##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:distinct.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings distinct_1.21.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/distinct.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘distinct/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘distinct’ version ‘1.21.0’
* 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 ‘distinct’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking C++ specification ... OK
* checking installed package size ... INFO
  installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   1.0Mb
    libs   5.9Mb
* 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 ... NOTE
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
perm_test_parallel_R: no visible binding for global variable ‘cl_id’
perm_test_parallel_covariates_R: no visible binding for global variable
  ‘cl_id’
plot_cdfs: no visible binding for global variable ‘group’
plot_densities: no visible binding for global variable ‘group’
Undefined global functions or variables:
  cl_id group
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Kang_subset.Rd: SingleCellExperiment-class
  plot_cdfs.Rd: ggplot, SummarizedExperiment-class,
    SingleCellExperiment-class, stat_ecdf
  plot_densities.Rd: ggplot, SummarizedExperiment-class,
    SingleCellExperiment-class, stat_density
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘distinct-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: distinct_test
> ### Title: Test for differential state between two groups of samples, based
> ###   on scRNA-seq data.
> ### Aliases: distinct_test
> 
> ### ** Examples
> 
> # load the input data:
> data("Kang_subset", package = "distinct")
> Kang_subset
class: SingleCellExperiment 
dim: 100 9517 
metadata(1): experiment_info
assays(2): logcounts cpm
rownames(100): ISG15 SYF2 ... MX2 PDXK
rowData names(0):
colnames: NULL
colData names(3): stim cell sample_id
Loading required namespace: GenomeInfoDb
Failed with error:  ‘there is no package called ‘GenomeInfoDb’’
Error in .requirePackage(package) : 
  unable to load required package ‘GenomeInfoDb’
Calls: <Anonymous> ... .extendsForS3 -> extends -> getClassDef -> .requirePackage
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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 ‘distinct.Rmd’ using rmarkdown
Failed with error:  'there is no package called 'GenomeInfoDb''

Quitting from distinct.Rmd:66-70 [load-example-data]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `.requirePackage()`:
! unable to load required package 'GenomeInfoDb'
---
Backtrace:
     ▆
  1. ├─tools::buildVignettes(...)
  2. │ ├─base::tryCatch(...)
  3. │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  4. │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
  5. │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
  6. │ └─engine$weave(file, quiet = quiet, encoding = enc)
  7. │   └─knitr:::vweave_rmarkdown(...)
  8. │     └─rmarkdown::render(...)
  9. │       └─knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
 10. │         └─knitr:::process_file(text, output)
 11. │           ├─xfun:::handle_error(...)
 12. │           ├─base::withCallingHandlers(...)
 13. │           └─knitr:::process_group(group)
 14. │             └─knitr:::call_block(x)
 15. │               └─knitr:::block_exec(params)
 16. │                 └─knitr:::eng_r(options)
 17. │                   ├─knitr:::in_input_dir(...)
 18. │                   │ └─knitr:::in_dir(input_dir(), expr)
 19. │                   └─knitr (local) evaluate(...)
 20. │                     └─evaluate::evaluate(...)
 21. │                       ├─base::withRestarts(...)
 22. │                       │ └─base (local) withRestartList(expr, restarts)
 23. │                       │   ├─base (local) withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
 24. │                       │   │ └─base (local) doWithOneRestart(return(expr), restart)
 25. │                       │   └─base (local) withRestartList(expr, restarts[-nr])
 26. │                       │     └─base (local) withOneRestart(expr, restarts[[1L]])
 27. │                       │       └─base (local) doWithOneRestart(return(expr), restart)
 28. │                       ├─evaluate:::with_handlers(...)
 29. │                       │ ├─base::eval(call)
 30. │                       │ │ └─base::eval(call)
 31. │                       │ └─base::withCallingHandlers(...)
 32. │                       └─watcher$print_value(ev$value, ev$visible, envir)
 33. │                         ├─base::withVisible(handle_value(handler, value, visible, envir))
 34. │                         └─evaluate:::handle_value(handler, value, visible, envir)
 35. │                           └─handler$value(value, visible)
 36. │                             └─knitr (local) fun(x, options = options)
 37. │                               ├─base::withVisible(knit_print(x, ...))
 38. │                               ├─knitr::knit_print(x, ...)
 39. │                               └─knitr:::knit_print.default(x, ...)
 40. │                                 └─knitr::normal_print(x)
 41. │                                   ├─methods::show(x)
 42. │                                   └─methods::show(x)
 43. │                                     ├─S4Vectors::coolcat("reducedDimNames(%d): %s\n", reducedDimNames(object))
 44. │                                     │ └─base::ifelse(nzchar(vals), vals, "''")
 45. │                                     ├─SingleCellExperiment::reducedDimNames(object)
 46. │                                     └─SingleCellExperiment::reducedDimNames(object)
 47. │                                       └─SingleCellExperiment:::.get_internal_names(...)
 48. │                                         ├─BiocGenerics::updateObject(x)
 49. │                                         └─SingleCellExperiment::updateObject(x)
 50. │                                           ├─methods::callNextMethod()
 51. │                                           └─SummarizedExperiment (local) .nextMethod(object = object)
 52. │                                             ├─BiocGenerics::updateObject(object@rowRanges, ..., verbose = verbose)
 53. │                                             └─GenomicRanges::updateObject(object@rowRanges, ..., verbose = verbose)
 54. │                                               ├─BiocGenerics::updateObject(object@unlistData, ..., verbose = verbose)
 55. │                                               └─GenomicRanges::updateObject(object@unlistData, ..., verbose = verbose)
 56. │                                                 └─BiocGenerics::updateObject(object@seqinfo, ..., verbose = verbose)
 57. └─methods:::.extendsForS3(`<chr>`)
 58.   └─methods::extends(Class, maybe = FALSE)
 59.     └─methods::getClassDef(class1)
 60.       └─methods:::.requirePackage(package)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'distinct.Rmd' failed with diagnostics:
unable to load required package 'GenomeInfoDb'
--- failed re-building ‘distinct.Rmd’

SUMMARY: processing the following file failed:
  ‘distinct.Rmd’

Error: Vignette re-building failed.
Execution halted

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

Status: 2 ERRORs, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/distinct.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL distinct
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘distinct’ ...
** this is package ‘distinct’ version ‘1.21.0’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
using C++17
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c Perm.cpp -o Perm.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c Perm_covariates.cpp -o Perm_covariates.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c Perm_covariates_parallel.cpp -o Perm_covariates_parallel.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c Perm_parallel.cpp -o Perm_parallel.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o distinct.so Perm.o Perm_covariates.o Perm_covariates_parallel.o Perm_parallel.o RcppExports.o -llapack -L/home/biocbuild/bbs-3.22-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-distinct/00new/distinct/libs
** R
** data
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (distinct)

R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 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(testthat)
> library(distinct)
> test_check("distinct")
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 8 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 8 ]
> 
> proc.time()
   user  system elapsed 
 10.155   0.561  83.575