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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:dcanr.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings dcanr_1.15.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/dcanr.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘dcanr/DESCRIPTION’ ... OK
* this is package ‘dcanr’ version ‘1.15.0’
* 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 ‘dcanr’ can be installed ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ...Warning in person1(given = given[[i]], family = family[[i]], middle = middle[[i]],  :
  It is recommended to use ‘given’ instead of ‘middle’.
 OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... WARNING
Invalid citation information in ‘inst/CITATION’:
  Warning message:
  In utils::packageDescription(basename(dir), dirname(dir)) :
    no package 'dcanr' was found
* 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 loading without being on the library search path ... WARNING
Error in library(dcanr, lib.loc = "/home/biocbuild/bbs-3.17-bioc/R/library") : 
  there is no package called ‘dcanr’
Execution halted

It looks like this package has a loading problem when not on .libPaths:
see the messages for details.
* 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 ... NOTE
ftgi.score: no visible binding for global variable ‘i’
ftgi.score: no visible binding for global variable ‘j’
Undefined global functions or variables:
  i j
* 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 ... SKIPPED
* 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 ...
  ‘dcanr_evaluation_vignette.Rmd’ using ‘UTF-8’... OK
  ‘dcanr_vignette.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/dcanr.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL dcanr
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* installing *source* package ‘dcanr’ ...
** using staged installation
Warning in person1(given = given[[i]], family = family[[i]], middle = middle[[i]],  :
  It is recommended to use ‘given’ instead of ‘middle’.
Warning in person1(given = given[[i]], family = family[[i]], middle = middle[[i]],  :
  It is recommended to use ‘given’ instead of ‘middle’.
** R
** data
** inst
** byte-compile and prepare package for lazy loading
in method for ‘dcScore’ with signature ‘"Matrix","ANY","ANY"’: no definition for class “Matrix”
in method for ‘dcScore’ with signature ‘"ExpressionSet","ANY","ANY"’: no definition for class “ExpressionSet”
in method for ‘dcScore’ with signature ‘"SummarizedExperiment","ANY","ANY"’: no definition for class “SummarizedExperiment”
in method for ‘dcScore’ with signature ‘"DGEList","ANY","ANY"’: no definition for class “DGEList”
** 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 (dcanr)

R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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(dcanr)
> 
> test_check("dcanr")
Begin Phase I (Initial E-Step) ...
Begin Phase II (M2-Step) ...
Begin Phase III ([E M1] Cycle) ...
Iteration: 1 
Iteration: 2 
One-Stepper Time: 0.0109999999999992 
Estimating optimal shrinkage intensity lambda (correlation matrix): 0.6287 

Estimating optimal shrinkage intensity lambda (correlation matrix): 1 

Estimate (local) false discovery rates (partial correlations):
Estimate (local) false discovery rates (partial correlations):
Begin Phase I (Initial E-Step) ...
Begin Phase II (M2-Step) ...
Begin Phase III ([E M1] Cycle) ...
Iteration: 1 
Iteration: 2 
One-Stepper Time: 0.00900000000000034 
Estimating optimal shrinkage intensity lambda (correlation matrix): 0.6287 

Estimating optimal shrinkage intensity lambda (correlation matrix): 1 

Estimate (local) false discovery rates (partial correlations):
Estimate (local) false discovery rates (partial correlations):
Begin Phase I (Initial E-Step) ...
Begin Phase II (M2-Step) ...
Begin Phase III ([E M1] Cycle) ...
Iteration: 1 
Iteration: 2 
One-Stepper Time: 0.00900000000000034 
Estimating optimal shrinkage intensity lambda (correlation matrix): 0.6287 

Estimating optimal shrinkage intensity lambda (correlation matrix): 1 

Estimate (local) false discovery rates (partial correlations):
Estimate (local) false discovery rates (partial correlations):
Begin Phase I (Initial E-Step) ...
Begin Phase II (M2-Step) ...
Begin Phase III ([E M1] Cycle) ...
Iteration: 1 
Iteration: 2 
One-Stepper Time: 0.0100000000000016 
Estimating optimal shrinkage intensity lambda (correlation matrix): 0.6287 

Estimating optimal shrinkage intensity lambda (correlation matrix): 1 

Estimate (local) false discovery rates (partial correlations):
Estimate (local) false discovery rates (partial correlations):
Begin Phase I (Initial E-Step) ...
Begin Phase II (M2-Step) ...
Begin Phase III ([E M1] Cycle) ...
Iteration: 1 
Iteration: 2 
One-Stepper Time: 0.00900000000000034 
Begin Phase I (Initial E-Step) ...
Begin Phase II (M2-Step) ...
Begin Phase III ([E M1] Cycle) ...
Iteration: 1 
Iteration: 2 
One-Stepper Time: 0.00900000000000034 
Estimating optimal shrinkage intensity lambda (correlation matrix): 0.6287 

Estimating optimal shrinkage intensity lambda (correlation matrix): 1 

Estimate (local) false discovery rates (partial correlations):
Estimate (local) false discovery rates (partial correlations):
Estimating optimal shrinkage intensity lambda (correlation matrix): 0.6287 

Estimating optimal shrinkage intensity lambda (correlation matrix): 1 

Estimate (local) false discovery rates (partial correlations):
Estimate (local) false discovery rates (partial correlations):
Begin Phase I (Initial E-Step) ...
Begin Phase II (M2-Step) ...
Begin Phase III ([E M1] Cycle) ...
Iteration: 1 
Iteration: 2 
One-Stepper Time: 0.00999999999999801 
Begin Phase I (Initial E-Step) ...
Begin Phase II (M2-Step) ...
Begin Phase III ([E M1] Cycle) ...
Iteration: 1 
Iteration: 2 
One-Stepper Time: 0.00900000000000034 
[ FAIL 0 | WARN 313 | SKIP 0 | PASS 172 ]

[ FAIL 0 | WARN 313 | SKIP 0 | PASS 172 ]
> 
> proc.time()
   user  system elapsed 
 20.998   0.435  21.475