##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:spicyR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings spicyR_1.19.3.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/spicyR.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* 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 ‘spicyR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘spicyR’ version ‘1.19.3’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 28 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 ‘spicyR’ 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 ... NOTE
.format_data: no visible binding for global variable ‘imageID’
.format_data: no visible binding for global variable ‘cellType’
bubblePlot: no visible binding for global variable ‘parent’
bubblePlot: no visible binding for global variable ‘cellTypeB_id’
bubblePlot: no visible binding for global variable ‘cellTypeB_numeric’
bubblePlot: no visible binding for global variable ‘condition’
convPairs: no visible binding for global variable ‘rowname’
convPairs: no visible binding for global variable ‘cellType_from’
convPairs: no visible binding for global variable ‘cellType_to’
convPairs: no visible binding for global variable ‘one’
convPairs: no visible binding for global variable ‘n_close’
convPairs: no visible binding for global variable ‘n’
convPairs: no visible binding for global variable ‘test’
convPairs: no visible binding for global variable ‘association’
getCellSummary: no visible binding for global variable ‘cellID’
getCellSummary: no visible binding for global variable ‘imageCellID’
getCellSummary: no visible binding for global variable ‘x’
getCellSummary: no visible binding for global variable ‘y’
getCellSummary: no visible binding for global variable ‘cellType’
getCellSummary: no visible binding for global variable ‘.’
getCellType: no visible binding for global variable ‘cellType’
inhomL: no visible binding for global variable ‘j’
inhomL: no visible binding for global variable ‘value’
inhomL: no visible binding for global variable ‘i’
inhomL: no visible binding for global variable ‘d’
inhomL: no visible binding for global variable ‘cellTypeI’
inhomL: no visible binding for global variable ‘cellTypeJ’
inhomL: no visible global function definition for ‘.’
inhomL: no visible binding for global variable ‘wt’
inhomLPair: no visible binding for global variable ‘cellTypeI’
inhomLPair: no visible binding for global variable ‘cellTypeJ’
spatialSurv : <anonymous>: no visible global function definition for
  ‘pchisq’
spatialSurv: no visible binding for global variable ‘test’
spatialSurv: no visible binding for global variable ‘coef’
spatialSurv: no visible binding for global variable ‘se.coef’
spatialSurv: no visible binding for global variable ‘p.value’
spicyBoxPlot: no visible binding for global variable ‘condition’
survBubble: no visible binding for global variable ‘test’
survBubble: no visible binding for global variable ‘parent’
survBubble: no visible binding for global variable ‘to’
survBubble: no visible binding for global variable ‘from’
survBubble: no visible global function definition for ‘filter’
survBubble: no visible binding for global variable ‘p.value’
survBubble: no visible binding for global variable ‘logP’
survBubble: no visible binding for global variable ‘coef’
survBubble: no visible binding for global variable ‘sig’
Undefined global functions or variables:
  . association cellID cellType cellTypeB_id cellTypeB_numeric
  cellTypeI cellTypeJ cellType_from cellType_to coef condition d filter
  from i imageCellID imageID j logP n n_close one p.value parent pchisq
  rowname se.coef sig test to value wt x y
Consider adding
  importFrom("stats", "coef", "filter", "pchisq")
to your NAMESPACE file.
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
       user system elapsed
spicy 5.068  0.078   5.157
* 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:
   [1] 0.900716577           - 0.900716396             [1]             
   [2] 0.872831518           - 0.872831224             [2]             
   [3] 0.985083470           - 0.985083010             [3]             
   [4] 1.056566405           - 1.056565888             [4]             
   [5] 0.885611269           - 0.885610907             [5]             
   [6] 0.917185360           - 0.917185203             [6]             
   [7] 1.291070495           - 1.291071205             [7]             
   [8] 0.966434151           - 0.966433660             [8]             
   [9] 0.910787063           - 0.910786914             [9]             
  [10] 1.130604144           - 1.130603861             [10]            
   ... ...                     ...                     and 110 more ...
  
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 2 ]
  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-3.21-bioc/meat/spicyR.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL spicyR
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘spicyR’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (spicyR)

R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"
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.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
> 
> library(testthat)
> library(spicyR)
> 
> test_check("spicyR")
Skipping argument checks as `getPairwise()` is being called within `spicy()`
[ FAIL 1 | WARN 0 | SKIP 1 | PASS 2 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test-utilities.R:1:1'

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-spicyR.R:7:9'): the output is equal to previous version ──────
suppressWarnings(...) (`actual`) not equal to `original_result` (`expected`).

actual@.Data[[1]] vs expected@.Data[[1]]
                           (Intercept) conditionOnset conditionLong-duration
- actual@.Data[[1]][1, ]      1.622665       5.961819               10.58897
+ expected@.Data[[1]][1, ]    1.622667       5.961804               10.58897

  `actual@.Data[[1]]$(Intercept)`: 1.6226650
`expected@.Data[[1]]$(Intercept)`: 1.6226675

  `actual@.Data[[1]]$conditionOnset`: 5.961819
`expected@.Data[[1]]$conditionOnset`: 5.961804

  `actual@.Data[[1]]$conditionLong-duration`: 10.58896862
`expected@.Data[[1]]$conditionLong-duration`: 10.58896896

actual@.Data[[3]] vs expected@.Data[[3]]
                           (Intercept) conditionOnset conditionLong-duration
- actual@.Data[[3]][1, ]     0.8528760      0.6122504              0.3825388
+ expected@.Data[[3]][1, ]   0.8528758      0.6122512              0.3825387

  `actual@.Data[[3]]$(Intercept)`: 0.85287599
`expected@.Data[[3]]$(Intercept)`: 0.85287576

  `actual@.Data[[3]]$conditionOnset`: 0.61225038
`expected@.Data[[3]]$conditionOnset`: 0.61225121

  `actual@.Data[[3]]$conditionLong-duration`: 0.382538768
`expected@.Data[[3]]$conditionLong-duration`: 0.382538702

  `actual@.Data[[4]]$(Intercept)`: 8.73055236
`expected@.Data[[4]]$(Intercept)`: 8.73055175

  `actual@.Data[[4]]$conditionOnset`: 11.7306002
`expected@.Data[[4]]$conditionOnset`: 11.7305984

  `actual@.Data[[4]]$conditionLong-duration`: 12.0805714
`expected@.Data[[4]]$conditionLong-duration`: 12.0805702

actual@.Data[[5]] vs expected@.Data[[5]]
                           (Intercept) conditionOnset conditionLong-duration
- actual@.Data[[5]][1, ]     0.1858605      0.5082280              0.8765288
+ expected@.Data[[5]][1, ]   0.1858608      0.5082268              0.8765289

  `actual@.Data[[5]]$(Intercept)`: 0.18586052
`expected@.Data[[5]]$(Intercept)`: 0.18586082

  `actual@.Data[[5]]$conditionOnset`: 0.5082280
`expected@.Data[[5]]$conditionOnset`: 0.5082268

  `actual@.Data[[5]]$conditionLong-duration`: 0.87652879
`expected@.Data[[5]]$conditionLong-duration`: 0.87652891

     actual@.Data[[8]]$Tc__Th | expected@.Data[[8]]$Tc__Th     
[67] 14.828620658             | 14.828620658               [67]
[68] 7.864179684              | 7.864179684                [68]
[69] 2.798068612              | 2.798068612                [69]
[70] 10.447586876             - 10.447060880               [70]
[71] 68.398894238             | 68.398894238               [71]
[72] -170.000000000           | -170.000000000             [72]
[73] 71.405466103             | 71.405466103               [73]

     actual@.Data[[10]]$Tc__Th | expected@.Data[[10]]$Tc__Th                 
 [1] 0.900716577               - 0.900716396                 [1]             
 [2] 0.872831518               - 0.872831224                 [2]             
 [3] 0.985083470               - 0.985083010                 [3]             
 [4] 1.056566405               - 1.056565888                 [4]             
 [5] 0.885611269               - 0.885610907                 [5]             
 [6] 0.917185360               - 0.917185203                 [6]             
 [7] 1.291070495               - 1.291071205                 [7]             
 [8] 0.966434151               - 0.966433660                 [8]             
 [9] 0.910787063               - 0.910786914                 [9]             
[10] 1.130604144               - 1.130603861                 [10]            
 ... ...                         ...                         and 110 more ...

actual$coefficient vs expected$coefficient
                            (Intercept) conditionOnset conditionLong-duration
- actual$coefficient[1, ]      1.622665       5.961819               10.58897
+ expected$coefficient[1, ]    1.622667       5.961804               10.58897

  `actual$coefficient$(Intercept)`: 1.6226650
`expected$coefficient$(Intercept)`: 1.6226675

  `actual$coefficient$conditionOnset`: 5.961819
`expected$coefficient$conditionOnset`: 5.961804

  `actual$coefficient$conditionLong-duration`: 10.58896862
`expected$coefficient$conditionLong-duration`: 10.58896896

actual$p.value vs expected$p.value
                        (Intercept) conditionOnset conditionLong-duration
- actual$p.value[1, ]     0.8528760      0.6122504              0.3825388
+ expected$p.value[1, ]   0.8528758      0.6122512              0.3825387

  `actual$p.value$(Intercept)`: 0.85287599
`expected$p.value$(Intercept)`: 0.85287576

  `actual$p.value$conditionOnset`: 0.61225038
`expected$p.value$conditionOnset`: 0.61225121

  `actual$p.value$conditionLong-duration`: 0.382538768
`expected$p.value$conditionLong-duration`: 0.382538702

  `actual$se$(Intercept)`: 8.73055236
`expected$se$(Intercept)`: 8.73055175

  `actual$se$conditionOnset`: 11.7306002
`expected$se$conditionOnset`: 11.7305984

  `actual$se$conditionLong-duration`: 12.0805714
`expected$se$conditionLong-duration`: 12.0805702

actual$statistic vs expected$statistic
                          (Intercept) conditionOnset conditionLong-duration
- actual$statistic[1, ]     0.1858605      0.5082280              0.8765288
+ expected$statistic[1, ]   0.1858608      0.5082268              0.8765289

  `actual$statistic$(Intercept)`: 0.18586052
`expected$statistic$(Intercept)`: 0.18586082

  `actual$statistic$conditionOnset`: 0.5082280
`expected$statistic$conditionOnset`: 0.5082268

  `actual$statistic$conditionLong-duration`: 0.87652879
`expected$statistic$conditionLong-duration`: 0.87652891

     actual$pairwiseAssoc$Tc__Th | expected$pairwiseAssoc$Tc__Th     
[67] 14.828620658                | 14.828620658                  [67]
[68] 7.864179684                 | 7.864179684                   [68]
[69] 2.798068612                 | 2.798068612                   [69]
[70] 10.447586876                - 10.447060880                  [70]
[71] 68.398894238                | 68.398894238                  [71]
[72] -170.000000000              | -170.000000000                [72]
[73] 71.405466103                | 71.405466103                  [73]

     actual$weights$Tc__Th | expected$weights$Tc__Th                 
 [1] 0.900716577           - 0.900716396             [1]             
 [2] 0.872831518           - 0.872831224             [2]             
 [3] 0.985083470           - 0.985083010             [3]             
 [4] 1.056566405           - 1.056565888             [4]             
 [5] 0.885611269           - 0.885610907             [5]             
 [6] 0.917185360           - 0.917185203             [6]             
 [7] 1.291070495           - 1.291071205             [7]             
 [8] 0.966434151           - 0.966433660             [8]             
 [9] 0.910787063           - 0.910786914             [9]             
[10] 1.130604144           - 1.130603861             [10]            
 ... ...                     ...                     and 110 more ...

[ FAIL 1 | WARN 0 | SKIP 1 | PASS 2 ]
Error: Test failures
Execution halted