##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:condiments.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings condiments_1.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/condiments.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘condiments/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘condiments’ version ‘1.13.0’
* 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 ‘condiments’ 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
.condition_sling: no visible binding for global variable ‘.’
.condition_sling : <anonymous>: no visible binding for global variable
  ‘.’
.distinct_inputs: no visible binding for global variable ‘Samples’
.distinct_inputs: no visible binding for global variable ‘.’
.fateSelectionTest: no visible binding for global variable ‘pair’
.fateSelectionTest: no visible binding for global variable ‘statistic’
.fateSelectionTest: no visible binding for global variable ‘p.value’
.multiple_samples: no visible binding for global variable ‘p.value’
.progressionTest: no visible binding for global variable ‘lineage’
.progressionTest: no visible binding for global variable ‘statistic’
.progressionTest: no visible binding for global variable ‘p.value’
.topologyTest_multipleSamples: no visible binding for global variable
  ‘p.value’
fateSelectionTest_multipleSamples,SlingshotDataSet: no visible binding
  for global variable ‘condition’
progressionTest_multipleSamples,SlingshotDataSet: no visible binding
  for global variable ‘condition’
Undefined global functions or variables:
  . Samples condition lineage p.value pair statistic
* 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 data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘condiments-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: differentiationTest
> ### Title: Differential differentiation
> ### Aliases: differentiationTest
> 
> ### ** Examples
> 
> data('slingshotExample', package = "slingshot")
> rd <- slingshotExample$rd
> cl <- slingshotExample$cl
> condition <- factor(rep(c('A','B'), length.out = nrow(rd)))
> condition[110:139] <- 'A'
> sds <- slingshot::slingshot(rd, cl)
Error in loadNamespace(x) : 
  there is no package called ‘DelayedMatrixStats’
Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
* 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:
    9. │       └─slingshot::getLineages(...)
   10. │         └─slingshot (local) .local(data, clusterLabels, ...)
   11. │           ├─TrajectoryUtils::createClusterMST(...)
   12. │           └─TrajectoryUtils::createClusterMST(...)
   13. │             └─TrajectoryUtils (local) .local(x, ...)
   14. │               └─TrajectoryUtils (local) FUN(x, clusters)
   15. │                 └─TrajectoryUtils:::.rowstats_w(...)
   16. └─base::loadNamespace(x)
   17.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   18.     └─base (local) withOneRestart(expr, restarts[[1L]])
   19.       └─base (local) doWithOneRestart(return(expr), restart)
  
  [ FAIL 9 | WARN 0 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘condiments.Rmd’ using rmarkdown

Quitting from lines 124-129 [unnamed-chunk-9] (condiments.Rmd)
Error: processing vignette 'condiments.Rmd' failed with diagnostics:
there is no package called 'DelayedMatrixStats'
--- failed re-building ‘condiments.Rmd’

--- re-building ‘controls.Rmd’ using rmarkdown

Quitting from lines 38-42 [unnamed-chunk-2] (controls.Rmd)
Error: processing vignette 'controls.Rmd' failed with diagnostics:
there is no package called 'DelayedMatrixStats'
--- failed re-building ‘controls.Rmd’

--- re-building ‘examples.Rmd’ using rmarkdown
--- finished re-building ‘examples.Rmd’

SUMMARY: processing the following files failed:
  ‘condiments.Rmd’ ‘controls.Rmd’

Error: Vignette re-building failed.
Execution halted

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

Status: 3 ERRORs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/condiments.Rcheck/00check.log’
for details.

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL condiments
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘condiments’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (condiments)

R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-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.

> library(condiments)
> library(testthat)
> test_check("condiments")
[ FAIL 9 | WARN 0 | SKIP 0 | PASS 0 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_1Lineage.R:14:1'): (code run outside of `test_that()`) ─────────
<packageNotFoundError/error/condition>
Error in `loadNamespace(x)`: there is no package called 'DelayedMatrixStats'
Backtrace:
     ▆
  1. ├─slingshot::slingshot(rd, cl) at test_1Lineage.R:14:1
  2. ├─slingshot::slingshot(rd, cl)
  3. │ ├─slingshot::slingshot(...)
  4. │ └─slingshot::slingshot(...)
  5. │   └─slingshot (local) .local(data, clusterLabels, ...)
  6. │     ├─slingshot::getLineages(...)
  7. │     └─slingshot::getLineages(...)
  8. │       ├─slingshot::getLineages(...)
  9. │       └─slingshot::getLineages(...)
 10. │         └─slingshot (local) .local(data, clusterLabels, ...)
 11. │           ├─TrajectoryUtils::createClusterMST(...)
 12. │           └─TrajectoryUtils::createClusterMST(...)
 13. │             └─TrajectoryUtils (local) .local(x, ...)
 14. │               └─TrajectoryUtils (local) FUN(x, clusters)
 15. │                 └─TrajectoryUtils:::.rowstats_w(...)
 16. └─base::loadNamespace(x)
 17.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
 18.     └─base (local) withOneRestart(expr, restarts[[1L]])
 19.       └─base (local) doWithOneRestart(return(expr), restart)
── Error ('test_3lineages.R:11:1'): (code run outside of `test_that()`) ────────
<packageNotFoundError/error/condition>
Error in `loadNamespace(x)`: there is no package called 'DelayedMatrixStats'
Backtrace:
     ▆
  1. ├─slingshot::slingshot(rd, cl, end.clus = 3) at test_3lineages.R:11:1
  2. ├─slingshot::slingshot(rd, cl, end.clus = 3)
  3. │ ├─slingshot::slingshot(...)
  4. │ └─slingshot::slingshot(...)
  5. │   └─slingshot (local) .local(data, clusterLabels, ...)
  6. │     ├─slingshot::getLineages(...)
  7. │     └─slingshot::getLineages(...)
  8. │       ├─slingshot::getLineages(...)
  9. │       └─slingshot::getLineages(...)
 10. │         └─slingshot (local) .local(data, clusterLabels, ...)
 11. │           ├─TrajectoryUtils::createClusterMST(...)
 12. │           └─TrajectoryUtils::createClusterMST(...)
 13. │             └─TrajectoryUtils (local) .local(x, ...)
 14. │               └─TrajectoryUtils (local) FUN(x, clusters)
 15. │                 └─TrajectoryUtils:::.rowstats_w(...)
 16. └─base::loadNamespace(x)
 17.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
 18.     └─base (local) withOneRestart(expr, restarts[[1L]])
 19.       └─base (local) doWithOneRestart(return(expr), restart)
── Error ('test_diff_lengths.R:15:1'): (code run outside of `test_that()`) ─────
<packageNotFoundError/error/condition>
Error in `loadNamespace(x)`: there is no package called 'DelayedMatrixStats'
Backtrace:
     ▆
  1. ├─slingshot::slingshot(rd, cl) at test_diff_lengths.R:15:1
  2. ├─slingshot::slingshot(rd, cl)
  3. │ ├─slingshot::slingshot(...)
  4. │ └─slingshot::slingshot(...)
  5. │   └─slingshot (local) .local(data, clusterLabels, ...)
  6. │     ├─slingshot::getLineages(...)
  7. │     └─slingshot::getLineages(...)
  8. │       ├─slingshot::getLineages(...)
  9. │       └─slingshot::getLineages(...)
 10. │         └─slingshot (local) .local(data, clusterLabels, ...)
 11. │           ├─TrajectoryUtils::createClusterMST(...)
 12. │           └─TrajectoryUtils::createClusterMST(...)
 13. │             └─TrajectoryUtils (local) .local(x, ...)
 14. │               └─TrajectoryUtils (local) FUN(x, clusters)
 15. │                 └─TrajectoryUtils:::.rowstats_w(...)
 16. └─base::loadNamespace(x)
 17.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
 18.     └─base (local) withOneRestart(expr, restarts[[1L]])
 19.       └─base (local) doWithOneRestart(return(expr), restart)
── Error ('test_fateSelection.R:12:1'): (code run outside of `test_that()`) ────
<packageNotFoundError/error/condition>
Error in `loadNamespace(x)`: there is no package called 'DelayedMatrixStats'
Backtrace:
     ▆
  1. ├─slingshot::slingshot(rd, cl) at test_fateSelection.R:12:1
  2. ├─slingshot::slingshot(rd, cl)
  3. │ ├─slingshot::slingshot(...)
  4. │ └─slingshot::slingshot(...)
  5. │   └─slingshot (local) .local(data, clusterLabels, ...)
  6. │     ├─slingshot::getLineages(...)
  7. │     └─slingshot::getLineages(...)
  8. │       ├─slingshot::getLineages(...)
  9. │       └─slingshot::getLineages(...)
 10. │         └─slingshot (local) .local(data, clusterLabels, ...)
 11. │           ├─TrajectoryUtils::createClusterMST(...)
 12. │           └─TrajectoryUtils::createClusterMST(...)
 13. │             └─TrajectoryUtils (local) .local(x, ...)
 14. │               └─TrajectoryUtils (local) FUN(x, clusters)
 15. │                 └─TrajectoryUtils:::.rowstats_w(...)
 16. └─base::loadNamespace(x)
 17.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
 18.     └─base (local) withOneRestart(expr, restarts[[1L]])
 19.       └─base (local) doWithOneRestart(return(expr), restart)
── Error ('test_multipleSamples.R:12:1'): (code run outside of `test_that()`) ──
<packageNotFoundError/error/condition>
Error in `loadNamespace(x)`: there is no package called 'DelayedMatrixStats'
Backtrace:
     ▆
  1. ├─slingshot::slingshot(rd, cl) at test_multipleSamples.R:12:1
  2. ├─slingshot::slingshot(rd, cl)
  3. │ ├─slingshot::slingshot(...)
  4. │ └─slingshot::slingshot(...)
  5. │   └─slingshot (local) .local(data, clusterLabels, ...)
  6. │     ├─slingshot::getLineages(...)
  7. │     └─slingshot::getLineages(...)
  8. │       ├─slingshot::getLineages(...)
  9. │       └─slingshot::getLineages(...)
 10. │         └─slingshot (local) .local(data, clusterLabels, ...)
 11. │           ├─TrajectoryUtils::createClusterMST(...)
 12. │           └─TrajectoryUtils::createClusterMST(...)
 13. │             └─TrajectoryUtils (local) .local(x, ...)
 14. │               └─TrajectoryUtils (local) FUN(x, clusters)
 15. │                 └─TrajectoryUtils:::.rowstats_w(...)
 16. └─base::loadNamespace(x)
 17.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
 18.     └─base (local) withOneRestart(expr, restarts[[1L]])
 19.       └─base (local) doWithOneRestart(return(expr), restart)
── Error ('test_progression.R:12:1'): (code run outside of `test_that()`) ──────
<packageNotFoundError/error/condition>
Error in `loadNamespace(x)`: there is no package called 'DelayedMatrixStats'
Backtrace:
     ▆
  1. ├─slingshot::slingshot(rd, cl) at test_progression.R:12:1
  2. ├─slingshot::slingshot(rd, cl)
  3. │ ├─slingshot::slingshot(...)
  4. │ └─slingshot::slingshot(...)
  5. │   └─slingshot (local) .local(data, clusterLabels, ...)
  6. │     ├─slingshot::getLineages(...)
  7. │     └─slingshot::getLineages(...)
  8. │       ├─slingshot::getLineages(...)
  9. │       └─slingshot::getLineages(...)
 10. │         └─slingshot (local) .local(data, clusterLabels, ...)
 11. │           ├─TrajectoryUtils::createClusterMST(...)
 12. │           └─TrajectoryUtils::createClusterMST(...)
 13. │             └─TrajectoryUtils (local) .local(x, ...)
 14. │               └─TrajectoryUtils (local) FUN(x, clusters)
 15. │                 └─TrajectoryUtils:::.rowstats_w(...)
 16. └─base::loadNamespace(x)
 17.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
 18.     └─base (local) withOneRestart(expr, restarts[[1L]])
 19.       └─base (local) doWithOneRestart(return(expr), restart)
── Error ('test_sds_objects.R:12:1'): (code run outside of `test_that()`) ──────
<packageNotFoundError/error/condition>
Error in `loadNamespace(x)`: there is no package called 'DelayedMatrixStats'
Backtrace:
     ▆
  1. ├─slingshot::slingshot(rd, cl) at test_sds_objects.R:12:1
  2. ├─slingshot::slingshot(rd, cl)
  3. │ ├─slingshot::slingshot(...)
  4. │ └─slingshot::slingshot(...)
  5. │   └─slingshot (local) .local(data, clusterLabels, ...)
  6. │     ├─slingshot::getLineages(...)
  7. │     └─slingshot::getLineages(...)
  8. │       ├─slingshot::getLineages(...)
  9. │       └─slingshot::getLineages(...)
 10. │         └─slingshot (local) .local(data, clusterLabels, ...)
 11. │           ├─TrajectoryUtils::createClusterMST(...)
 12. │           └─TrajectoryUtils::createClusterMST(...)
 13. │             └─TrajectoryUtils (local) .local(x, ...)
 14. │               └─TrajectoryUtils (local) FUN(x, clusters)
 15. │                 └─TrajectoryUtils:::.rowstats_w(...)
 16. └─base::loadNamespace(x)
 17.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
 18.     └─base (local) withOneRestart(expr, restarts[[1L]])
 19.       └─base (local) doWithOneRestart(return(expr), restart)
── Error ('test_topology.R:12:1'): (code run outside of `test_that()`) ─────────
<packageNotFoundError/error/condition>
Error in `loadNamespace(x)`: there is no package called 'DelayedMatrixStats'
Backtrace:
     ▆
  1. ├─slingshot::slingshot(rd, cl) at test_topology.R:12:1
  2. ├─slingshot::slingshot(rd, cl)
  3. │ ├─slingshot::slingshot(...)
  4. │ └─slingshot::slingshot(...)
  5. │   └─slingshot (local) .local(data, clusterLabels, ...)
  6. │     ├─slingshot::getLineages(...)
  7. │     └─slingshot::getLineages(...)
  8. │       ├─slingshot::getLineages(...)
  9. │       └─slingshot::getLineages(...)
 10. │         └─slingshot (local) .local(data, clusterLabels, ...)
 11. │           ├─TrajectoryUtils::createClusterMST(...)
 12. │           └─TrajectoryUtils::createClusterMST(...)
 13. │             └─TrajectoryUtils (local) .local(x, ...)
 14. │               └─TrajectoryUtils (local) FUN(x, clusters)
 15. │                 └─TrajectoryUtils:::.rowstats_w(...)
 16. └─base::loadNamespace(x)
 17.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
 18.     └─base (local) withOneRestart(expr, restarts[[1L]])
 19.       └─base (local) doWithOneRestart(return(expr), restart)
── Error ('test_utils.R:12:1'): (code run outside of `test_that()`) ────────────
<packageNotFoundError/error/condition>
Error in `loadNamespace(x)`: there is no package called 'DelayedMatrixStats'
Backtrace:
     ▆
  1. ├─slingshot::slingshot(rd, cl) at test_utils.R:12:1
  2. ├─slingshot::slingshot(rd, cl)
  3. │ ├─slingshot::slingshot(...)
  4. │ └─slingshot::slingshot(...)
  5. │   └─slingshot (local) .local(data, clusterLabels, ...)
  6. │     ├─slingshot::getLineages(...)
  7. │     └─slingshot::getLineages(...)
  8. │       ├─slingshot::getLineages(...)
  9. │       └─slingshot::getLineages(...)
 10. │         └─slingshot (local) .local(data, clusterLabels, ...)
 11. │           ├─TrajectoryUtils::createClusterMST(...)
 12. │           └─TrajectoryUtils::createClusterMST(...)
 13. │             └─TrajectoryUtils (local) .local(x, ...)
 14. │               └─TrajectoryUtils (local) FUN(x, clusters)
 15. │                 └─TrajectoryUtils:::.rowstats_w(...)
 16. └─base::loadNamespace(x)
 17.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
 18.     └─base (local) withOneRestart(expr, restarts[[1L]])
 19.       └─base (local) doWithOneRestart(return(expr), restart)

[ FAIL 9 | WARN 0 | SKIP 0 | PASS 0 ]
Error: Test failures
Execution halted