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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:COMPASS.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings COMPASS_1.49.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/COMPASS.Rcheck’
* using R Under development (unstable) (2026-03-05 r89546)
* 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 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-03-14 02:18:44 UTC
* checking for file ‘COMPASS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘COMPASS’ version ‘1.49.0’
* 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 ... WARNING
Found the following significant warnings:
  mat2vec.c:38:18: warning: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
  melt_dataframe.c:57:21: warning: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
See ‘/home/biocbuild/bbs-3.23-bioc/meat/COMPASS.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
* checking installed package size ... INFO
  installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   3.9Mb
* 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 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 ... WARNING
Note: information on .o files is not available
File ‘COMPASS/libs/COMPASS.so’:
  Found non-API calls to R: ‘DATAPTR’, ‘STRING_PTR’
These entry points may be removed soon:
‘STRING_PTR’, ‘DATAPTR’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
* checking sizes of PDF files under ‘inst/doc’ ...* 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: CellCounts
> ### Title: Compute Number of Cells Positive for Certain Cytokine
> ###   Combinations
> ### Aliases: CellCounts
> 
> ### ** Examples
> 
> set.seed(123)
> ## generate 10 simulated matrices of flow data
> K <- 6 ## number of markers
> data <- replicate(10, simplify=FALSE, {
+   m <- matrix( rnorm(1E4 * K, 2000, 1000 ), ncol=K )
+   m[m < 2500] <- 0
+   colnames(m) <- c("IL2", "IL4", "IL6", "Mip1B", "IFNg", "TNFa")
+   return(m)
+ })
> names(data) <- sample(letters, 10)
> head( data[[1]] )
          IL2      IL4 IL6    Mip1B     IFNg     TNFa
[1,]    0.000 4370.725   0    0.000    0.000    0.000
[2,]    0.000    0.000   0    0.000 2721.365 2917.511
[3,] 3558.708 2926.961   0    0.000    0.000    0.000
[4,]    0.000    0.000   0    0.000    0.000    0.000
[5,]    0.000    0.000   0 2900.647 3302.121    0.000
[6,] 3715.065 3131.986   0    0.000    0.000 4257.013
> 
> ## generate counts over all available combinations of markers in data
> str(CellCounts(data)) ## 64 columns, as all 2^6 combinations expressed
 int [1:10, 1:64] 1094 1059 1108 1086 1103 1083 1129 1086 1119 1095 ...
 - attr(*, "dimnames")=List of 2
  ..$ : chr [1:10] "h" "g" "e" "a" ...
  ..$ : chr [1:64] "!IL2&!IL4&!IL6&!Mip1B&!IFNg&!TNFa" "IL2&!IL4&!IL6&!Mip1B&!IFNg&!TNFa" "!IL2&IL4&!IL6&!Mip1B&!IFNg&!TNFa" "!IL2&!IL4&IL6&!Mip1B&!IFNg&!TNFa" ...
> 
> ## generate marginal counts
> combos <- list(1, 2, 3, 4, 5, 6) ## marginal cell counts
> cc <- CellCounts(data, combos)
> 
> ## a base R way of doing the same thing
> f <- function(data) {
+   do.call(rbind, lapply(data, function(x) apply(x, 2, function(x) sum(x > 0))))
+ }
> cc2 <- f(data)
> 
> ## check that they're identical
> stopifnot(identical( unname(cc), unname(cc2) ))
> 
> ## We can also generate cell counts by expressing various combinations
> ## of markers (names) in the data.
> 
> ## count cells expressing IL2 or IL4
> CellCounts(data, "IL2|IL4")

 *** caught segfault ***
address 0xffffffffd2ec4b40, cause 'memory not mapped'

Traceback:
 1: .CellCounts_character(data, combinations)
 2: CellCounts.default(data, "IL2|IL4")
 3: CellCounts(data, "IL2|IL4")
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault (core dumped)
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’
 ERROR
Running the tests in ‘tests/test-all.R’ failed.
Last 13 lines of output:
  28: withRestarts(tryCatch(withCallingHandlers({    eval(code, test_env)    new_expectations <- the$test_expectations > starting_expectations    if (snapshot_skipped) {        skip("On CRAN")    }    else if (!new_expectations && skip_on_empty) {        skip_empty()    }}, expectation = handle_expectation, packageNotFoundError = function(e) {    if (on_cran()) {        skip(paste0("{", e$package, "} is not installed."))    }}, snapshot_on_cran = function(cnd) {    snapshot_skipped <<- TRUE    invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message,     error = handle_error, interrupt = handle_interrupt), error = handle_fatal),     end_test = function() {    })
  29: test_code(code = exprs, env = env, reporter = get_reporter() %||%     StopReporter$new())
  30: source_file(path, env = env(env), desc = desc, shuffle = shuffle,     error_call = error_call)
  31: FUN(X[[i]], ...)
  32: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle,     error_call = error_call)
  33: doTryCatch(return(expr), name, parentenv, handler)
  34: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  35: tryCatchList(expr, classes, parentenv, handlers)
  36: tryCatch(code, testthat_abort_reporter = function(cnd) {    cat(conditionMessage(cnd), "\n")    NULL})
  37: with_reporter(reporters$multi, lapply(test_paths, test_one_file,     env = env, desc = desc, shuffle = shuffle, error_call = error_call))
  38: test_files_serial(test_dir = test_dir, test_package = test_package,     test_paths = test_paths, load_helpers = load_helpers, reporter = reporter,     env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,     desc = desc, load_package = load_package, shuffle = shuffle,     error_call = error_call)
  39: test_files(test_dir = path, test_paths = test_paths, test_package = package,     reporter = reporter, load_helpers = load_helpers, env = env,     stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,     load_package = load_package, parallel = parallel, shuffle = shuffle)
  40: test_dir("testthat")
  An irrecoverable exception occurred. R is aborting now ...
  Segmentation fault (core dumped)
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 2 WARNINGs, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/COMPASS.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL COMPASS
###
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* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘COMPASS’ ...
** this is package ‘COMPASS’ version ‘1.49.0’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c COMPASS_init.c -o COMPASS_init.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c CellCounts.cpp -o CellCounts.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c CellCounts_character.cpp -o CellCounts_character.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c digamma.c -o digamma.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c mat2vec.c -o mat2vec.o
mat2vec.c: In function ‘mat2vec’:
mat2vec.c:38:18: warning: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
   38 |           (char*)DATAPTR(elt), (char*)DATAPTR(x) + (i* nRow* sz), nRow* sz); \
      |                  ^~~~~~~
mat2vec.c:45:7: note: in expansion of macro ‘HANDLE_CASE_MEMCPY’
   45 |       HANDLE_CASE_MEMCPY(INTEGER, int);
      |       ^~~~~~~~~~~~~~~~~~
mat2vec.c:38:11: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
   38 |           (char*)DATAPTR(elt), (char*)DATAPTR(x) + (i* nRow* sz), nRow* sz); \
      |           ^
mat2vec.c:45:7: note: in expansion of macro ‘HANDLE_CASE_MEMCPY’
   45 |       HANDLE_CASE_MEMCPY(INTEGER, int);
      |       ^~~~~~~~~~~~~~~~~~
mat2vec.c:38:32: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
   38 |           (char*)DATAPTR(elt), (char*)DATAPTR(x) + (i* nRow* sz), nRow* sz); \
      |                                ^
mat2vec.c:45:7: note: in expansion of macro ‘HANDLE_CASE_MEMCPY’
   45 |       HANDLE_CASE_MEMCPY(INTEGER, int);
      |       ^~~~~~~~~~~~~~~~~~
mat2vec.c:38:11: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
   38 |           (char*)DATAPTR(elt), (char*)DATAPTR(x) + (i* nRow* sz), nRow* sz); \
      |           ^
mat2vec.c:47:7: note: in expansion of macro ‘HANDLE_CASE_MEMCPY’
   47 |       HANDLE_CASE_MEMCPY(REAL, double);
      |       ^~~~~~~~~~~~~~~~~~
mat2vec.c:38:32: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
   38 |           (char*)DATAPTR(elt), (char*)DATAPTR(x) + (i* nRow* sz), nRow* sz); \
      |                                ^
mat2vec.c:47:7: note: in expansion of macro ‘HANDLE_CASE_MEMCPY’
   47 |       HANDLE_CASE_MEMCPY(REAL, double);
      |       ^~~~~~~~~~~~~~~~~~
mat2vec.c:38:11: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
   38 |           (char*)DATAPTR(elt), (char*)DATAPTR(x) + (i* nRow* sz), nRow* sz); \
      |           ^
mat2vec.c:49:7: note: in expansion of macro ‘HANDLE_CASE_MEMCPY’
   49 |       HANDLE_CASE_MEMCPY(INTEGER, int);
      |       ^~~~~~~~~~~~~~~~~~
mat2vec.c:38:32: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
   38 |           (char*)DATAPTR(elt), (char*)DATAPTR(x) + (i* nRow* sz), nRow* sz); \
      |                                ^
mat2vec.c:49:7: note: in expansion of macro ‘HANDLE_CASE_MEMCPY’
   49 |       HANDLE_CASE_MEMCPY(INTEGER, int);
      |       ^~~~~~~~~~~~~~~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c melt_dataframe.c -o melt_dataframe.o
melt_dataframe.c: In function ‘stack_vector’:
melt_dataframe.c:57:21: warning: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
   57 |       memcpy((char*)DATAPTR(out) + (i* len* sz), (char*)DATAPTR(x), len* sz); \
      |                     ^~~~~~~
melt_dataframe.c:67:5: note: in expansion of macro ‘HANDLE_CASE’
   67 |     HANDLE_CASE(INTSXP, int);
      |     ^~~~~~~~~~~
melt_dataframe.c:57:14: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
   57 |       memcpy((char*)DATAPTR(out) + (i* len* sz), (char*)DATAPTR(x), len* sz); \
      |              ^
melt_dataframe.c:67:5: note: in expansion of macro ‘HANDLE_CASE’
   67 |     HANDLE_CASE(INTSXP, int);
      |     ^~~~~~~~~~~
melt_dataframe.c:57:50: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
   57 |       memcpy((char*)DATAPTR(out) + (i* len* sz), (char*)DATAPTR(x), len* sz); \
      |                                                  ^
melt_dataframe.c:67:5: note: in expansion of macro ‘HANDLE_CASE’
   67 |     HANDLE_CASE(INTSXP, int);
      |     ^~~~~~~~~~~
melt_dataframe.c:57:14: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
   57 |       memcpy((char*)DATAPTR(out) + (i* len* sz), (char*)DATAPTR(x), len* sz); \
      |              ^
melt_dataframe.c:68:5: note: in expansion of macro ‘HANDLE_CASE’
   68 |     HANDLE_CASE(REALSXP, double);
      |     ^~~~~~~~~~~
melt_dataframe.c:57:50: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
   57 |       memcpy((char*)DATAPTR(out) + (i* len* sz), (char*)DATAPTR(x), len* sz); \
      |                                                  ^
melt_dataframe.c:68:5: note: in expansion of macro ‘HANDLE_CASE’
   68 |     HANDLE_CASE(REALSXP, double);
      |     ^~~~~~~~~~~
melt_dataframe.c:57:14: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
   57 |       memcpy((char*)DATAPTR(out) + (i* len* sz), (char*)DATAPTR(x), len* sz); \
      |              ^
melt_dataframe.c:69:5: note: in expansion of macro ‘HANDLE_CASE’
   69 |     HANDLE_CASE(LGLSXP, int);
      |     ^~~~~~~~~~~
melt_dataframe.c:57:50: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
   57 |       memcpy((char*)DATAPTR(out) + (i* len* sz), (char*)DATAPTR(x), len* sz); \
      |                                                  ^
melt_dataframe.c:69:5: note: in expansion of macro ‘HANDLE_CASE’
   69 |     HANDLE_CASE(LGLSXP, int);
      |     ^~~~~~~~~~~
melt_dataframe.c: In function ‘melt_dataframe’:
melt_dataframe.c:147:14: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
  147 |       memcpy((char*)DATAPTR(value_SEXP) + (i* nRow * sizeof(CTYPE)), \
      |              ^
melt_dataframe.c:160:5: note: in expansion of macro ‘HANDLE_CASE’
  160 |     HANDLE_CASE(INTSXP, int);
      |     ^~~~~~~~~~~
melt_dataframe.c:148:14: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
  148 |              (char*)DATAPTR(tmp),                                    \
      |              ^
melt_dataframe.c:160:5: note: in expansion of macro ‘HANDLE_CASE’
  160 |     HANDLE_CASE(INTSXP, int);
      |     ^~~~~~~~~~~
melt_dataframe.c:147:14: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
  147 |       memcpy((char*)DATAPTR(value_SEXP) + (i* nRow * sizeof(CTYPE)), \
      |              ^
melt_dataframe.c:161:5: note: in expansion of macro ‘HANDLE_CASE’
  161 |     HANDLE_CASE(REALSXP, double);
      |     ^~~~~~~~~~~
melt_dataframe.c:148:14: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
  148 |              (char*)DATAPTR(tmp),                                    \
      |              ^
melt_dataframe.c:161:5: note: in expansion of macro ‘HANDLE_CASE’
  161 |     HANDLE_CASE(REALSXP, double);
      |     ^~~~~~~~~~~
melt_dataframe.c:147:14: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
  147 |       memcpy((char*)DATAPTR(value_SEXP) + (i* nRow * sizeof(CTYPE)), \
      |              ^
melt_dataframe.c:162:5: note: in expansion of macro ‘HANDLE_CASE’
  162 |     HANDLE_CASE(LGLSXP, int);
      |     ^~~~~~~~~~~
melt_dataframe.c:148:14: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
  148 |              (char*)DATAPTR(tmp),                                    \
      |              ^
melt_dataframe.c:162:5: note: in expansion of macro ‘HANDLE_CASE’
  162 |     HANDLE_CASE(LGLSXP, int);
      |     ^~~~~~~~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c melt_matrix.c -o melt_matrix.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c samplePuPs.cpp -o samplePuPs.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c transpose_list.c -o transpose_list.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c updatealphas_Exp.cpp -o updatealphas_Exp.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c updatealphas_Exp_MH.cpp -o updatealphas_Exp_MH.o
updatealphas_Exp_MH.cpp: In function ‘SEXPREC* updatealphas_Exp_MH(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
updatealphas_Exp_MH.cpp:26:10: warning: variable ‘psik’ set but not used [-Wunused-but-set-variable]
   26 |   double psik = 0.;
      |          ^~~~
updatealphas_Exp_MH.cpp:35:7: warning: variable ‘flagkk’ set but not used [-Wunused-but-set-variable]
   35 |   int flagkk = 0;
      |       ^~~~~~
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c updatealphau.cpp -o updatealphau.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c updatealphau_noPu_Exp.cpp -o updatealphau_noPu_Exp.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c updatealphau_noPu_Exp_MH.cpp -o updatealphau_noPu_Exp_MH.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c updatebeta_RW.cpp -o updatebeta_RW.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c updategammak_noPu.cpp -o updategammak_noPu.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c utils.c -o utils.o
g++ -std=gnu++20 -shared -L/home/biocbuild/bbs-3.23-bioc/R/lib -L/usr/local/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 -llapack -L/home/biocbuild/bbs-3.23-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.23-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.23-bioc/R/site-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 Under development (unstable) (2026-03-05 r89546) -- "Unsuffered Consequences"
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Platform: x86_64-pc-linux-gnu

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> 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

⠏ |          0 | COMPASSPlot                                                    
⠏ |          0 | test plotCOMPASSResultStack                                    
⠋ |          1 | test plotCOMPASSResultStack                                    
⠹ |          3 | test plotCOMPASSResultStack                                    
✔ |          6 | test plotCOMPASSResultStack [45.0s]

⠏ |          0 | CellCounts                                                     
⠏ |          0 | CellCounts                                                     
 *** caught segfault ***
address 0x45975a10, cause 'memory not mapped'

Traceback:
 1: .CellCounts_character(data, combinations)
 2: CellCounts.default(data, combinations)
 3: CellCounts(data, combinations)
 4: eval_bare(expr, quo_get_env(quo))
 5: quasi_label(enquo(object), label)
 6: expect_identical(CellCounts(data, combinations), CellCounts(data,     1:6))
 7: eval(code, test_env)
 8: eval(code, test_env)
 9: withCallingHandlers({    eval(code, test_env)    new_expectations <- the$test_expectations > starting_expectations    if (snapshot_skipped) {        skip("On CRAN")    }    else if (!new_expectations && skip_on_empty) {        skip_empty()    }}, expectation = handle_expectation, packageNotFoundError = function(e) {    if (on_cran()) {        skip(paste0("{", e$package, "} is not installed."))    }}, snapshot_on_cran = function(cnd) {    snapshot_skipped <<- TRUE    invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message,     error = handle_error, interrupt = handle_interrupt)
10: doTryCatch(return(expr), name, parentenv, handler)
11: tryCatchOne(expr, names, parentenv, handlers[[1L]])
12: tryCatchList(expr, classes, parentenv, handlers)
13: tryCatch(withCallingHandlers({    eval(code, test_env)    new_expectations <- the$test_expectations > starting_expectations    if (snapshot_skipped) {        skip("On CRAN")    }    else if (!new_expectations && skip_on_empty) {        skip_empty()    }}, expectation = handle_expectation, packageNotFoundError = function(e) {    if (on_cran()) {        skip(paste0("{", e$package, "} is not installed."))    }}, snapshot_on_cran = function(cnd) {    snapshot_skipped <<- TRUE    invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message,     error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
14: doWithOneRestart(return(expr), restart)
15: withOneRestart(expr, restarts[[1L]])
16: withRestarts(tryCatch(withCallingHandlers({    eval(code, test_env)    new_expectations <- the$test_expectations > starting_expectations    if (snapshot_skipped) {        skip("On CRAN")    }    else if (!new_expectations && skip_on_empty) {        skip_empty()    }}, expectation = handle_expectation, packageNotFoundError = function(e) {    if (on_cran()) {        skip(paste0("{", e$package, "} is not installed."))    }}, snapshot_on_cran = function(cnd) {    snapshot_skipped <<- TRUE    invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message,     error = handle_error, interrupt = handle_interrupt), error = handle_fatal),     end_test = function() {    })
17: test_code(code, parent.frame())
18: test_that("The integer and character interfaces for CellCounts match up",     {        expect_identical(CellCounts(data, combinations), CellCounts(data,             1:6))        expect_identical(CellCounts(data, list(c(1, 2, 3))),             CellCounts(data, list("A&B&C")))        y <- "A&B&C"        expect_identical(CellCounts(data, list(c(1, 2, 3))),             CellCounts(data, list(y)))        expect_identical(CellCounts(data, 1:6), marginal_counts(data))    })
19: eval(code, test_env)
20: eval(code, test_env)
21: withCallingHandlers({    eval(code, test_env)    new_expectations <- the$test_expectations > starting_expectations    if (snapshot_skipped) {        skip("On CRAN")    }    else if (!new_expectations && skip_on_empty) {        skip_empty()    }}, expectation = handle_expectation, packageNotFoundError = function(e) {    if (on_cran()) {        skip(paste0("{", e$package, "} is not installed."))    }}, snapshot_on_cran = function(cnd) {    snapshot_skipped <<- TRUE    invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message,     error = handle_error, interrupt = handle_interrupt)
22: doTryCatch(return(expr), name, parentenv, handler)
23: tryCatchOne(expr, names, parentenv, handlers[[1L]])
24: tryCatchList(expr, classes, parentenv, handlers)
25: tryCatch(withCallingHandlers({    eval(code, test_env)    new_expectations <- the$test_expectations > starting_expectations    if (snapshot_skipped) {        skip("On CRAN")    }    else if (!new_expectations && skip_on_empty) {        skip_empty()    }}, expectation = handle_expectation, packageNotFoundError = function(e) {    if (on_cran()) {        skip(paste0("{", e$package, "} is not installed."))    }}, snapshot_on_cran = function(cnd) {    snapshot_skipped <<- TRUE    invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message,     error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
26: doWithOneRestart(return(expr), restart)
27: withOneRestart(expr, restarts[[1L]])
28: withRestarts(tryCatch(withCallingHandlers({    eval(code, test_env)    new_expectations <- the$test_expectations > starting_expectations    if (snapshot_skipped) {        skip("On CRAN")    }    else if (!new_expectations && skip_on_empty) {        skip_empty()    }}, expectation = handle_expectation, packageNotFoundError = function(e) {    if (on_cran()) {        skip(paste0("{", e$package, "} is not installed."))    }}, snapshot_on_cran = function(cnd) {    snapshot_skipped <<- TRUE    invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message,     error = handle_error, interrupt = handle_interrupt), error = handle_fatal),     end_test = function() {    })
29: test_code(code = exprs, env = env, reporter = get_reporter() %||%     StopReporter$new())
30: source_file(path, env = env(env), desc = desc, shuffle = shuffle,     error_call = error_call)
31: FUN(X[[i]], ...)
32: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle,     error_call = error_call)
33: doTryCatch(return(expr), name, parentenv, handler)
34: tryCatchOne(expr, names, parentenv, handlers[[1L]])
35: tryCatchList(expr, classes, parentenv, handlers)
36: tryCatch(code, testthat_abort_reporter = function(cnd) {    cat(conditionMessage(cnd), "\n")    NULL})
37: with_reporter(reporters$multi, lapply(test_paths, test_one_file,     env = env, desc = desc, shuffle = shuffle, error_call = error_call))
38: test_files_serial(test_dir = test_dir, test_package = test_package,     test_paths = test_paths, load_helpers = load_helpers, reporter = reporter,     env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,     desc = desc, load_package = load_package, shuffle = shuffle,     error_call = error_call)
39: test_files(test_dir = path, test_paths = test_paths, test_package = package,     reporter = reporter, load_helpers = load_helpers, env = env,     stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,     load_package = load_package, parallel = parallel, shuffle = shuffle)
40: test_dir("testthat")
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault (core dumped)