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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:infercnv.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings infercnv_1.4.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/infercnv.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (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       248.840  1.328 208.426
run                     11.542  0.036  11.579
apply_median_filtering   8.352  0.027   8.384
* 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
  ‘/home/biocbuild/bbs-3.11-bioc/meat/infercnv.Rcheck/00check.log’
for details.

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###
### Running command:
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###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL infercnv
###
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* installing to library ‘/home/biocbuild/bbs-3.11-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)

R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 02:29:39] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2020-10-17 02:29:39] subtracting mean(normal) per gene per cell across all data
INFO [2020-10-17 02:29:39] -subtracting expr per gene, use_bounds=TRUE
INFO [2020-10-17 02:29:39] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2020-10-17 02:29:39] subtracting mean(normal) per gene per cell across all data
INFO [2020-10-17 02:29:39] -subtracting expr per gene, use_bounds=TRUE
INFO [2020-10-17 02:29:39] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2020-10-17 02:29:39] subtracting mean(normal) per gene per cell across all data
INFO [2020-10-17 02:29:39] -subtracting expr per gene, use_bounds=TRUE
INFO [2020-10-17 02:29:39] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2020-10-17 02:29:39] subtracting mean(normal) per gene per cell across all data
INFO [2020-10-17 02:29:39] -subtracting expr per gene, use_bounds=TRUE
INFO [2020-10-17 02:29:39] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2020-10-17 02:29:39] subtracting mean(normal) per gene per cell across all data
INFO [2020-10-17 02:29:39] -subtracting expr per gene, use_bounds=TRUE
INFO [2020-10-17 02:29:39] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2020-10-17 02:29:39] subtracting mean(normal) per gene per cell across all data
INFO [2020-10-17 02:29:39] -subtracting expr per gene, use_bounds=TRUE
WARN [2020-10-17 02:29:39] window length < 2, returning original unmodified data
WARN [2020-10-17 02:29:39] window length < 2, returning original unmodified data
INFO [2020-10-17 02:29:39] ::remove_outlier_norm:Start out_method: average_bound lower_bound: -1 upper_bound: 30
INFO [2020-10-17 02:29:39] ::remove_outlier_norm: using hard thresholds:  lower_bound: -1 upper_bound: 30
INFO [2020-10-17 02:29:39] ::remove_outlier_norm:Start out_method: average_bound lower_bound: 5 upper_bound: 15
INFO [2020-10-17 02:29:39] ::remove_outlier_norm: using hard thresholds:  lower_bound: 5 upper_bound: 15
INFO [2020-10-17 02:29:39] ::remove_outlier_norm:Start out_method: average_bound lower_bound: NA upper_bound: NA
INFO [2020-10-17 02:29:39] ::remove_outlier_norm using method: average_bound for defining outliers.
INFO [2020-10-17 02:29:39] outlier bounds defined between: -0.5 - 17.75
INFO [2020-10-17 02:29:39] ::order_reduce:Start.
INFO [2020-10-17 02:29:39] ::order_reduce:Start.
INFO [2020-10-17 02:29:39] .order_reduce(): expr and order match.
INFO [2020-10-17 02:29:39] ::process_data:order_reduce:Reduction from positional data, new dimensions (r,c) = 10,2 Total=110 Min=1 Max=10.
INFO [2020-10-17 02:29:39] ::order_reduce:Start.
INFO [2020-10-17 02:29:39] .order_reduce(): expr and order match.
INFO [2020-10-17 02:29:39] ::process_data:order_reduce:Reduction from positional data, new dimensions (r,c) = 10,2 Total=110 Min=1 Max=10.
INFO [2020-10-17 02:29:39] ::order_reduce:Start.
INFO [2020-10-17 02:29:39] ::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 
 10.431   0.335  10.757