##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:randRotation.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings randRotation_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/randRotation.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘randRotation/DESCRIPTION’ ... OK
* this is package ‘randRotation’ version ‘1.18.0’
* 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 ‘randRotation’ 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 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 ... OK
* checking Rd files ... NOTE
checkRd: (-1) qqunif.Rd:35: Lost braces; missing escapes or markup?
    35 | A list of \code{x} and {y} coordinates, as in \code{\link[stats:qqnorm]{qqplot}}.
       |                        ^
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
      user system elapsed
pFdr 8.858   0.26   9.135
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  [3] 0.958 - 0.993 == -0.035391
  [4] 0.991 - 0.998 == -0.007912
  [5] 1.000 - 1.000 == -0.000377
  ── Failure ('test_rotateStat_pFdr.R:33:3'): Test execution of rotateStat (including parallel computation mode), pFdr with "fdr.q" and "fdr.qu" ──
  sort(pFdr(res1, "fdr.qu"))[1:10] not equal to c(0.87, 0.94, 0.99303, 0.99844, 0.99992, 0.99999, 1, 1, 1, 1).
  5/10 mismatches (average diff: 0.143)
  [1] 0.210 - 0.870 == -0.660000
  [2] 0.950 - 0.940 ==  0.010000
  [3] 0.958 - 0.993 == -0.035391
  [4] 0.991 - 0.998 == -0.007912
  [5] 1.000 - 1.000 == -0.000377
  
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 16 ]
  Error: Test failures
  Execution halted
* 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 ERROR, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/randRotation.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL randRotation
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘randRotation’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
Loading required namespace: randRotation
*** 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 (randRotation)

R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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(randRotation)
> 
> test_check("randRotation")
[ FAIL 3 | WARN 0 | SKIP 0 | PASS 16 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_rotateStat_pFdr.R:31:3'): Test execution of rotateStat (including parallel computation mode), pFdr with "fdr.q" and "fdr.qu" ──
sort(pFdr(res1))[1:10] not equal to c(...).
9/10 mismatches (average diff: 0.00167)
[1]  0.0022 - 0.0088 == -6.60e-03
[2]  0.0096 - 0.0095 ==  9.99e-05
[3]  0.0163 - 0.0151 ==  1.20e-03
[5]  0.0258 - 0.0259 == -1.00e-04
[6]  0.0263 - 0.0268 == -5.00e-04
[7]  0.0373 - 0.0362 ==  1.10e-03
[8]  0.0395 - 0.0394 ==  1.00e-04
[9]  0.0416 - 0.0457 == -4.10e-03
[10] 0.0461 - 0.0473 == -1.20e-03
── Failure ('test_rotateStat_pFdr.R:32:3'): Test execution of rotateStat (including parallel computation mode), pFdr with "fdr.q" and "fdr.qu" ──
sort(pFdr(res1, "fdr.q"))[1:10] not equal to c(0.87, 0.94, 0.99303, 0.99844, 0.99992, 0.99999, 1, 1, 1, 1).
5/10 mismatches (average diff: 0.143)
[1] 0.210 - 0.870 == -0.660000
[2] 0.950 - 0.940 ==  0.010000
[3] 0.958 - 0.993 == -0.035391
[4] 0.991 - 0.998 == -0.007912
[5] 1.000 - 1.000 == -0.000377
── Failure ('test_rotateStat_pFdr.R:33:3'): Test execution of rotateStat (including parallel computation mode), pFdr with "fdr.q" and "fdr.qu" ──
sort(pFdr(res1, "fdr.qu"))[1:10] not equal to c(0.87, 0.94, 0.99303, 0.99844, 0.99992, 0.99999, 1, 1, 1, 1).
5/10 mismatches (average diff: 0.143)
[1] 0.210 - 0.870 == -0.660000
[2] 0.950 - 0.940 ==  0.010000
[3] 0.958 - 0.993 == -0.035391
[4] 0.991 - 0.998 == -0.007912
[5] 1.000 - 1.000 == -0.000377

[ FAIL 3 | WARN 0 | SKIP 0 | PASS 16 ]
Error: Test failures
Execution halted