Build/check report for BioC 3.24 - INSTALL results for COMPASS on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.4 LTS)	x86_64	4.6.0 RC (2026-04-17 r89917) -- "Because it was There"	4796
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INSTALL results for COMPASS on nebbiolo2

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: 1.49.0
Command: /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD INSTALL COMPASS
StartedAt: 2026-04-21 15:57:52 -0400 (Tue, 21 Apr 2026)
EndedAt: 2026-04-21 15:58:07 -0400 (Tue, 21 Apr 2026)
EllapsedTime: 15.3 seconds
RetCode: 1
Status: ERROR
Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD INSTALL COMPASS
###
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* installing to library ‘/home/biocbuild/bbs-3.24-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-3.24-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.24-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-3.24-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.24-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-3.24-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.24-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-3.24-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.24-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-3.24-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.24-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-3.24-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.24-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);
      |       ^~~~~~~~~~~~~~~~~~
mat2vec.c:51:19: warning: implicit declaration of function ‘STRING_PTR’; did you mean ‘STRING_ELT’? [-Wimplicit-function-declaration]
   51 |       HANDLE_CASE(STRING_PTR, SEXP);
      |                   ^~~~~~~~~~
mat2vec.c:22:27: note: in definition of macro ‘HANDLE_CASE’
   22 |       CTYPE* output_ptr = ACCESSOR(VECTOR_ELT(output, i)); \
      |                           ^~~~~~~~
mat2vec.c:51:19: warning: initialization of ‘struct SEXPREC **’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
   51 |       HANDLE_CASE(STRING_PTR, SEXP);
      |                   ^~~~~~~~~~
mat2vec.c:22:27: note: in definition of macro ‘HANDLE_CASE’
   22 |       CTYPE* output_ptr = ACCESSOR(VECTOR_ELT(output, i)); \
      |                           ^~~~~~~~
mat2vec.c:51:19: warning: initialization of ‘struct SEXPREC **’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
   51 |       HANDLE_CASE(STRING_PTR, SEXP);
      |                   ^~~~~~~~~~
mat2vec.c:23:22: note: in definition of macro ‘HANDLE_CASE’
   23 |       CTYPE* x_ptr = ACCESSOR(x);                          \
      |                      ^~~~~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.24-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.24-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 ‘rep_each_char’:
melt_dataframe.c:20:15: warning: implicit declaration of function ‘STRING_PTR’; did you mean ‘STRING_ELT’? [-Wimplicit-function-declaration]
   20 |   SEXP* ptr = STRING_PTR(x);
      |               ^~~~~~~~~~
      |               STRING_ELT
melt_dataframe.c:20:15: warning: initialization of ‘struct SEXPREC **’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
melt_dataframe.c:21:19: warning: initialization of ‘struct SEXPREC **’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
   21 |   SEXP* out_ptr = STRING_PTR(out);
      |                   ^~~~~~~~~~
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:40:17: warning: initialization of ‘struct SEXPREC **’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
   40 |     SEXP* ptr = STRING_PTR(x);                       \
      |                 ^~~~~~~~~~
melt_dataframe.c:70:5: note: in expansion of macro ‘HANDLE_CASE_STRING’
   70 |     HANDLE_CASE_STRING;
      |     ^~~~~~~~~~~~~~~~~~
melt_dataframe.c:41:21: warning: initialization of ‘struct SEXPREC **’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
   41 |     SEXP* out_ptr = STRING_PTR(out);                 \
      |                     ^~~~~~~~~~
melt_dataframe.c:70:5: note: in expansion of macro ‘HANDLE_CASE_STRING’
   70 |     HANDLE_CASE_STRING;
      |     ^~~~~~~~~~~~~~~~~~
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);
      |     ^~~~~~~~~~~
melt_dataframe.c:176:28: warning: assignment to ‘struct SEXPREC **’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
  176 |           curr_str_vec_ptr = STRING_PTR(tmp);
      |                            ^
melt_dataframe.c:178:28: warning: assignment to ‘struct SEXPREC **’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
  178 |           curr_str_vec_ptr = STRING_PTR(curr_str_vec);
      |                            ^
melt_dataframe.c:181:32: warning: initialization of ‘struct SEXPREC **’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
  181 |         SEXP* value_SEXP_ptr = STRING_PTR(value_SEXP);
      |                                ^~~~~~~~~~
melt_dataframe.c:235:21: warning: initialization of ‘struct SEXPREC **’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
  235 |   SEXP* names_ptr = STRING_PTR(names);
      |                     ^~~~~~~~~~
melt_dataframe.c:236:25: warning: initialization of ‘struct SEXPREC **’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
  236 |   SEXP* names_out_ptr = STRING_PTR(names_out);
      |                         ^~~~~~~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.24-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.24-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
melt_matrix.c: In function ‘rep_row_names’:
melt_matrix.c:11:17: warning: implicit declaration of function ‘STRING_PTR’; did you mean ‘STRING_ELT’? [-Wimplicit-function-declaration]
   11 |   SEXP* x_ptr = STRING_PTR(x);
      |                 ^~~~~~~~~~
      |                 STRING_ELT
melt_matrix.c:11:17: warning: initialization of ‘struct SEXPREC **’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
melt_matrix.c:12:19: warning: initialization of ‘struct SEXPREC **’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
   12 |   SEXP* out_ptr = STRING_PTR(out);
      |                   ^~~~~~~~~~
melt_matrix.c: In function ‘rep_col_names’:
melt_matrix.c:28:15: warning: initialization of ‘struct SEXPREC **’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
   28 |   SEXP* ptr = STRING_PTR(x);
      |               ^~~~~~~~~~
melt_matrix.c:29:19: warning: initialization of ‘struct SEXPREC **’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
   29 |   SEXP* out_ptr = STRING_PTR(out);
      |                   ^~~~~~~~~~
melt_matrix.c: In function ‘matrix_to_vector’:
melt_matrix.c:77:23: warning: initialization of ‘struct SEXPREC **’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
   77 |       SEXP* mat_ptr = STRING_PTR(x);
      |                       ^~~~~~~~~~
melt_matrix.c:78:23: warning: initialization of ‘struct SEXPREC **’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
   78 |       SEXP* out_ptr = STRING_PTR(out);
      |                       ^~~~~~~~~~
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.24-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.24-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-3.24-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.24-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
transpose_list.c: In function ‘transpose_list’:
transpose_list.c:38:33: warning: implicit declaration of function ‘STRING_PTR’; did you mean ‘STRING_ELT’? [-Wimplicit-function-declaration]
   38 |       HANDLE_CASE(STRSXP, SEXP, STRING_PTR);
      |                                 ^~~~~~~~~~
transpose_list.c:19:18: note: in definition of macro ‘HANDLE_CASE’
   19 |     CTYPE* ptr = ACCESSOR(tmp);                  \
      |                  ^~~~~~~~
transpose_list.c:38:33: warning: initialization of ‘struct SEXPREC **’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
   38 |       HANDLE_CASE(STRSXP, SEXP, STRING_PTR);
      |                                 ^~~~~~~~~~
transpose_list.c:19:18: note: in definition of macro ‘HANDLE_CASE’
   19 |     CTYPE* ptr = ACCESSOR(tmp);                  \
      |                  ^~~~~~~~
transpose_list.c:22:44: error: subscripted value is neither array nor pointer nor vector
   22 |         ptr[i] = ACCESSOR(VECTOR_ELT(x, i))[j];  \
      |                                            ^
transpose_list.c:38:7: note: in expansion of macro ‘HANDLE_CASE’
   38 |       HANDLE_CASE(STRSXP, SEXP, STRING_PTR);
      |       ^~~~~~~~~~~
make: *** [/home/biocbuild/bbs-3.24-bioc/R/etc/Makeconf:190: transpose_list.o] Error 1
ERROR: compilation failed for package ‘COMPASS’
* removing ‘/home/biocbuild/bbs-3.24-bioc/R/site-library/COMPASS’