##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:COMPASS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings COMPASS_1.44.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/COMPASS.Rcheck’
* using R version 4.4.3 (2025-02-28)
* 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 ‘COMPASS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘COMPASS’ version ‘1.44.0’
* 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 ‘COMPASS’ can be installed ... OK
* used C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
  ‘BiocStyle’ ‘foreach’ ‘rmarkdown’
  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
.CellCounts: no visible binding for global variable
  ‘_COMPASS_CellCounts’
COMPASSfitToCountsTable: no visible binding for global variable
  ‘population’
COMPASSfitToCountsTable: no visible binding for global variable ‘Count’
COMPASSfitToCountsTable: no visible binding for global variable ‘id’
CellCounts_character: no visible binding for global variable
  ‘_COMPASS_CellCounts_character’
GetThresholdedIntensities : <anonymous>: no visible global function
  definition for ‘gh_pop_is_bool_gate’
Undefined global functions or variables:
  Count _COMPASS_CellCounts _COMPASS_CellCounts_character
  gh_pop_is_bool_gate id population
* 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 line endings in shell scripts ... 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘COMPASS-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: GetThresholdedIntensities
> ### Title: Extract Thresholded Intensities from a GatingSet
> ### Aliases: GetThresholdedIntensities
> 
> ### ** Examples
> 
> if (require("flowWorkspace")&require("flowCore")&require("tidyr")) {
+ 
+   ## Generate an example GatingSet that could be used with COMPASS
+   ## We then pull out the 'data' and 'counts' components that could
+   ## be used within a COMPASSContainer
+ 
+   n <- 10 ## number of samples
+   k <- 4 ## number of markers
+ 
+   sid_vec <- paste0("sid_", 1:n) ## sample ids; unique names used to denote samples
+   iid_vec <- rep_len( paste0("iid_", 1:(n/10) ), n ) ## individual ids
+   marker_names <- c("TNFa", "IL2", "IL4", "IL6")
+ 
+   ## Generate n sets of 'flow' data -- a list of matrices, each row
+   ## is a cell, each column is fluorescence intensities on a particular
+   ## channel / marker
+   data <- replicate(n, {
+     nrow <- round(runif(1) * 1E4 + 1000)
+     ncol <- k
+     vals <- rexp( nrow * ncol, runif(1, 1E-5, 1E-3) )
+     output <- matrix(vals, nrow, ncol)
+     colnames(output) <- marker_names
+     return(output)
+   })
+   names(data) <- sid_vec
+ 
+   ## Put it into a GatingSet
+   fs <- flowSet( lapply(data, flowFrame) )
+   gs <- GatingSet(fs)
+ 
+   ## Add some dummy metadata
+   meta <- pData(gs)
+   meta$PTID <- 1:10
+   pData(gs) <- meta
+ 
+   gate <- rectangleGate( list(TNFa=c(-Inf,Inf)))
+   gs_pop_add(gs, gate, parent="root", name="dummy")
+ 
+   ## Add dummy gate
+ 
+   ## Make some gates, and apply them
+   invisible(lapply(marker_names, function(marker) {
+     .gate <- setNames( list( c( rexp(1, runif(1, 1E-5, 1E-3)), Inf) ), marker )
+     gate <- rectangleGate(.gate=.gate)
+     gs_pop_add(gs, gate, parent="dummy", name=paste0(marker, "+"))
+   }))
+ 
+   recompute(gs)
+ 
+   ## Map node names to channel names
+   map=list(
+     "TNFa+"="TNFa",
+     "IL2+"="IL2",
+     "IL4+"="IL4",
+     "IL6+"="IL6"
+   )
+ 
+   ## Pull out the data as a COMPASS-friendly dataset
+   node <- "dummy"
+   map <- map
+   system.time(
+     output <- GetThresholdedIntensities(gs, "dummy", map)
+   )
+ 
+   system.time(
+     output <- COMPASSContainerFromGatingSet(gs, "dummy", individual_id="PTID")
+   )
+ 
+   str(output)
+ 
+ }
Loading required package: flowWorkspace
As part of improvements to flowWorkspace, some behavior of
GatingSet objects has changed. For details, please read the section
titled "The cytoframe and cytoset classes" in the package vignette:

  vignette("flowWorkspace-Introduction", "flowWorkspace")
Loading required package: flowCore
Loading required package: tidyr
done!
Fetching data from children of '/dummy'.
Extracting cell counts
Looking for expected children nodes
We will extract data from the following nodes:

TNFa+, IL2+, IL4+, IL6+
Channel names were matched to the 'desc' column.
Extracting cell intensities and thresholding...
Done!
Extracting cell counts
Fetching dummy
Fetching child nodes
common markers are: 
TNFa IL2 IL4 IL6 
We will map the following nodes to markers:
Extracting single cell data for TNFa+|IL2+|IL4+|IL6+
..........Creating COMPASS Container
Filtering low counts
Filtering 4 samples due to low counts
Error in if (any(sapply(data, function(x) any(x < 0)))) { : 
  missing value where TRUE/FALSE needed
Calls: system.time -> COMPASSContainerFromGatingSet -> COMPASSContainer
Timing stopped at: 0.304 0.027 0.337
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’
 OK
* 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, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/COMPASS.Rcheck/00check.log’
for details.

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL COMPASS
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘COMPASS’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c COMPASS_init.c -o COMPASS_init.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c CellCounts.cpp -o CellCounts.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c CellCounts_character.cpp -o CellCounts_character.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c digamma.c -o digamma.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c mat2vec.c -o mat2vec.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c melt_dataframe.c -o melt_dataframe.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c melt_matrix.c -o melt_matrix.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c samplePuPs.cpp -o samplePuPs.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c transpose_list.c -o transpose_list.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c updatealphas_Exp.cpp -o updatealphas_Exp.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c updatealphas_Exp_MH.cpp -o updatealphas_Exp_MH.o
updatealphas_Exp_MH.cpp:26:10: warning: variable 'psik' set but not used [-Wunused-but-set-variable]
  double psik = 0.;
         ^
updatealphas_Exp_MH.cpp:35:7: warning: variable 'flagkk' set but not used [-Wunused-but-set-variable]
  int flagkk = 0;
      ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c updatealphau.cpp -o updatealphau.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c updatealphau_noPu_Exp.cpp -o updatealphau_noPu_Exp.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c updatealphau_noPu_Exp_MH.cpp -o updatealphau_noPu_Exp_MH.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c updatebeta_RW.cpp -o updatebeta_RW.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c updategammak_noPu.cpp -o updategammak_noPu.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c utils.c -o utils.o
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o COMPASS.so COMPASS_init.o CellCounts.o CellCounts_character.o RcppExports.o digamma.o mat2vec.o melt_dataframe.o melt_matrix.o samplePuPs.o transpose_list.o updatealphas_Exp.o updatealphas_Exp_MH.o updatealphau.o updatealphau_noPu_Exp.o updatealphau_noPu_Exp_MH.o updatebeta_RW.o updategammak_noPu.o utils.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lemutls_w -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-COMPASS/00new/COMPASS/libs
** 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
** 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 (COMPASS)

R version 4.4.3 (2025-02-28) -- "Trophy Case"
Copyright (C) 2025 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.

> library(testthat)
> library(COMPASS)
> library(flowWorkspace)
As part of improvements to flowWorkspace, some behavior of
GatingSet objects has changed. For details, please read the section
titled "The cytoframe and cytoset classes" in the package vignette:

  vignette("flowWorkspace-Introduction", "flowWorkspace")
> if (file.exists("testthat")) {
+   test_dir("testthat")
+ }
✔ | F W  S  OK | Context

⠏ |          0 | COMPASS                                                        
⠏ |          0 | COMPASS Interface                                              
⠋ |          1 | COMPASS Interface                                              
✔ |          1 | COMPASS Interface [1.1s]

⠏ |          0 | COMPASSPlot                                                    
⠏ |          0 | test plotCOMPASSResultStack                                    
⠋ |          1 | test plotCOMPASSResultStack                                    
⠹ |          3 | test plotCOMPASSResultStack                                    
✔ |          6 | test plotCOMPASSResultStack [62.8s]

⠏ |          0 | CellCounts                                                     
⠏ |          0 | CellCounts                                                     
✔ |          7 | CellCounts

⠏ |          0 | FunctionalityScore                                             
⠏ |          0 | FS, PFS                                                        
✔ |          8 | FS, PFS

⠏ |          0 | GatingSet2COMPASS                                              
⠏ |          0 | test COMPASSContainerFromGatingSet                             
⠋ |   1      0 | test COMPASSContainerFromGatingSet                             
⠴ |   1      5 | test COMPASSContainerFromGatingSet                             
✔ |   1      7 | test COMPASSContainerFromGatingSet
────────────────────────────────────────────────────────────────────────────────
Warning ('test-GatingSet2COMPASS.R:15:3'): COMPASSContainerFromGatingSet
There appear to be negative intensities in the 'data' supplied.
Backtrace:
    ▆
 1. └─COMPASS::COMPASSContainerFromGatingSet(...) at test-GatingSet2COMPASS.R:15:3
 2.   └─COMPASS::COMPASSContainer(...)
────────────────────────────────────────────────────────────────────────────────

══ Results ═════════════════════════════════════════════════════════════════════
Duration: 64.6 s

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 29 ]
> 
> proc.time()
   user  system elapsed 
 69.964   1.401  69.263