 -0500 (Sat, 27 Nov 2021)
EndedAt: 2021-11-27 04:17:43 -0500 (Sat, 27 Nov 2021)
EllapsedTime: 626.9 seconds
RetCode: 0
Status:   OK  
CheckDir: infercnv.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### 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_1.11.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/infercnv.Rcheck’
* using R Under development (unstable) (2021-11-01 r81125)
* 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 ‘1.11.1’
* 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 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
.parameterize_random_cluster_heights: no visible global function
  definition for ‘parllelDist’
Undefined global functions or variables:
  parllelDist
* 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       312.662  3.630 275.533
run                     17.567  0.429  18.021
apply_median_filtering  11.367  0.089  11.472
* 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-3.15-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/4.2/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 Under development (unstable) (2021-11-01 r81125) -- "Unsuffered Consequences"
Copyright (C) 2021 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 [2021-11-27 04:17:33] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2021-11-27 04:17:33] subtracting mean(normal) per gene per cell across all data
INFO [2021-11-27 04:17:33] -subtracting expr per gene, use_bounds=TRUE
INFO [2021-11-27 04:17:33] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2021-11-27 04:17:33] subtracting mean(normal) per gene per cell across all data
INFO [2021-11-27 04:17:33] -subtracting expr per gene, use_bounds=TRUE
INFO [2021-11-27 04:17:33] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2021-11-27 04:17:33] subtracting mean(normal) per gene per cell across all data
INFO [2021-11-27 04:17:33] -subtracting expr per gene, use_bounds=TRUE
INFO [2021-11-27 04:17:33] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2021-11-27 04:17:33] subtracting mean(normal) per gene per cell across all data
INFO [2021-11-27 04:17:33] -subtracting expr per gene, use_bounds=TRUE
INFO [2021-11-27 04:17:33] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2021-11-27 04:17:33] subtracting mean(normal) per gene per cell across all data
INFO [2021-11-27 04:17:33] -subtracting expr per gene, use_bounds=TRUE
INFO [2021-11-27 04:17:33] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2021-11-27 04:17:33] subtracting mean(normal) per gene per cell across all data
INFO [2021-11-27 04:17:33] -subtracting expr per gene, use_bounds=TRUE
WARN [2021-11-27 04:17:33] window length < 2, returning original unmodified data
WARN [2021-11-27 04:17:33] window length < 2, returning original unmodified data
INFO [2021-11-27 04:17:33] ::remove_outlier_norm:Start out_method: average_bound lower_bound: -1 upper_bound: 30
INFO [2021-11-27 04:17:33] ::remove_outlier_norm: using hard thresholds:  lower_bound: -1 upper_bound: 30
INFO [2021-11-27 04:17:33] ::remove_outlier_norm:Start out_method: average_bound lower_bound: 5 upper_bound: 15
INFO [2021-11-27 04:17:33] ::remove_outlier_norm: using hard thresholds:  lower_bound: 5 upper_bound: 15
INFO [2021-11-27 04:17:33] ::remove_outlier_norm:Start out_method: average_bound lower_bound: NA upper_bound: NA
INFO [2021-11-27 04:17:33] ::remove_outlier_norm using method: average_bound for defining outliers.
INFO [2021-11-27 04:17:33] outlier bounds defined between: -0.5 - 17.75
INFO [2021-11-27 04:17:33] ::order_reduce:Start.
INFO [2021-11-27 04:17:33] ::order_reduce:Start.
INFO [2021-11-27 04:17:33] .order_reduce(): expr and order match.
INFO [2021-11-27 04:17:33] ::process_data:order_reduce:Reduction from positional data, new dimensions (r,c) = 10,2 Total=110 Min=1 Max=10.
INFO [2021-11-27 04:17:33] ::order_reduce:Start.
INFO [2021-11-27 04:17:33] .order_reduce(): expr and order match.
INFO [2021-11-27 04:17:33] ::process_data:order_reduce:Reduction from positional data, new dimensions (r,c) = 10,2 Total=110 Min=1 Max=10.
INFO [2021-11-27 04:17:33] ::order_reduce:Start.
INFO [2021-11-27 04:17:33] ::process_data:order_reduce:The position file  and the expression file row (gene) names do not match.
══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (3)

[ FAIL 0 | WARN 0 | SKIP 3 | PASS 39 ]
> 
> proc.time()
   user  system elapsed 
 14.035   0.665  14.703 

Example timings

infercnv.Rcheck/infercnv-Ex.timings

nameusersystemelapsed
CreateInfercnvObject0.1610.0150.176
apply_median_filtering11.367 0.08911.472
color.palette0.0050.0000.005
filterHighPNormals0.0360.0020.038
inferCNVBayesNet312.662 3.630275.533
plot_cnv1.3350.0781.421
plot_per_group2.4790.0552.550
run17.567 0.42918.021
sample_object0.0450.0020.047