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###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:uSORT.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings uSORT_1.32.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/uSORT.Rcheck'
* using R version 4.4.2 (2024-10-31 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'uSORT/DESCRIPTION' ... OK
* this is package 'uSORT' version '1.32.0'
* 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 whether package 'uSORT' can be installed ... WARNING
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'F:/biocbuild/bbs-3.20-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 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 ... 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 21.75   1.19   22.94
autoSPIN    14.31   0.58   14.89
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'runTests.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: 1 WARNING, 1 NOTE
See
  'F:/biocbuild/bbs-3.20-bioc/meat/uSORT.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL uSORT
###
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* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/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 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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 -- Fri Dec 20 07:07:15 2024 
*********************************************** 
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 
   5.12    0.62    5.79