##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:spicyR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings spicyR_1.18.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/spicyR.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘spicyR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘spicyR’ version ‘1.18.0’
* 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 ‘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 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
.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       23.729  0.123  23.854
convPairs   16.151  0.479  16.695
getPairwise  9.206  0.148   9.312
* 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] 0.90071658            - 0.90071640              [1]             
   [2] 0.87283152            - 0.87283122              [2]             
   [3] 0.98508347            - 0.98508301              [3]             
   [4] 1.05656640            - 1.05656589              [4]             
   [5] 0.88561127            - 0.88561091              [5]             
   [6] 0.91718536            - 0.91718520              [6]             
   [7] 1.29107050            - 1.29107120              [7]             
   [8] 0.96643415            - 0.96643366              [8]             
   [9] 0.91078706            - 0.91078691              [9]             
  [10] 1.13060414            - 1.13060386              [10]            
   ... ...                     ...                     and 110 more ...
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 5 ]
  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
  ‘/home/biocbuild/bbs-3.20-bioc/meat/spicyR.Rcheck/00check.log’
for details.

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL spicyR
###
##############################################################################
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* installing to library ‘/home/biocbuild/R/R-4.4.1/site-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 version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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")
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 5 ]

══ 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]]$(Intercept)`: 1.622665
`expected@.Data[[1]]$(Intercept)`: 1.622667

  `actual@.Data[[1]]$conditionOnset`: 5.96182
`expected@.Data[[1]]$conditionOnset`: 5.96180

  `actual@.Data[[1]]$conditionLong-duration`: 10.5889686
`expected@.Data[[1]]$conditionLong-duration`: 10.5889690

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]]$(Intercept)`: 0.8528760
`expected@.Data[[3]]$(Intercept)`: 0.8528758

  `actual@.Data[[3]]$conditionOnset`: 0.6122504
`expected@.Data[[3]]$conditionOnset`: 0.6122512

  `actual@.Data[[3]]$conditionLong-duration`: 0.38253877
`expected@.Data[[3]]$conditionLong-duration`: 0.38253870

  `actual@.Data[[4]]$(Intercept)`: 8.7305524
`expected@.Data[[4]]$(Intercept)`: 8.7305517

  `actual@.Data[[4]]$conditionOnset`: 11.730600
`expected@.Data[[4]]$conditionOnset`: 11.730598

  `actual@.Data[[4]]$conditionLong-duration`: 12.080571
`expected@.Data[[4]]$conditionLong-duration`: 12.080570

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]]$(Intercept)`: 0.1858605
`expected@.Data[[5]]$(Intercept)`: 0.1858608

  `actual@.Data[[5]]$conditionOnset`: 0.508228
`expected@.Data[[5]]$conditionOnset`: 0.508227

  `actual@.Data[[5]]$conditionLong-duration`: 0.8765288
`expected@.Data[[5]]$conditionLong-duration`: 0.8765289

     actual@.Data[[8]]$Tc__Th | expected@.Data[[8]]$Tc__Th     
[67] 14.82862066              | 14.82862066                [67]
[68] 7.86417968               | 7.86417968                 [68]
[69] 2.79806861               | 2.79806861                 [69]
[70] 10.44758688              - 10.44706088                [70]
[71] 68.39889424              | 68.39889424                [71]
[72] -170.00000000            | -170.00000000              [72]
[73] 71.40546610              | 71.40546610                [73]

     actual@.Data[[10]]$Tc__Th | expected@.Data[[10]]$Tc__Th                 
 [1] 0.90071658                - 0.90071640                  [1]             
 [2] 0.87283152                - 0.87283122                  [2]             
 [3] 0.98508347                - 0.98508301                  [3]             
 [4] 1.05656640                - 1.05656589                  [4]             
 [5] 0.88561127                - 0.88561091                  [5]             
 [6] 0.91718536                - 0.91718520                  [6]             
 [7] 1.29107050                - 1.29107120                  [7]             
 [8] 0.96643415                - 0.96643366                  [8]             
 [9] 0.91078706                - 0.91078691                  [9]             
[10] 1.13060414                - 1.13060386                  [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)`: 1.622665
`expected$coefficient$(Intercept)`: 1.622667

  `actual$coefficient$conditionOnset`: 5.96182
`expected$coefficient$conditionOnset`: 5.96180

  `actual$coefficient$conditionLong-duration`: 10.5889686
`expected$coefficient$conditionLong-duration`: 10.5889690

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)`: 0.8528760
`expected$p.value$(Intercept)`: 0.8528758

  `actual$p.value$conditionOnset`: 0.6122504
`expected$p.value$conditionOnset`: 0.6122512

  `actual$p.value$conditionLong-duration`: 0.38253877
`expected$p.value$conditionLong-duration`: 0.38253870

  `actual$se$(Intercept)`: 8.7305524
`expected$se$(Intercept)`: 8.7305517

  `actual$se$conditionOnset`: 11.730600
`expected$se$conditionOnset`: 11.730598

  `actual$se$conditionLong-duration`: 12.080571
`expected$se$conditionLong-duration`: 12.080570

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)`: 0.1858605
`expected$statistic$(Intercept)`: 0.1858608

  `actual$statistic$conditionOnset`: 0.508228
`expected$statistic$conditionOnset`: 0.508227

  `actual$statistic$conditionLong-duration`: 0.8765288
`expected$statistic$conditionLong-duration`: 0.8765289

     actual$pairwiseAssoc$Tc__Th | expected$pairwiseAssoc$Tc__Th     
[67] 14.82862066                 | 14.82862066                   [67]
[68] 7.86417968                  | 7.86417968                    [68]
[69] 2.79806861                  | 2.79806861                    [69]
[70] 10.44758688                 - 10.44706088                   [70]
[71] 68.39889424                 | 68.39889424                   [71]
[72] -170.00000000               | -170.00000000                 [72]
[73] 71.40546610                 | 71.40546610                   [73]

     actual$weights$Tc__Th | expected$weights$Tc__Th                 
 [1] 0.90071658            - 0.90071640              [1]             
 [2] 0.87283152            - 0.87283122              [2]             
 [3] 0.98508347            - 0.98508301              [3]             
 [4] 1.05656640            - 1.05656589              [4]             
 [5] 0.88561127            - 0.88561091              [5]             
 [6] 0.91718536            - 0.91718520              [6]             
 [7] 1.29107050            - 1.29107120              [7]             
 [8] 0.96643415            - 0.96643366              [8]             
 [9] 0.91078706            - 0.91078691              [9]             
[10] 1.13060414            - 1.13060386              [10]            
 ... ...                     ...                     and 110 more ...

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 5 ]
Error: Test failures
Execution halted