##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:XDE.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings XDE_2.57.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/XDE.Rcheck’
* using R Under development (unstable) (2026-03-20 r89666)
* using platform: aarch64-apple-darwin23
* R was compiled by
    Apple clang version 17.0.0 (clang-1700.3.19.1)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.3.1
* using session charset: UTF-8
* current time: 2026-03-23 02:34:31 UTC
* using option ‘--no-vignettes’
* checking for file ‘XDE/DESCRIPTION’ ... OK
* this is package ‘XDE’ version ‘2.57.0’
* 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 ‘XDE’ can be installed ... WARNING
Found the following significant warnings:
  ./Matrix_v2.h:4:17: warning: using directive refers to implicitly-defined namespace 'std'
  Potential_v2.cpp:374:34: warning: equality comparison result unused [-Wunused-comparison]
  Structure.cpp:1971:4: warning: ignoring return value of function declared with 'nodiscard' attribute [-Wunused-result]
  Structure.cpp:1983:7: warning: ignoring return value of function declared with 'nodiscard' attribute [-Wunused-result]
  Structure.cpp:1990:7: warning: ignoring return value of function declared with 'nodiscard' attribute [-Wunused-result]
  Structure.cpp:1996:7: warning: ignoring return value of function declared with 'nodiscard' attribute [-Wunused-result]
  Structure.cpp:2002:7: warning: ignoring return value of function declared with 'nodiscard' attribute [-Wunused-result]
  Structure.cpp:2008:7: warning: ignoring return value of function declared with 'nodiscard' attribute [-Wunused-result]
  Structure.cpp:2014:7: warning: ignoring return value of function declared with 'nodiscard' attribute [-Wunused-result]
  Structure.cpp:2020:7: warning: ignoring return value of function declared with 'nodiscard' attribute [-Wunused-result]
  Structure.cpp:2026:7: warning: ignoring return value of function declared with 'nodiscard' attribute [-Wunused-result]
  Structure.cpp:2032:7: warning: ignoring return value of function declared with 'nodiscard' attribute [-Wunused-result]
  Structure.cpp:2038:7: warning: ignoring return value of function declared with 'nodiscard' attribute [-Wunused-result]
  Structure.cpp:2044:7: warning: ignoring return value of function declared with 'nodiscard' attribute [-Wunused-result]
  Structure.cpp:2050:7: warning: ignoring return value of function declared with 'nodiscard' attribute [-Wunused-result]
  Structure.cpp:2056:7: warning: ignoring return value of function declared with 'nodiscard' attribute [-Wunused-result]
  Structure.cpp:2062:7: warning: ignoring return value of function declared with 'nodiscard' attribute [-Wunused-result]
  Structure.cpp:2068:7: warning: ignoring return value of function declared with 'nodiscard' attribute [-Wunused-result]
  Structure.cpp:2074:7: warning: ignoring return value of function declared with 'nodiscard' attribute [-Wunused-result]
  Structure.cpp:2080:7: warning: ignoring return value of function declared with 'nodiscard' attribute [-Wunused-result]
  Structure.cpp:2086:7: warning: ignoring return value of function declared with 'nodiscard' attribute [-Wunused-result]
  Structure.cpp:2092:7: warning: ignoring return value of function declared with 'nodiscard' attribute [-Wunused-result]
  Structure.cpp:2098:7: warning: ignoring return value of function declared with 'nodiscard' attribute [-Wunused-result]
  Structure.cpp:2104:7: warning: ignoring return value of function declared with 'nodiscard' attribute [-Wunused-result]
  Structure.cpp:2110:7: warning: ignoring return value of function declared with 'nodiscard' attribute [-Wunused-result]
See ‘/Users/biocbuild/bbs-3.23-bioc/meat/XDE.Rcheck/00install.out’ for details.
* used C compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’
* used C++ compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’
* used SDK: ‘MacOSX26.2.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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Non-topic package-anchored link(s) in Rd file 'ExpressionSetList-class.Rd':
  ‘[Biobase]{class.AssayData}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 include directives in Makefiles ... OK
* checking compiled code ... INFO
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘doRUnit.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 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.23-bioc/meat/XDE.Rcheck/00check.log’
for details.

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library’
* installing *source* package ‘XDE’ ...
** this is package ‘XDE’ version ‘2.57.0’
** using staged installation
** libs
using C compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’
using C++ compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’
using SDK: ‘MacOSX26.2.sdk’
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c Cholesky.cpp -o Cholesky.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c Matrix_v2.cpp -o Matrix_v2.o
In file included from Matrix_v2.cpp:1:
./Matrix_v2.h:4:17: warning: using directive refers to implicitly-defined namespace 'std'
    4 | using namespace std;
      |                 ^
Matrix_v2.cpp:148:7: warning: variable 'signDet' set but not used [-Wunused-but-set-variable]
  148 |   int signDet = 1;
      |       ^
Matrix_v2.cpp:244:7: warning: unused variable 'k' [-Wunused-variable]
  244 |   int k = 1;
      |       ^
Matrix_v2.cpp:246:9: warning: unused variable 'j' [-Wunused-variable]
  246 |   int i,j,r;
      |         ^
4 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c Potential_v2.cpp -o Potential_v2.o
Potential_v2.cpp:374:34: warning: equality comparison result unused [-Wunused-comparison]
  374 |         if (theGene[k][i] == 1) include == 1;
      |                                 ~~~~~~~~^~~~
Potential_v2.cpp:374:34: note: use '=' to turn this equality comparison into an assignment
  374 |         if (theGene[k][i] == 1) include == 1;
      |                                         ^~
      |                                         =
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c Random_v2.cpp -o Random_v2.o
Random_v2.cpp:12:16: warning: variable 'temp' set but not used [-Wunused-but-set-variable]
   12 |   unsigned int temp = UINT_MAX - 1;
      |                ^
Random_v2.cpp:1847:10: warning: unused variable 'x' [-Wunused-variable]
 1847 |   double x,y,tt,sum;
      |          ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c Rinterface_v2.cpp -o Rinterface_v2.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c Structure.cpp -o Structure.o
Structure.cpp:526:12: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  526 |   char buf[bufSize];
      |            ^~~~~~~
Structure.cpp:526:12: note: read of non-const variable 'bufSize' is not allowed in a constant expression
Structure.cpp:525:7: note: declared here
  525 |   int bufSize = 1000;
      |       ^
Structure.cpp:536:13: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  536 |   char var1[bufSize];
      |             ^~~~~~~
Structure.cpp:536:13: note: read of non-const variable 'bufSize' is not allowed in a constant expression
Structure.cpp:525:7: note: declared here
  525 |   int bufSize = 1000;
      |       ^
Structure.cpp:537:13: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  537 |   char var2[bufSize];
      |             ^~~~~~~
Structure.cpp:537:13: note: read of non-const variable 'bufSize' is not allowed in a constant expression
Structure.cpp:525:7: note: declared here
  525 |   int bufSize = 1000;
      |       ^
Structure.cpp:538:13: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  538 |   char var3[bufSize];
      |             ^~~~~~~
Structure.cpp:538:13: note: read of non-const variable 'bufSize' is not allowed in a constant expression
Structure.cpp:525:7: note: declared here
  525 |   int bufSize = 1000;
      |       ^
Structure.cpp:539:13: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  539 |   char var4[bufSize];
      |             ^~~~~~~
Structure.cpp:539:13: note: read of non-const variable 'bufSize' is not allowed in a constant expression
Structure.cpp:525:7: note: declared here
  525 |   int bufSize = 1000;
      |       ^
Structure.cpp:528:8: warning: unused variable 'c' [-Wunused-variable]
  528 |   char c;
      |        ^
Structure.cpp:1577:16: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
 1577 |       char buf[bufSize];
      |                ^~~~~~~
Structure.cpp:1577:16: note: read of non-const variable 'bufSize' is not allowed in a constant expression
Structure.cpp:1576:11: note: declared here
 1576 |       int bufSize = 1000;
      |           ^
Structure.cpp:1587:17: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
 1587 |       char var1[bufSize];
      |                 ^~~~~~~
Structure.cpp:1587:17: note: read of non-const variable 'bufSize' is not allowed in a constant expression
Structure.cpp:1576:11: note: declared here
 1576 |       int bufSize = 1000;
      |           ^
Structure.cpp:1588:17: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
 1588 |       char var2[bufSize];
      |                 ^~~~~~~
Structure.cpp:1588:17: note: read of non-const variable 'bufSize' is not allowed in a constant expression
Structure.cpp:1576:11: note: declared here
 1576 |       int bufSize = 1000;
      |           ^
Structure.cpp:1642:8: warning: unused variable 'nRead' [-Wunused-variable]
 1642 |           int nRead = sscanf(var1,"%d",&value);
      |               ^~~~~
Structure.cpp:1668:12: warning: unused variable 'nRead' [-Wunused-variable]
 1668 |               int nRead = sscanf(var2,"%le",&value);
      |                   ^~~~~
Structure.cpp:1579:12: warning: unused variable 'c' [-Wunused-variable]
 1579 |       char c;
      |            ^
Structure.cpp:1726:16: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
 1726 |       char buf[bufSize];
      |                ^~~~~~~
Structure.cpp:1726:16: note: read of non-const variable 'bufSize' is not allowed in a constant expression
Structure.cpp:1725:11: note: declared here
 1725 |       int bufSize = 1000;
      |           ^
Structure.cpp:1736:16: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
 1736 |       char var[bufSize];
      |                ^~~~~~~
Structure.cpp:1736:16: note: read of non-const variable 'bufSize' is not allowed in a constant expression
Structure.cpp:1725:11: note: declared here
 1725 |       int bufSize = 1000;
      |           ^
Structure.cpp:1811:18: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
 1811 |               char name[bufSize];
      |                         ^~~~~~~
Structure.cpp:1811:18: note: read of non-const variable 'bufSize' is not allowed in a constant expression
Structure.cpp:1725:11: note: declared here
 1725 |       int bufSize = 1000;
      |           ^
Structure.cpp:1728:12: warning: unused variable 'c' [-Wunused-variable]
 1728 |       char c;
      |            ^
Structure.cpp:1971:4: warning: ignoring return value of function declared with 'nodiscard' attribute [-Wunused-result]
 1971 |           filename.empty();
      |           ^~~~~~~~~~~~~~
Structure.cpp:1983:7: warning: ignoring return value of function declared with 'nodiscard' attribute [-Wunused-result]
 1983 |       filename.empty();
      |       ^~~~~~~~~~~~~~
Structure.cpp:1990:7: warning: ignoring return value of function declared with 'nodiscard' attribute [-Wunused-result]
 1990 |       filename.empty();
      |       ^~~~~~~~~~~~~~
Structure.cpp:1996:7: warning: ignoring return value of function declared with 'nodiscard' attribute [-Wunused-result]
 1996 |       filename.empty();
      |       ^~~~~~~~~~~~~~
Structure.cpp:2002:7: warning: ignoring return value of function declared with 'nodiscard' attribute [-Wunused-result]
 2002 |       filename.empty();
      |       ^~~~~~~~~~~~~~
Structure.cpp:2008:7: warning: ignoring return value of function declared with 'nodiscard' attribute [-Wunused-result]
 2008 |       filename.empty();
      |       ^~~~~~~~~~~~~~
Structure.cpp:2014:7: warning: ignoring return value of function declared with 'nodiscard' attribute [-Wunused-result]
 2014 |       filename.empty();
      |       ^~~~~~~~~~~~~~
Structure.cpp:2020:7: warning: ignoring return value of function declared with 'nodiscard' attribute [-Wunused-result]
 2020 |       filename.empty();
      |       ^~~~~~~~~~~~~~
Structure.cpp:2026:7: warning: ignoring return value of function declared with 'nodiscard' attribute [-Wunused-result]
 2026 |       filename.empty();
      |       ^~~~~~~~~~~~~~
Structure.cpp:2032:7: warning: ignoring return value of function declared with 'nodiscard' attribute [-Wunused-result]
 2032 |       filename.empty();
      |       ^~~~~~~~~~~~~~
Structure.cpp:2038:7: warning: ignoring return value of function declared with 'nodiscard' attribute [-Wunused-result]
 2038 |       filename.empty();
      |       ^~~~~~~~~~~~~~
Structure.cpp:2044:7: warning: ignoring return value of function declared with 'nodiscard' attribute [-Wunused-result]
 2044 |       filename.empty();
      |       ^~~~~~~~~~~~~~
Structure.cpp:2050:7: warning: ignoring return value of function declared with 'nodiscard' attribute [-Wunused-result]
 2050 |       filename.empty();
      |       ^~~~~~~~~~~~~~
Structure.cpp:2056:7: warning: ignoring return value of function declared with 'nodiscard' attribute [-Wunused-result]
 2056 |       filename.empty();
      |       ^~~~~~~~~~~~~~
Structure.cpp:2062:7: warning: ignoring return value of function declared with 'nodiscard' attribute [-Wunused-result]
 2062 |       filename.empty();
      |       ^~~~~~~~~~~~~~
Structure.cpp:2068:7: warning: ignoring return value of function declared with 'nodiscard' attribute [-Wunused-result]
 2068 |       filename.empty();
      |       ^~~~~~~~~~~~~~
Structure.cpp:2074:7: warning: ignoring return value of function declared with 'nodiscard' attribute [-Wunused-result]
 2074 |       filename.empty();
      |       ^~~~~~~~~~~~~~
Structure.cpp:2080:7: warning: ignoring return value of function declared with 'nodiscard' attribute [-Wunused-result]
 2080 |       filename.empty();
      |       ^~~~~~~~~~~~~~
Structure.cpp:2086:7: warning: ignoring return value of function declared with 'nodiscard' attribute [-Wunused-result]
 2086 |       filename.empty();
      |       ^~~~~~~~~~~~~~
Structure.cpp:2092:7: warning: ignoring return value of function declared with 'nodiscard' attribute [-Wunused-result]
 2092 |       filename.empty();
      |       ^~~~~~~~~~~~~~
Structure.cpp:2098:7: warning: ignoring return value of function declared with 'nodiscard' attribute [-Wunused-result]
 2098 |       filename.empty();
      |       ^~~~~~~~~~~~~~
Structure.cpp:2104:7: warning: ignoring return value of function declared with 'nodiscard' attribute [-Wunused-result]
 2104 |       filename.empty();
      |       ^~~~~~~~~~~~~~
Structure.cpp:2110:7: warning: ignoring return value of function declared with 'nodiscard' attribute [-Wunused-result]
 2110 |       filename.empty();
      |       ^~~~~~~~~~~~~~
39 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c Update_v2.cpp -o Update_v2.o
Update_v2.cpp:2314:9: warning: variable 'nOn' set but not used [-Wunused-but-set-variable]
 2314 |     int nOn = 0;
      |         ^
Update_v2.cpp:2464:9: warning: variable 'nOn' set but not used [-Wunused-but-set-variable]
 2464 |     int nOn = 0;
      |         ^
Update_v2.cpp:3293:9: warning: variable 'nOn' set but not used [-Wunused-but-set-variable]
 3293 |     int nOn = 0;
      |         ^
Update_v2.cpp:3404:9: warning: variable 'nOn' set but not used [-Wunused-but-set-variable]
 3404 |     int nOn = 0;
      |         ^
Update_v2.cpp:3919:10: warning: unused variable 'pot' [-Wunused-variable]
 3919 |   double pot = - OmegaGibbs(df,D,oldClique,oldComponents,Q,G,Delta,
      |          ^~~
Update_v2.cpp:3973:10: warning: unused variable 'pot' [-Wunused-variable]
 3973 |   double pot = DeltaStarGibbs(oldClique,oldComponents,Q,G,S,newValues,
      |          ^~~
Update_v2.cpp:4526:9: warning: variable 'nOn' set but not used [-Wunused-but-set-variable]
 4526 |     int nOn = 0;
      |         ^
Update_v2.cpp:4657:9: warning: variable 'nOn' set but not used [-Wunused-but-set-variable]
 4657 |     int nOn = 0;
      |         ^
8 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c Utility_v2.cpp -o Utility_v2.o
Utility_v2.cpp:221:12: warning: unused variable 'detPrior' [-Wunused-variable]
  221 |     double detPrior = inverse(var,varInv);
      |            ^~~~~~~~
Utility_v2.cpp:228:12: warning: unused variable 'detPosterior' [-Wunused-variable]
  228 |     double detPosterior = 1.0 /inverse(varInv,var);
      |            ^~~~~~~~~~~~
Utility_v2.cpp:303:9: warning: unused variable 's' [-Wunused-variable]
  303 |     int s;
      |         ^
Utility_v2.cpp:328:12: warning: unused variable 'detPrior' [-Wunused-variable]
  328 |     double detPrior = inverse(var,varInv);
      |            ^~~~~~~~
Utility_v2.cpp:334:12: warning: unused variable 'detPosterior' [-Wunused-variable]
  334 |     double detPosterior = 1.0 / inverse(varInv,var);
      |            ^~~~~~~~~~~~
Utility_v2.cpp:764:6: warning: unused variable 'ngg' [-Wunused-variable]
  764 |         int ngg = neighbour[gg].size();
      |             ^~~
Utility_v2.cpp:954:8: warning: unused variable 'ngg' [-Wunused-variable]
  954 |           int ngg = neighbour[gg].size();
      |               ^~~
Utility_v2.cpp:1463:33: warning: unused variable 'itextra' [-Wunused-variable]
 1463 |       map<int,double>::iterator itextra = VinvSparse[k].end();
      |                                 ^~~~~~~
8 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c diffExpressed_main.cpp -o diffExpressed_main.o
In file included from diffExpressed_main.cpp:38:
./UpdateGamma2Gibbs.h:112:14: warning: variable 'pot' set but not used [-Wunused-but-set-variable]
  112 |       double pot = - model->potential(ran);
      |              ^
In file included from diffExpressed_main.cpp:42:
./UpdateXiGibbs.h:95:11: warning: variable 'pot' set but not used [-Wunused-but-set-variable]
   95 |           double pot = - model->potential(ran);
      |                  ^
./UpdateXiGibbs.h:162:15: warning: variable 'pot' set but not used [-Wunused-but-set-variable]
  162 |               double pot = - model->potential(ran);
      |                      ^
3 warnings generated.
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c registerDynamicSymbol.c -o registerDynamicSymbol.o
clang++ -arch arm64 -std=gnu++20 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o XDE.so Cholesky.o Matrix_v2.o Potential_v2.o Random_v2.o Rinterface_v2.o Structure.o Update_v2.o Utility_v2.o diffExpressed_main.o registerDynamicSymbol.o -lm -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.6/Resources/library/00LOCK-XDE/00new/XDE/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘qqplot’ in package ‘XDE’
** 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 (XDE)

R Under development (unstable) (2026-03-20 r89666) -- "Unsuffered Consequences"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin23

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.

> ## from xmapcore package
> if( require( "RUnit", quietly=TRUE ) ) {
+ 	pkg <- "XDE"
+ 
+ 	if( Sys.getenv( "RCMDCHECK" ) == "FALSE" ) {
+ 		path <- file.path( getwd(), "..", "inst", "unitTests" )
+ 	} else {
+ 		path <- system.file( package=pkg, "unitTests" )
+ 	}
+ 
+ 	cat( "\nRunning unit tests\n" )
+ 	print( list( pkg=pkg, getwd=getwd(), pathToUnitTests=path ) )
+ 	library( package=pkg, character.only=TRUE )
+ 
+ 	##xmap.clear.cache()
+ 
+ 	##Fail on warnings
+ 	options( warn=2 )
+ 
+ 	## Get the pattern (if there is one?)
+ 	patt <- Sys.getenv( "RUNITFILEPATTERN" )
+ 	if( is.null( patt ) || nchar( patt ) == 0 ) {
+ 		testSuite <- defineTestSuite(name=paste( pkg, "unit testing" ),
+ 					     dirs=path,
+ 					     testFileRegexp=paste( "^test.+", patt, "\\.[rR]$", sep="" ))
+ 	} else {
+ 		##testSuite <- defineTestSuite( name=paste( pkg, "unit testing" ), testFileRegexp=paste( "^runit\\.", patt, "\\.[rR]$", sep="" ), dirs=path )
+ 		testSuite <- defineTestSuite(name=paste( pkg, "unit testing" ),
+ 					     testFileRegexp=paste( "^test.+", patt, "\\.[rR]$", sep="" ),
+ 					     dirs=path )
+ 	}
+ 	tests <- runTestSuite( testSuite )
+ 
+ 	pathReport <- file.path( path, "report" )
+ 
+ 	cat( "------------------- UNIT TEST SUMMARY ---------------------\n\n" )
+ 	printTextProtocol( tests, showDetails=FALSE )
+ 	printTextProtocol( tests, showDetails=FALSE, fileName=paste( pathReport, "Summary.txt", sep="" ) )
+ 	printTextProtocol( tests, showDetails=TRUE,  fileName=paste( pathReport, ".txt", sep="" ) )
+ 
+ 	printHTMLProtocol( tests, fileName=paste( pathReport, ".html", sep="" ) )
+ 
+ 	tmp <- getErrors( tests )
+ 	if( tmp$nFail > 0 | tmp$nErr > 0 ){
+ 		stop( paste( "\n\nunit testing failed (#test failures: ", tmp$nFail, ", #R errors: ",  tmp$nErr, ")\n\n", sep=""))
+ 	}
+ } else {
+ 	warning( "cannot run unit tests -- package RUnit is not available" )
+ }

Running unit tests
$pkg
[1] "XDE"

$getwd
[1] "/Users/biocbuild/bbs-3.23-bioc/meat/XDE.Rcheck/tests"

$pathToUnitTests
[1] "/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpVkeJI3/RLIBS_32249b778cb/XDE/unitTests"

Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

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

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


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, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Welcome to Bioconductor

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

Welcome to XDE version 2.57.0
------------------- UNIT TEST SUMMARY ---------------------

RUNIT TEST PROTOCOL -- Sun Mar 22 22:35:45 2026 
*********************************************** 
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
XDE unit testing - 0 test functions, 0 errors, 0 failures
> 
> proc.time()
   user  system elapsed 
  2.327   0.171   2.561