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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:deconvR.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings deconvR_1.2.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/deconvR.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘deconvR/DESCRIPTION’ ... OK
* this is package ‘deconvR’ version ‘1.2.0’
* package encoding: UTF-8
* 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 ‘deconvR’ 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
* 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:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL deconvR
###
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* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘deconvR’ ...
** 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 (deconvR)

R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 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(deconvR)
Loading required package: data.table
> 
> test_check("deconvR")
Received list of locations.
Reading file.
Reading file.
uniting...
BSmeth2Probe couldn't find any match between the probe IDs and
        WGBS data you have provided. Please make sure that you're using an
        appropriate probe ID locations with your WGBS data.
Received list of locations.
Reading file.
Reading file.
Received list of locations.
Reading file.
Reading file.
uniting...
BSmeth2Probe couldn't find any match between the probe IDs and
        WGBS data you have provided. Please make sure that you're using an
        appropriate probe ID locations with your WGBS data.
Received list of locations.
Reading file.
Reading file.
uniting...
BSmeth2Probe couldn't find any match between the probe IDs and
        WGBS data you have provided. Please make sure that you're using an
        appropriate probe ID locations with your WGBS data.
DECONVOLUTION WITH NNLS
SUMMARY OF PARTIAL R-SQUARED VALUES FOR NNLS: 
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
      1       1       1       1       1       1 
DECONVOLUTION WITH NNLS
SUMMARY OF PARTIAL R-SQUARED VALUES FOR NNLS: 
DECONVOLUTION WITH NNLS
DECONVOLUTION WITH NNLS
SUMMARY OF PARTIAL R-SQUARED VALUES FOR NNLS: 
SUMMARY OF PARTIAL R-SQUARED VALUES FOR NNLS : 
DECONVOLUTION WITH NNLS
SUMMARY OF PARTIAL R-SQUARED VALUES FOR NNLS: 
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
      1       1       1       1       1       1 
[1] "double"
DECONVOLUTION WITH NNLS
DECONVOLUTION WITH NNLS
SUMMARY OF PARTIAL R-SQUARED VALUES FOR NNLS: 
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
      1       1       1       1       1       1 
DECONVOLUTION WITH NNLS
DECONVOLUTION WITH NNLS
DECONVOLUTION WITH NNLS
DECONVOLUTION WITH SVR
SUMMARY OF PARTIAL R-SQUARED VALUES FOR SVR: 
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
      1       1       1       1       1       1 
DECONVOLUTION WITH SVR
SUMMARY OF PARTIAL R-SQUARED VALUES FOR SVR: 
DECONVOLUTION WITH SVR
DECONVOLUTION WITH SVR
SUMMARY OF PARTIAL R-SQUARED VALUES FOR SVR: 
SUMMARY OF PARTIAL R-SQUARED VALUES FOR SVR : 
DECONVOLUTION WITH SVR
SUMMARY OF PARTIAL R-SQUARED VALUES FOR SVR: 
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
      1       1       1       1       1       1 
[1] "double"
DECONVOLUTION WITH SVR
DECONVOLUTION WITH SVR
SUMMARY OF PARTIAL R-SQUARED VALUES FOR SVR: 
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
      1       1       1       1       1       1 
DECONVOLUTION WITH SVR
DECONVOLUTION WITH SVR
DECONVOLUTION WITH QP
SUMMARY OF PARTIAL R-SQUARED VALUES FOR QP: 
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
      1       1       1       1       1       1 
DECONVOLUTION WITH QP
SUMMARY OF PARTIAL R-SQUARED VALUES FOR QP: 
DECONVOLUTION WITH QP
DECONVOLUTION WITH QP
SUMMARY OF PARTIAL R-SQUARED VALUES FOR QP: 
SUMMARY OF PARTIAL R-SQUARED VALUES FOR QP : 
DECONVOLUTION WITH QP
SUMMARY OF PARTIAL R-SQUARED VALUES FOR QP: 
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
      1       1       1       1       1       1 
[1] "double"
DECONVOLUTION WITH QP
DECONVOLUTION WITH QP
SUMMARY OF PARTIAL R-SQUARED VALUES FOR QP: 
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
      1       1       1       1       1       1 
DECONVOLUTION WITH QP
DECONVOLUTION WITH QP
DECONVOLUTION WITH RLM
SUMMARY OF PARTIAL R-SQUARED VALUES FOR RLM: 
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
      1       1       1       1       1       1 
DECONVOLUTION WITH RLM
SUMMARY OF PARTIAL R-SQUARED VALUES FOR RLM: 
DECONVOLUTION WITH RLM

DECONVOLUTION WITH RLM
SUMMARY OF PARTIAL R-SQUARED VALUES FOR RLM: 
SUMMARY OF PARTIAL R-SQUARED VALUES FOR RLM : 
DECONVOLUTION WITH RLM
SUMMARY OF PARTIAL R-SQUARED VALUES FOR RLM: 
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
      1       1       1       1       1       1 
[1] "double"
DECONVOLUTION WITH RLM
DECONVOLUTION WITH RLM
SUMMARY OF PARTIAL R-SQUARED VALUES FOR RLM: 
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
      1       1       1       1       1       1 
DECONVOLUTION WITH RLM
DECONVOLUTION WITH RLM
CELL TYPES IN EXTENDED ATLAS: 
example_cell_type 
CELL TYPES IN EXTENDED ATLAS: 
else 
this 
that 
CELL TYPES IN EXTENDED ATLAS: 
else 
this 
that 
CELL TYPES IN EXTENDED ATLAS: 
else 
else_v2 
this_v2 
that_v2 
that 
this 
Monocytes_EPIC 
[ FAIL 0 | WARN 182 | SKIP 0 | PASS 146 ]

[ FAIL 0 | WARN 182 | SKIP 0 | PASS 146 ]
> 
> proc.time()
   user  system elapsed 
183.831   2.172 186.657