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### Running command:
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###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:BEARscc.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings BEARscc_1.10.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/BEARscc.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 ‘BEARscc/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BEARscc’ version ‘1.10.0’
* 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 ‘BEARscc’ 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 ... OK
* 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 ... 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
estimate_noiseparameters 15.380  0.112  14.710
simulate_replicates       7.648  0.028   7.862
* 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: OK

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### Running command:
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###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL BEARscc
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘BEARscc’ ...
** using staged installation
** R
** data
** 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 (BEARscc)

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.

> library(testthat)
> library(BEARscc)
> 
> test_check("BEARscc")

[1] "Running BEARscc on example data to test for correct installation."

[1] "Fitting parameter alpha to establish spike-in derived noise model."
[1] "Estimating error for spike-ins with alpha = 0"
[1] "Estimating error for spike-ins with alpha = 0.25"
[1] "Estimating error for spike-ins with alpha = 0.5"
[1] "Estimating error for spike-ins with alpha = 0.75"
[1] "Estimating error for spike-ins with alpha = 1"
[1] "There are adequate spike-in drop-outs to build the drop-out model. Estimating the drop-out model now."

[1] "Injecting noise for testing..."
[1] "Creating a simulated replicated counts matrix: 1."
[1] "Creating a simulated replicated counts matrix: 2."
[1] "Creating a simulated replicated counts matrix: 3."

[1] "Creating consensus matrix for testing..."

[1] "Computing cluster and cell metrics for testing..."
══ Warnings ════════════════════════════════════════════════════════════════════
── Warning (test_noise.R:75:1): (code run outside of `test_that()`) ────────────
The melt generic in data.table has been passed a list and will attempt to redirect to the relevant reshape2 method; please note that reshape2 is deprecated, and this redirection is now deprecated as well. To continue using melt methods from reshape2 while both libraries are attached, e.g. melt.list, you can prepend the namespace like reshape2::melt(metric_list). In the next version, this warning will become an error.
Backtrace:
 1. BEARscc::report_cluster_metrics(...) test_noise.R:75:0
 3. base::lapply(...)
 4. BEARscc:::FUN(X[[i]], ...)
 5. data.table::melt(metric_list, id.vars = c("size"))
── Warning (test_noise.R:75:1): (code run outside of `test_that()`) ────────────
The melt generic in data.table has been passed a list and will attempt to redirect to the relevant reshape2 method; please note that reshape2 is deprecated, and this redirection is now deprecated as well. To continue using melt methods from reshape2 while both libraries are attached, e.g. melt.list, you can prepend the namespace like reshape2::melt(metric_list). In the next version, this warning will become an error.
Backtrace:
 1. BEARscc::report_cluster_metrics(...) test_noise.R:75:0
 3. base::lapply(...)
 4. BEARscc:::FUN(X[[i]], ...)
 5. data.table::melt(metric_list, id.vars = c("size"))
── Warning (test_noise.R:75:1): (code run outside of `test_that()`) ────────────
The melt generic in data.table has been passed a list and will attempt to redirect to the relevant reshape2 method; please note that reshape2 is deprecated, and this redirection is now deprecated as well. To continue using melt methods from reshape2 while both libraries are attached, e.g. melt.list, you can prepend the namespace like reshape2::melt(metric_list). In the next version, this warning will become an error.
Backtrace:
 1. BEARscc::report_cluster_metrics(...) test_noise.R:75:0
 3. base::lapply(...)
 4. BEARscc:::FUN(X[[i]], ...)
 5. data.table::melt(metric_list, id.vars = c("size"))
── Warning (test_noise.R:75:1): (code run outside of `test_that()`) ────────────
The melt generic in data.table has been passed a list and will attempt to redirect to the relevant reshape2 method; please note that reshape2 is deprecated, and this redirection is now deprecated as well. To continue using melt methods from reshape2 while both libraries are attached, e.g. melt.list, you can prepend the namespace like reshape2::melt(metric_list). In the next version, this warning will become an error.
Backtrace:
 1. BEARscc::report_cluster_metrics(...) test_noise.R:75:0
 3. base::lapply(...)
 4. BEARscc:::FUN(X[[i]], ...)
 5. data.table::melt(metric_list, id.vars = c("size"))
── Warning (test_noise.R:75:1): (code run outside of `test_that()`) ────────────
The melt generic in data.table has been passed a list and will attempt to redirect to the relevant reshape2 method; please note that reshape2 is deprecated, and this redirection is now deprecated as well. To continue using melt methods from reshape2 while both libraries are attached, e.g. melt.list, you can prepend the namespace like reshape2::melt(metric_list). In the next version, this warning will become an error.
Backtrace:
 1. BEARscc::report_cluster_metrics(...) test_noise.R:75:0
 3. base::lapply(...)
 4. BEARscc:::FUN(X[[i]], ...)
 5. data.table::melt(metric_list, id.vars = c("size"))
── Warning (test_noise.R:75:1): (code run outside of `test_that()`) ────────────
The melt generic in data.table has been passed a list and will attempt to redirect to the relevant reshape2 method; please note that reshape2 is deprecated, and this redirection is now deprecated as well. To continue using melt methods from reshape2 while both libraries are attached, e.g. melt.list, you can prepend the namespace like reshape2::melt(cluster.scores). In the next version, this warning will become an error.
Backtrace:
 1. BEARscc::report_cluster_metrics(...) test_noise.R:75:0
 3. data.table::melt(cluster.scores, id.var = c("rn", "size", "metric"))
── Warning (test_noise.R:77:1): (code run outside of `test_that()`) ────────────
The melt generic in data.table has been passed a list and will attempt to redirect to the relevant reshape2 method; please note that reshape2 is deprecated, and this redirection is now deprecated as well. To continue using melt methods from reshape2 while both libraries are attached, e.g. melt.list, you can prepend the namespace like reshape2::melt(lapply(cluster_names, calculate_cell_metrics_by_cluster, consensus_matrix = consensus_matrix,     cluster_labels = cluster_labels)). In the next version, this warning will become an error.
Backtrace:
 1. BEARscc::report_cell_metrics(BEARscc_clusts.df, noise_consensus) test_noise.R:77:0
 2. base::lapply(...)
 3. BEARscc:::FUN(X[[i]], ...)
 5. data.table::melt(...)
── Warning (test_noise.R:77:1): (code run outside of `test_that()`) ────────────
The melt generic in data.table has been passed a list and will attempt to redirect to the relevant reshape2 method; please note that reshape2 is deprecated, and this redirection is now deprecated as well. To continue using melt methods from reshape2 while both libraries are attached, e.g. melt.list, you can prepend the namespace like reshape2::melt(lapply(cluster_names, calculate_cell_metrics_by_cluster, consensus_matrix = consensus_matrix,     cluster_labels = cluster_labels)). In the next version, this warning will become an error.
Backtrace:
 1. BEARscc::report_cell_metrics(BEARscc_clusts.df, noise_consensus) test_noise.R:77:0
 2. base::lapply(...)
 3. BEARscc:::FUN(X[[i]], ...)
 5. data.table::melt(...)
── Warning (test_noise.R:77:1): (code run outside of `test_that()`) ────────────
The melt generic in data.table has been passed a list and will attempt to redirect to the relevant reshape2 method; please note that reshape2 is deprecated, and this redirection is now deprecated as well. To continue using melt methods from reshape2 while both libraries are attached, e.g. melt.list, you can prepend the namespace like reshape2::melt(lapply(cluster_names, calculate_cell_metrics_by_cluster, consensus_matrix = consensus_matrix,     cluster_labels = cluster_labels)). In the next version, this warning will become an error.
Backtrace:
 1. BEARscc::report_cell_metrics(BEARscc_clusts.df, noise_consensus) test_noise.R:77:0
 2. base::lapply(...)
 3. BEARscc:::FUN(X[[i]], ...)
 5. data.table::melt(...)
── Warning (test_noise.R:77:1): (code run outside of `test_that()`) ────────────
The melt generic in data.table has been passed a list and will attempt to redirect to the relevant reshape2 method; please note that reshape2 is deprecated, and this redirection is now deprecated as well. To continue using melt methods from reshape2 while both libraries are attached, e.g. melt.list, you can prepend the namespace like reshape2::melt(lapply(cluster_names, calculate_cell_metrics_by_cluster, consensus_matrix = consensus_matrix,     cluster_labels = cluster_labels)). In the next version, this warning will become an error.
Backtrace:
 1. BEARscc::report_cell_metrics(BEARscc_clusts.df, noise_consensus) test_noise.R:77:0
 2. base::lapply(...)
 3. BEARscc:::FUN(X[[i]], ...)
 5. data.table::melt(...)
── Warning (test_noise.R:77:1): (code run outside of `test_that()`) ────────────
The melt generic in data.table has been passed a list and will attempt to redirect to the relevant reshape2 method; please note that reshape2 is deprecated, and this redirection is now deprecated as well. To continue using melt methods from reshape2 while both libraries are attached, e.g. melt.list, you can prepend the namespace like reshape2::melt(lapply(cluster_names, calculate_cell_metrics_by_cluster, consensus_matrix = consensus_matrix,     cluster_labels = cluster_labels)). In the next version, this warning will become an error.
Backtrace:
 1. BEARscc::report_cell_metrics(BEARscc_clusts.df, noise_consensus) test_noise.R:77:0
 2. base::lapply(...)
 3. BEARscc:::FUN(X[[i]], ...)
 5. data.table::melt(...)
── Warning (test_noise.R:77:1): (code run outside of `test_that()`) ────────────
The melt generic in data.table has been passed a list and will attempt to redirect to the relevant reshape2 method; please note that reshape2 is deprecated, and this redirection is now deprecated as well. To continue using melt methods from reshape2 while both libraries are attached, e.g. melt.list, you can prepend the namespace like reshape2::melt(lapply(cluster_names, calculate_cell_metrics_by_cluster, consensus_matrix = consensus_matrix,     cluster_labels = cluster_labels)). In the next version, this warning will become an error.
Backtrace:
 1. BEARscc::report_cell_metrics(BEARscc_clusts.df, noise_consensus) test_noise.R:77:0
 2. base::lapply(...)
 3. BEARscc:::FUN(X[[i]], ...)
 5. data.table::melt(...)
── Warning (test_noise.R:77:1): (code run outside of `test_that()`) ────────────
The melt generic in data.table has been passed a list and will attempt to redirect to the relevant reshape2 method; please note that reshape2 is deprecated, and this redirection is now deprecated as well. To continue using melt methods from reshape2 while both libraries are attached, e.g. melt.list, you can prepend the namespace like reshape2::melt(cell.scores). In the next version, this warning will become an error.
Backtrace:
 1. BEARscc::report_cell_metrics(BEARscc_clusts.df, noise_consensus) test_noise.R:77:0
 3. data.table::melt(...)

[ FAIL 0 | WARN 13 | SKIP 0 | PASS 25 ]
> 
> proc.time()
   user  system elapsed 
 26.116   0.412  26.837