R version 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes"
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Platform: x86_64-apple-darwin20 (64-bit)

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> library(testthat)
> library(clusterExperiment)
Loading required package: SingleCellExperiment
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

> test_check("clusterExperiment")
Found more than one class "Annotated" in cache; using the first, from namespace 'S4Vectors'
Also defined by 'RNeXML'
Note: Not all of the methods requested in 'reduceMethod' have been calculated. Will calculate all the methods requested (any pre-existing values -- filtering statistics or dimensionality reductions -- with these names will be recalculated and overwritten): PCA.
Found more than one class "Annotated" in cache; using the first, from namespace 'S4Vectors'
Also defined by 'RNeXML'
Note: Not all of the methods requested in 'reduceMethod' have been calculated. Will calculate all the methods requested (any pre-existing values -- filtering statistics or dimensionality reductions -- with these names will be recalculated and overwritten): PCA.
Found more than one class "Annotated" in cache; using the first, from namespace 'S4Vectors'
Also defined by 'RNeXML'
Note: Not all of the methods requested in 'reduceMethod' have been calculated. Will calculate all the methods requested (any pre-existing values -- filtering statistics or dimensionality reductions -- with these names will be recalculated and overwritten): var.
Note: Not all of the methods requested in 'reduceMethod' have been calculated. Will calculate all the methods requested (any pre-existing values -- filtering statistics or dimensionality reductions -- with these names will be recalculated and overwritten): var.
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 43 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-rsecFluidigm.R:17:5'): saved rsecFluidigm is still valid object ──
Error in `checkRsecFluidigmObject(rsecFluidigmNew)`: rsecFluidigm has changed -- makeConsensus
Backtrace:
    ▆
 1. ├─testthat::expect_silent(checkRsecFluidigmObject(rsecFluidigmNew)) at test-rsecFluidigm.R:17:5
 2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)
 3. │   ├─testthat (local) .capture(...)
 4. │   │ ├─withr::with_output_sink(...)
 5. │   │ │ └─base::force(code)
 6. │   │ ├─base::withCallingHandlers(...)
 7. │   │ └─base::withVisible(code)
 8. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
 9. └─clusterExperiment:::checkRsecFluidigmObject(rsecFluidigmNew)

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 43 ]
Error: Test failures
Execution halted

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no clusterExperiment_2.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-longtests/meat/clusterExperiment.Rcheck’
* using R version 4.3.2 Patched (2023-11-01 r85457)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘clusterExperiment/DESCRIPTION’ ... OK
* this is package ‘clusterExperiment’ version ‘2.22.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘clusterExperiment’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
  installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    data   3.6Mb
* checking package 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 R 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 ... NOTE
Foreign function calls to a different package:
  .C(ape::node_depth, ...)
  .C(ape::node_depth_edgelength, ...)
  .C(ape::node_height, ...)
  .C(ape::node_height_clado, ...)
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... SKIPPED
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... WARNING
Output for data("rsecFluidigm", package = "clusterExperiment"):
  Search path was changed
* 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 ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘longtests/testthat.R’ failed.
Last 13 lines of output:
  Backtrace:
      ▆
   1. ├─testthat::expect_silent(checkRsecFluidigmObject(rsecFluidigmNew)) at test-rsecFluidigm.R:17:5
   2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)
   3. │   ├─testthat (local) .capture(...)
   4. │   │ ├─withr::with_output_sink(...)
   5. │   │ │ └─base::force(code)
   6. │   │ ├─base::withCallingHandlers(...)
   7. │   │ └─base::withVisible(code)
   8. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
   9. └─clusterExperiment:::checkRsecFluidigmObject(rsecFluidigmNew)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 43 ]
  Error: Test failures
  Execution halted
* DONE

Status: 1 ERROR, 1 WARNING, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.18-bioc-longtests/meat/clusterExperiment.Rcheck/00check.log’
for details.

* installing *source* package ‘clusterExperiment’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c search_pairs.cpp -o search_pairs.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c subsampleLoop.cpp -o subsampleLoop.o
clang++ -arch x86_64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o clusterExperiment.so RcppExports.o search_pairs.o subsampleLoop.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.18-bioc-longtests/meat/clusterExperiment.Rcheck/00LOCK-clusterExperiment/00new/clusterExperiment/libs
** R
** data
** byte-compile and prepare package for lazy loading
Found more than one class "Annotated" in cache; using the first, from namespace 'S4Vectors'
Also defined by ‘RNeXML’
Found more than one class "Annotated" in cache; using the first, from namespace 'S4Vectors'
Also defined by ‘RNeXML’
Found more than one class "Annotated" in cache; using the first, from namespace 'S4Vectors'
Also defined by ‘RNeXML’
Found more than one class "Annotated" in cache; using the first, from namespace 'S4Vectors'
Also defined by ‘RNeXML’
** 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 (clusterExperiment)