##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:uSORT.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings uSORT_1.27.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/uSORT.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘uSORT/DESCRIPTION’ ... OK
* this is package ‘uSORT’ version ‘1.27.0’
* 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 ‘uSORT’ can be installed ... WARNING
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/home/biocbuild/bbs-3.18-bioc/meat/uSORT.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
* 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 loading without being on the library search path ... 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 ... NOTE
mcesApply1: no visible global function definition for ‘clusterEvalQ’
mcesApply1: no visible global function definition for ‘parRapply’
mcesApply1: no visible global function definition for ‘parCapply’
Undefined global functions or variables:
  clusterEvalQ parCapply parRapply
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
sWanderlust 28.994  0.522  29.554
autoSPIN    17.251  0.276  17.548
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘uSORT_quick_start.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘uSORT_quick_start.Rmd’ using rmarkdown
Error: processing vignette 'uSORT_quick_start.Rmd' failed with diagnostics:
there is no package called ‘BiocStyle’
--- failed re-building ‘uSORT_quick_start.Rmd’

SUMMARY: processing the following file failed:
  ‘uSORT_quick_start.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/uSORT.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL uSORT
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’
* installing *source* package ‘uSORT’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
No methods found in package ‘BiocGenerics’ for request: ‘clusterEvalQ’ when loading ‘uSORT’
No methods found in package ‘BiocGenerics’ for request: ‘parCapply’ when loading ‘uSORT’
No methods found in package ‘BiocGenerics’ for request: ‘parRapply’ when loading ‘uSORT’
Note: break used in wrong context: no loop is visible 
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
No methods found in package ‘BiocGenerics’ for request: ‘clusterEvalQ’ when loading ‘uSORT’
No methods found in package ‘BiocGenerics’ for request: ‘parCapply’ when loading ‘uSORT’
No methods found in package ‘BiocGenerics’ for request: ‘parRapply’ when loading ‘uSORT’
** testing if installed package can be loaded from final location
No methods found in package ‘BiocGenerics’ for request: ‘clusterEvalQ’ when loading ‘uSORT’
No methods found in package ‘BiocGenerics’ for request: ‘parCapply’ when loading ‘uSORT’
No methods found in package ‘BiocGenerics’ for request: ‘parRapply’ when loading ‘uSORT’
** testing if installed package keeps a record of temporary installation path
* DONE (uSORT)

R version 4.3.0 (2023-04-21) -- "Already Tomorrow"
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.

> BiocGenerics:::testPackage("uSORT")
No methods found in package 'BiocGenerics' for request: 'clusterEvalQ' when loading 'uSORT'
No methods found in package 'BiocGenerics' for request: 'parCapply' when loading 'uSORT'
No methods found in package 'BiocGenerics' for request: 'parRapply' when loading 'uSORT'
No starting point specified, the first row will be used!
  Building lNN graph...
    lNN computed in: 0 seconds
    Randomly Select waypoints...
    Flock waypoints...
  Iteratively realign trajectory: 
    Running iterations... 1
      Correlation with previous iteration: 0.985372
    Running iterations... 2
      Correlation with previous iteration: 0.99972
    Running iterations... 3
      Correlation with previous iteration: 0.999971
  Wanderlust Sorting Done!


RUNIT TEST PROTOCOL -- Tue Jun  6 09:14:08 2023 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
uSORT RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  6.237   0.483   6.724