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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_1.23.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/infercnv.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘infercnv/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘infercnv’ version ‘1.23.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 INFO
Imports includes 31 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 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 116.403  2.959 102.582
run               10.735  0.313  11.103
* 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 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-3.21-bioc/meat/infercnv.Rcheck/00check.log’
for details.

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###
### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL infercnv
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/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)

R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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 [2024-11-24 23:07:07] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2024-11-24 23:07:07] subtracting mean(normal) per gene per cell across all data
INFO [2024-11-24 23:07:07] -subtracting expr per gene, use_bounds=TRUE
INFO [2024-11-24 23:07:07] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2024-11-24 23:07:07] subtracting mean(normal) per gene per cell across all data
INFO [2024-11-24 23:07:08] -subtracting expr per gene, use_bounds=TRUE
INFO [2024-11-24 23:07:08] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2024-11-24 23:07:08] subtracting mean(normal) per gene per cell across all data
INFO [2024-11-24 23:07:08] -subtracting expr per gene, use_bounds=TRUE
INFO [2024-11-24 23:07:08] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2024-11-24 23:07:08] subtracting mean(normal) per gene per cell across all data
INFO [2024-11-24 23:07:08] -subtracting expr per gene, use_bounds=TRUE
INFO [2024-11-24 23:07:08] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2024-11-24 23:07:08] subtracting mean(normal) per gene per cell across all data
INFO [2024-11-24 23:07:08] -subtracting expr per gene, use_bounds=TRUE
INFO [2024-11-24 23:07:08] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2024-11-24 23:07:08] subtracting mean(normal) per gene per cell across all data
INFO [2024-11-24 23:07:08] -subtracting expr per gene, use_bounds=TRUE
WARN [2024-11-24 23:07:08] window length < 2, returning original unmodified data
WARN [2024-11-24 23:07:08] window length < 2, returning original unmodified data
INFO [2024-11-24 23:07:08] ::remove_outlier_norm:Start out_method: average_bound lower_bound: -1 upper_bound: 30
INFO [2024-11-24 23:07:08] ::remove_outlier_norm: using hard thresholds:  lower_bound: -1 upper_bound: 30
INFO [2024-11-24 23:07:08] ::remove_outlier_norm:Start out_method: average_bound lower_bound: 5 upper_bound: 15
INFO [2024-11-24 23:07:08] ::remove_outlier_norm: using hard thresholds:  lower_bound: 5 upper_bound: 15
INFO [2024-11-24 23:07:08] ::remove_outlier_norm:Start out_method: average_bound lower_bound: NA upper_bound: NA
INFO [2024-11-24 23:07:08] ::remove_outlier_norm using method: average_bound for defining outliers.
INFO [2024-11-24 23:07:08] outlier bounds defined between: -0.5 - 17.75
INFO [2024-11-24 23:07:08] ::order_reduce:Start.
INFO [2024-11-24 23:07:08] ::order_reduce:Start.
INFO [2024-11-24 23:07:08] .order_reduce(): expr and order match.
INFO [2024-11-24 23:07:08] ::process_data:order_reduce:Reduction from positional data, new dimensions (r,c) = 10,2 Total=110 Min=1 Max=10.
INFO [2024-11-24 23:07:08] ::order_reduce:Start.
INFO [2024-11-24 23:07:08] .order_reduce(): expr and order match.
INFO [2024-11-24 23:07:08] ::process_data:order_reduce:Reduction from positional data, new dimensions (r,c) = 10,2 Total=110 Min=1 Max=10.
INFO [2024-11-24 23:07:08] ::order_reduce:Start.
INFO [2024-11-24 23:07:08] ::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 
 10.602   0.920  11.594