Multiple platform build/check report for BioC 3.23 - INSTALL results for COMPASS on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.4 LTS)	x86_64	4.6.0 RC (2026-04-17 r89917) -- "Because it was There"	4988
kjohnson3	macOS 13.7.7 Ventura	arm64	4.6.0 Patched (2026-04-24 r89963) -- "Because it was There"	4718
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INSTALL results for COMPASS on kjohnson3

To the developers/maintainers of the COMPASS package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/COMPASS.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.
raw results
Summary

Package: COMPASS
Version: 1.50.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL COMPASS
StartedAt: 2026-05-01 15:05:24 -0400 (Fri, 01 May 2026)
EndedAt: 2026-05-01 15:05:30 -0400 (Fri, 01 May 2026)
EllapsedTime: 5.4 seconds
RetCode: 1
Status: ERROR
Command output

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###
### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL COMPASS
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library’
* installing *source* package ‘COMPASS’ ...
** this is package ‘COMPASS’ version ‘1.50.0’
** 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 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/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++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/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++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/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++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/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/4.6/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/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c mat2vec.c -o mat2vec.o
mat2vec.c:45:7: error: call to undeclared function 'DATAPTR'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]
   45 |       HANDLE_CASE_MEMCPY(INTEGER, int);
      |       ^
mat2vec.c:38:18: note: expanded from macro 'HANDLE_CASE_MEMCPY'
   38 |           (char*)DATAPTR(elt), (char*)DATAPTR(x) + (i* nRow* sz), nRow* sz); \
      |                  ^
mat2vec.c:45:7: warning: cast to 'char *' from smaller integer type 'int' [-Wint-to-pointer-cast]
   45 |       HANDLE_CASE_MEMCPY(INTEGER, int);
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mat2vec.c:38:11: note: expanded from macro 'HANDLE_CASE_MEMCPY'
   37 |       memcpy(                                                                \
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   38 |           (char*)DATAPTR(elt), (char*)DATAPTR(x) + (i* nRow* sz), nRow* sz); \
      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/secure/_string.h:234:40: note: expanded from macro 'memcpy'
  234 | #define memcpy(...) __memcpy_chk_func (__VA_ARGS__)
      |                     ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/secure/_string.h:127:27: note: expanded from macro '__memcpy_chk_func'
  127 |                 __builtin___memcpy_chk (dest, __VA_ARGS__, __darwin_obsz0 (dest))
      |                                         ^~~~
mat2vec.c:45:7: warning: cast to 'char *' from smaller integer type 'int' [-Wint-to-pointer-cast]
   45 |       HANDLE_CASE_MEMCPY(INTEGER, int);
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mat2vec.c:38:32: note: expanded from macro 'HANDLE_CASE_MEMCPY'
   38 |           (char*)DATAPTR(elt), (char*)DATAPTR(x) + (i* nRow* sz), nRow* sz); \
      |                                ^~~~~~~~~~~~~~~~~
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/secure/_string.h:234:40: note: expanded from macro 'memcpy'
  234 | #define memcpy(...) __memcpy_chk_func (__VA_ARGS__)
      |                                        ^~~~~~~~~~~
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/secure/_string.h:127:33: note: expanded from macro '__memcpy_chk_func'
  127 |                 __builtin___memcpy_chk (dest, __VA_ARGS__, __darwin_obsz0 (dest))
      |                                               ^~~~~~~~~~~
mat2vec.c:45:7: warning: cast to 'char *' from smaller integer type 'int' [-Wint-to-pointer-cast]
   45 |       HANDLE_CASE_MEMCPY(INTEGER, int);
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mat2vec.c:38:11: note: expanded from macro 'HANDLE_CASE_MEMCPY'
   37 |       memcpy(                                                                \
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   38 |           (char*)DATAPTR(elt), (char*)DATAPTR(x) + (i* nRow* sz), nRow* sz); \
      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/secure/_string.h:234:40: note: expanded from macro 'memcpy'
  234 | #define memcpy(...) __memcpy_chk_func (__VA_ARGS__)
      |                     ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/secure/_string.h:127:62: note: expanded from macro '__memcpy_chk_func'
  127 |                 __builtin___memcpy_chk (dest, __VA_ARGS__, __darwin_obsz0 (dest))
      |                                                            ~~~~~~~~~~~~~~~~^~~~~
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/secure/_common.h:40:55: note: expanded from macro '__darwin_obsz0'
   40 | #define __darwin_obsz0(object) __builtin_object_size (object, 0)
      |                                                       ^~~~~~
mat2vec.c:47:7: error: call to undeclared function 'DATAPTR'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]
   47 |       HANDLE_CASE_MEMCPY(REAL, double);
      |       ^
mat2vec.c:38:18: note: expanded from macro 'HANDLE_CASE_MEMCPY'
   38 |           (char*)DATAPTR(elt), (char*)DATAPTR(x) + (i* nRow* sz), nRow* sz); \
      |                  ^
mat2vec.c:47:7: warning: cast to 'char *' from smaller integer type 'int' [-Wint-to-pointer-cast]
   47 |       HANDLE_CASE_MEMCPY(REAL, double);
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mat2vec.c:38:11: note: expanded from macro 'HANDLE_CASE_MEMCPY'
   37 |       memcpy(                                                                \
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   38 |           (char*)DATAPTR(elt), (char*)DATAPTR(x) + (i* nRow* sz), nRow* sz); \
      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/secure/_string.h:234:40: note: expanded from macro 'memcpy'
  234 | #define memcpy(...) __memcpy_chk_func (__VA_ARGS__)
      |                     ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/secure/_string.h:127:27: note: expanded from macro '__memcpy_chk_func'
  127 |                 __builtin___memcpy_chk (dest, __VA_ARGS__, __darwin_obsz0 (dest))
      |                                         ^~~~
mat2vec.c:47:7: warning: cast to 'char *' from smaller integer type 'int' [-Wint-to-pointer-cast]
   47 |       HANDLE_CASE_MEMCPY(REAL, double);
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mat2vec.c:38:32: note: expanded from macro 'HANDLE_CASE_MEMCPY'
   38 |           (char*)DATAPTR(elt), (char*)DATAPTR(x) + (i* nRow* sz), nRow* sz); \
      |                                ^~~~~~~~~~~~~~~~~
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/secure/_string.h:234:40: note: expanded from macro 'memcpy'
  234 | #define memcpy(...) __memcpy_chk_func (__VA_ARGS__)
      |                                        ^~~~~~~~~~~
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/secure/_string.h:127:33: note: expanded from macro '__memcpy_chk_func'
  127 |                 __builtin___memcpy_chk (dest, __VA_ARGS__, __darwin_obsz0 (dest))
      |                                               ^~~~~~~~~~~
mat2vec.c:47:7: warning: cast to 'char *' from smaller integer type 'int' [-Wint-to-pointer-cast]
   47 |       HANDLE_CASE_MEMCPY(REAL, double);
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mat2vec.c:38:11: note: expanded from macro 'HANDLE_CASE_MEMCPY'
   37 |       memcpy(                                                                \
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   38 |           (char*)DATAPTR(elt), (char*)DATAPTR(x) + (i* nRow* sz), nRow* sz); \
      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/secure/_string.h:234:40: note: expanded from macro 'memcpy'
  234 | #define memcpy(...) __memcpy_chk_func (__VA_ARGS__)
      |                     ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/secure/_string.h:127:62: note: expanded from macro '__memcpy_chk_func'
  127 |                 __builtin___memcpy_chk (dest, __VA_ARGS__, __darwin_obsz0 (dest))
      |                                                            ~~~~~~~~~~~~~~~~^~~~~
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/secure/_common.h:40:55: note: expanded from macro '__darwin_obsz0'
   40 | #define __darwin_obsz0(object) __builtin_object_size (object, 0)
      |                                                       ^~~~~~
mat2vec.c:49:7: error: call to undeclared function 'DATAPTR'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]
   49 |       HANDLE_CASE_MEMCPY(INTEGER, int);
      |       ^
mat2vec.c:38:18: note: expanded from macro 'HANDLE_CASE_MEMCPY'
   38 |           (char*)DATAPTR(elt), (char*)DATAPTR(x) + (i* nRow* sz), nRow* sz); \
      |                  ^
mat2vec.c:49:7: warning: cast to 'char *' from smaller integer type 'int' [-Wint-to-pointer-cast]
   49 |       HANDLE_CASE_MEMCPY(INTEGER, int);
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mat2vec.c:38:11: note: expanded from macro 'HANDLE_CASE_MEMCPY'
   37 |       memcpy(                                                                \
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   38 |           (char*)DATAPTR(elt), (char*)DATAPTR(x) + (i* nRow* sz), nRow* sz); \
      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/secure/_string.h:234:40: note: expanded from macro 'memcpy'
  234 | #define memcpy(...) __memcpy_chk_func (__VA_ARGS__)
      |                     ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/secure/_string.h:127:27: note: expanded from macro '__memcpy_chk_func'
  127 |                 __builtin___memcpy_chk (dest, __VA_ARGS__, __darwin_obsz0 (dest))
      |                                         ^~~~
mat2vec.c:49:7: warning: cast to 'char *' from smaller integer type 'int' [-Wint-to-pointer-cast]
   49 |       HANDLE_CASE_MEMCPY(INTEGER, int);
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mat2vec.c:38:32: note: expanded from macro 'HANDLE_CASE_MEMCPY'
   38 |           (char*)DATAPTR(elt), (char*)DATAPTR(x) + (i* nRow* sz), nRow* sz); \
      |                                ^~~~~~~~~~~~~~~~~
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/secure/_string.h:234:40: note: expanded from macro 'memcpy'
  234 | #define memcpy(...) __memcpy_chk_func (__VA_ARGS__)
      |                                        ^~~~~~~~~~~
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/secure/_string.h:127:33: note: expanded from macro '__memcpy_chk_func'
  127 |                 __builtin___memcpy_chk (dest, __VA_ARGS__, __darwin_obsz0 (dest))
      |                                               ^~~~~~~~~~~
mat2vec.c:49:7: warning: cast to 'char *' from smaller integer type 'int' [-Wint-to-pointer-cast]
   49 |       HANDLE_CASE_MEMCPY(INTEGER, int);
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mat2vec.c:38:11: note: expanded from macro 'HANDLE_CASE_MEMCPY'
   37 |       memcpy(                                                                \
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   38 |           (char*)DATAPTR(elt), (char*)DATAPTR(x) + (i* nRow* sz), nRow* sz); \
      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/secure/_string.h:234:40: note: expanded from macro 'memcpy'
  234 | #define memcpy(...) __memcpy_chk_func (__VA_ARGS__)
      |                     ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/secure/_string.h:127:62: note: expanded from macro '__memcpy_chk_func'
  127 |                 __builtin___memcpy_chk (dest, __VA_ARGS__, __darwin_obsz0 (dest))
      |                                                            ~~~~~~~~~~~~~~~~^~~~~
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/secure/_common.h:40:55: note: expanded from macro '__darwin_obsz0'
   40 | #define __darwin_obsz0(object) __builtin_object_size (object, 0)
      |                                                       ^~~~~~
mat2vec.c:51:19: error: call to undeclared function 'STRING_PTR'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]
   51 |       HANDLE_CASE(STRING_PTR, SEXP);
      |                   ^
mat2vec.c:51:7: error: incompatible integer to pointer conversion initializing 'SEXP *' (aka 'struct SEXPREC **') with an expression of type 'int' [-Wint-conversion]
   51 |       HANDLE_CASE(STRING_PTR, SEXP);
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mat2vec.c:22:14: note: expanded from macro 'HANDLE_CASE'
   22 |       CTYPE* output_ptr = ACCESSOR(VECTOR_ELT(output, i)); \
      |              ^            ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mat2vec.c:51:7: error: incompatible integer to pointer conversion initializing 'SEXP *' (aka 'struct SEXPREC **') with an expression of type 'int' [-Wint-conversion]
   51 |       HANDLE_CASE(STRING_PTR, SEXP);
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mat2vec.c:23:14: note: expanded from macro 'HANDLE_CASE'
   23 |       CTYPE* x_ptr = ACCESSOR(x);                          \
      |              ^       ~~~~~~~~~~~
9 warnings and 6 errors generated.
make: *** [mat2vec.o] Error 1
ERROR: compilation failed for package ‘COMPASS’
* removing ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library/COMPASS’