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###
### Running command:
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### /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 COMPASS
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* checking for file ‘COMPASS/DESCRIPTION’ ... OK
* preparing ‘COMPASS’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* running ‘cleanup’
Warning in system2(command, args, stdout = NULL, stderr = NULL, ...) :
error in running command
* installing the package (it is needed to build vignettes)
-----------------------------------
* 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 ‘/tmp/RtmpwF4kns/Rinst358c4dcf8e613/COMPASS’
-----------------------------------
ERROR: package installation failed