[R-pkg-team] Bug#1103201: r-cran-genabel: FTBFS: fexact.c:181:37: error: implicit declaration of function 'Calloc'
Santiago Vila
sanvila at debian.org
Tue Apr 15 01:19:50 BST 2025
Package: src:r-cran-genabel
Version: 1.8-0-7
Severity: serious
Tags: ftbfs trixie sid
Dear maintainer:
During a rebuild of all packages in unstable, your package failed to build:
--------------------------------------------------------------------------------
[...]
debian/rules clean
dh clean --buildsystem R
dh_auto_clean -O--buildsystem=R
dh_autoreconf_clean -O--buildsystem=R
dh_clean -O--buildsystem=R
debian/rules binary
dh binary --buildsystem R
dh_update_autotools_config -O--buildsystem=R
dh_autoreconf -O--buildsystem=R
dh_auto_configure -O--buildsystem=R
dh_auto_build -O--buildsystem=R
dh_auto_test -O--buildsystem=R
create-stamp debian/debhelper-build-stamp
dh_testroot -O--buildsystem=R
dh_prep -O--buildsystem=R
dh_auto_install --destdir=debian/r-cran-genabel/ -O--buildsystem=R
I: R Package: GenABEL Version: 1.8-0
I: Building using R version 4.5.0-1
I: R API version: r-api-4.0
I: Using built-time from d/changelog: Fri, 18 Aug 2023 08:22:29 +0200
mkdir -p /<<PKGBUILDDIR>>/debian/r-cran-genabel/usr/lib/R/site-library
R CMD INSTALL -l /<<PKGBUILDDIR>>/debian/r-cran-genabel/usr/lib/R/site-library --clean . "--built-timestamp='Fri, 18 Aug 2023 08:22:29 +0200'"
* installing *source* package ‘GenABEL’ ...
** this is package ‘GenABEL’ version ‘1.8-0’
files ‘src/ctest.h’, ‘src/fexact.c’ have the wrong MD5 checksums
** using staged installation
** libs
using C compiler: ‘gcc (Debian 14.2.0-19) 14.2.0’
using C++ compiler: ‘g++ (Debian 14.2.0-19) 14.2.0’
make[1]: Entering directory '/<<PKGBUILDDIR>>/src'
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -DCOMPILE_WITH_R -fpic -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/r-base-4.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c AbstractMatrix.cpp -o AbstractMatrix.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -DCOMPILE_WITH_R -fpic -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/r-base-4.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c AbstractMatrix_R.cpp -o AbstractMatrix_R.o
AbstractMatrix_R.cpp: In function ‘SEXPREC* set_all_varnames_R(SEXP, SEXP)’:
AbstractMatrix_R.cpp:171:82: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘long unsigned int’ [-Wformat=]
171 | error_R("can not set variable name for variable %ul\n",i);
| ~^ ~
| | |
| | long unsigned int
| unsigned int
| %lu
AbstractMatrix_R.cpp: In function ‘SEXPREC* set_all_obsnames_R(SEXP, SEXP)’:
AbstractMatrix_R.cpp:247:88: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘long unsigned int’ [-Wformat=]
247 | error_R("can not set observation name for observation %ul\n",i);
| ~^ ~
| | |
| | long unsigned int
| unsigned int
| %lu
AbstractMatrix_R.cpp: In function ‘SEXPREC* write_variable_double_FileMatrix_R(SEXP, SEXP, SEXP)’:
AbstractMatrix_R.cpp:392:58: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘long unsigned int’ [-Wformat=]
392 | error_R("can not write variable %ul\n",nvariable);
| ~^ ~~~~~~~~~
| | |
| | long unsigned int
| unsigned int
| %lu
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -DCOMPILE_WITH_R -fpic -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/r-base-4.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c CastUtils.cpp -o CastUtils.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -DCOMPILE_WITH_R -fpic -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/r-base-4.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c Chip.cpp -o Chip.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -DCOMPILE_WITH_R -fpic -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/r-base-4.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c FileVector.cpp -o FileVector.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -DCOMPILE_WITH_R -fpic -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/r-base-4.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c FilteredMatrix.cpp -o FilteredMatrix.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -DCOMPILE_WITH_R -fpic -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/r-base-4.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c FilteredMatrix_R.cpp -o FilteredMatrix_R.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -DCOMPILE_WITH_R -fpic -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/r-base-4.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c Logger.cpp -o Logger.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -DCOMPILE_WITH_R -fpic -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/r-base-4.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c RealHandlerWrapper.cpp -o RealHandlerWrapper.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -DCOMPILE_WITH_R -fpic -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/r-base-4.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c ReusableFileHandle.cpp -o ReusableFileHandle.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -DCOMPILE_WITH_R -fpic -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/r-base-4.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c Transposer.cpp -o Transposer.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -DCOMPILE_WITH_R -fpic -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/r-base-4.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c chinv2.cpp -o chinv2.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -DCOMPILE_WITH_R -fpic -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/r-base-4.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c cholesky2.cpp -o cholesky2.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -DCOMPILE_WITH_R -fpic -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/r-base-4.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c chsolve2.cpp -o chsolve2.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -DCOMPILE_WITH_R -fpic -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/r-base-4.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c convert.snp.affymetrix.cpp -o convert.snp.affymetrix.o
convert.snp.affymetrix.cpp: In function ‘void convert_snp_affymetrix_C(char**, char**, unsigned int*, char**, char**, unsigned int*, char**, char*, unsigned int*)’:
convert.snp.affymetrix.cpp:93:30: warning: too many arguments for format [-Wformat-extra-args]
93 | if(!outfile.is_open()){error("Can not open file \"\"\n",outfilename);}
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
convert.snp.affymetrix.cpp:245:11: warning: format ‘%i’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=]
245 | Rprintf("%i SNPs excluded bacause of absent in annotation\n", snp_excludet_from_output_data);
| ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| | |
| int long unsigned int
| %li
convert.snp.affymetrix.cpp:246:17: warning: format ‘%i’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=]
246 | Rprintf("Total %i SNPs are written into output file\n", snp_amount-snp_excludet_from_output_data);
| ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| | |
| int long unsigned int
| %li
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -DCOMPILE_WITH_R -fpic -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/r-base-4.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c convert_snp_illumina.cpp -o convert_snp_illumina.o
convert_snp_illumina.cpp: In function ‘void convert_snp_illumina(char**, char**, int*, int*, char**, int*)’:
convert_snp_illumina.cpp:113:72: warning: format ‘%i’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=]
113 | error("First three fields are missing in line %i!\n",(nsnps+1));
| ~^ ~~~~~~~~~
| | |
| int long unsigned int
| %li
convert_snp_illumina.cpp:119:101: warning: format ‘%i’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=]
119 | if (!(datas >> tmp_strand)) error("Strand field is missing in line %i, SNP '%s'!\n",(nsnps+1),tmp_snpnam.c_str());
| ~^ ~~~~~~~~~
| | |
| int long unsigned int
| %li
convert_snp_illumina.cpp:130:100: warning: format ‘%i’ expects argument of type ‘int’, but argument 3 has type ‘long unsigned int’ [-Wformat=]
130 | if (!(datas >> tempstr)) error("Too few fields for SNP '%s', line %i (no. IDs = %li, no. fields = %li)!\n",snpnam[nsnps-1].c_str(),(nsnps+1),nids,(i+1));
| ~^ ~~~~~~~~~
| | |
| int long unsigned int
| %li
convert_snp_illumina.cpp:210:74: warning: format ‘%s’ expects a matching ‘char*’ argument [-Wformat=]
210 | error ("ran out of memory reading file '%s' line %li !");
| ~^
| |
| char*
convert_snp_illumina.cpp:210:84: warning: format ‘%li’ expects a matching ‘long int’ argument [-Wformat=]
210 | error ("ran out of memory reading file '%s' line %li !");
| ~~^
| |
| long int
convert_snp_illumina.cpp:213:74: warning: format ‘%s’ expects a matching ‘char*’ argument [-Wformat=]
213 | error ("ran out of memory reading file '%s' line %li !");
| ~^
| |
| char*
convert_snp_illumina.cpp:213:84: warning: format ‘%li’ expects a matching ‘long int’ argument [-Wformat=]
213 | error ("ran out of memory reading file '%s' line %li !");
| ~~^
| |
| long int
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -DCOMPILE_WITH_R -fpic -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/r-base-4.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c convert_snp_merlin.cpp -o convert_snp_merlin.o
convert_snp_merlin.cpp: In function ‘void convert_snp_merlin(char**, char**, char**, int*, int*, char**, int*, int*, int*, int*)’:
convert_snp_merlin.cpp:311:66: warning: format ‘%s’ expects a matching ‘char*’ argument [-Wformat=]
311 | error ("ran out of memory reading file '%s' line %li !");
| ~^
| |
| char*
convert_snp_merlin.cpp:311:76: warning: format ‘%li’ expects a matching ‘long int’ argument [-Wformat=]
311 | error ("ran out of memory reading file '%s' line %li !");
| ~~^
| |
| long int
convert_snp_merlin.cpp:314:66: warning: format ‘%s’ expects a matching ‘char*’ argument [-Wformat=]
314 | error ("ran out of memory reading file '%s' line %li !");
| ~^
| |
| char*
convert_snp_merlin.cpp:314:76: warning: format ‘%li’ expects a matching ‘long int’ argument [-Wformat=]
314 | error ("ran out of memory reading file '%s' line %li !");
| ~~^
| |
| long int
convert_snp_merlin.cpp:355:51: warning: format ‘%li’ expects argument of type ‘long int’, but argument 2 has type ‘int’ [-Wformat=]
355 | Rprintf(" ... analysed %li genotypes ...\n",((1+snp)*nids));
| ~~^ ~~~~~~~~~~~~~~
| | |
| long int int
| %i
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -DCOMPILE_WITH_R -fpic -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/r-base-4.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c convert_snp_merlin_wslash.cpp -o convert_snp_merlin_wslash.o
convert_snp_merlin_wslash.cpp: In function ‘void convert_snp_merlin_wslash(char**, char**, char**, int*, int*, char**, int*, int*, int*, int*)’:
convert_snp_merlin_wslash.cpp:335:66: warning: format ‘%s’ expects a matching ‘char*’ argument [-Wformat=]
335 | error ("ran out of memory reading file '%s' line %li !");
| ~^
| |
| char*
convert_snp_merlin_wslash.cpp:335:76: warning: format ‘%li’ expects a matching ‘long int’ argument [-Wformat=]
335 | error ("ran out of memory reading file '%s' line %li !");
| ~~^
| |
| long int
convert_snp_merlin_wslash.cpp:338:66: warning: format ‘%s’ expects a matching ‘char*’ argument [-Wformat=]
338 | error ("ran out of memory reading file '%s' line %li !");
| ~^
| |
| char*
convert_snp_merlin_wslash.cpp:338:76: warning: format ‘%li’ expects a matching ‘long int’ argument [-Wformat=]
338 | error ("ran out of memory reading file '%s' line %li !");
| ~~^
| |
| long int
convert_snp_merlin_wslash.cpp:379:51: warning: format ‘%li’ expects argument of type ‘long int’, but argument 2 has type ‘int’ [-Wformat=]
379 | Rprintf(" ... analysed %li genotypes ...\n",((1+snp)*nids));
| ~~^ ~~~~~~~~~~~~~~
| | |
| long int int
| %i
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -DCOMPILE_WITH_R -fpic -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/r-base-4.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c convert_snp_tped.cpp -o convert_snp_tped.o
convert_snp_tped.cpp: In function ‘void convert_snp_tped(char**, char**, char**, int*, int*, char**, int*)’:
convert_snp_tped.cpp:182:74: warning: format ‘%s’ expects a matching ‘char*’ argument [-Wformat=]
182 | error ("ran out of memory reading file '%s' line %li !");
| ~^
| |
| char*
convert_snp_tped.cpp:182:84: warning: format ‘%li’ expects a matching ‘long int’ argument [-Wformat=]
182 | error ("ran out of memory reading file '%s' line %li !");
| ~~^
| |
| long int
convert_snp_tped.cpp:185:74: warning: format ‘%s’ expects a matching ‘char*’ argument [-Wformat=]
185 | error ("ran out of memory reading file '%s' line %li !");
| ~^
| |
| char*
convert_snp_tped.cpp:185:84: warning: format ‘%li’ expects a matching ‘long int’ argument [-Wformat=]
185 | error ("ran out of memory reading file '%s' line %li !");
| ~~^
| |
| long int
convert_snp_tped.cpp:237:42: warning: format ‘%i’ expects argument of type ‘int’, but argument 2 has type ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wformat=]
237 | Rprintf("...done. Read %i SNPs from file '%s'\n",chrom.size(),tpedfilename[0]);
| ~^ ~~~~~~~~~~~~
| | |
| int std::vector<std::__cxx11::basic_string<char> >::size_type {aka long unsigned int}
| %li
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -DCOMPILE_WITH_R -fpic -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/r-base-4.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c convert_util.cpp -o convert_util.o
In file included from /usr/include/stdio.h:970,
from /usr/include/c++/14/cstdio:42,
from /usr/include/c++/14/ext/string_conversions.h:45,
from /usr/include/c++/14/bits/basic_string.h:4154,
from /usr/include/c++/14/string:54,
from convert_util.cpp:2:
In function ‘int sprintf(char*, const char*, ...)’,
inlined from ‘void text2fvf(std::string, std::string, std::string, std::string, std::string, int, int, long unsigned int, long unsigned int, int, int, short unsigned int, bool, std::string)’ at convert_util.cpp:299:20:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull]
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function ‘int __builtin___sprintf_chk(char*, int, long unsigned int, const char*, ...)’
In function ‘int sprintf(char*, const char*, ...)’,
inlined from ‘void text2fvf(std::string, std::string, std::string, std::string, std::string, int, int, long unsigned int, long unsigned int, int, int, short unsigned int, bool, std::string)’ at convert_util.cpp:307:20:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull]
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function ‘int __builtin___sprintf_chk(char*, int, long unsigned int, const char*, ...)’
/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=]
In function ‘int sprintf(char*, const char*, ...)’,
inlined from ‘void text2fvf(std::string, std::string, std::string, std::string, std::string, int, int, long unsigned int, long unsigned int, int, int, short unsigned int, bool, std::string)’ at convert_util.cpp:299:20:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=]
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -DCOMPILE_WITH_R -fpic -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/r-base-4.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c coxfit2.cpp -o coxfit2.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -DCOMPILE_WITH_R -fpic -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/r-base-4.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c dautil.cpp -o dautil.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -DCOMPILE_WITH_R -fpic -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/r-base-4.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c dmatrix.cpp -o dmatrix.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -DCOMPILE_WITH_R -fpic -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/r-base-4.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c dometa.cpp -o dometa.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -DCOMPILE_WITH_R -fpic -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/r-base-4.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c export_plink.cpp -o export_plink.o
gcc -std=gnu23 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/r-base-4.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c fexact.c -o fexact.o
fexact.c: In function ‘fexact’:
fexact.c:181:37: error: implicit declaration of function ‘Calloc’; did you mean ‘calloc’? [-Wimplicit-function-declaration]
181 | equiv = (double *) Calloc(iwkmax / 2, double); // call Free(equiv) at the end.
| ^~~~~~
| calloc
fexact.c:181:56: error: expected expression before ‘double’
181 | equiv = (double *) Calloc(iwkmax / 2, double); // call Free(equiv) at the end.
| ^~~~~~
fexact.c:305:17: error: implicit declaration of function ‘Free’; did you mean ‘free’? [-Wimplicit-function-declaration]
305 | Free(equiv);
| ^~~~
| free
make[1]: *** [/usr/lib/R/etc/Makeconf:202: fexact.o] Error 1
make[1]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[1]: Entering directory '/<<PKGBUILDDIR>>/src'
make[1]: Leaving directory '/<<PKGBUILDDIR>>/src'
ERROR: compilation failed for package ‘GenABEL’
* removing ‘/<<PKGBUILDDIR>>/debian/r-cran-genabel/usr/lib/R/site-library/GenABEL’
dh_auto_install: error: R CMD INSTALL -l /<<PKGBUILDDIR>>/debian/r-cran-genabel/usr/lib/R/site-library --clean . "--built-timestamp='Fri, 18 Aug 2023 08:22:29 +0200'" returned exit code 1
make: *** [debian/rules:7: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------
The above is just how the build ends and not necessarily the most relevant part.
If required, the full build log is available here:
https://people.debian.org/~sanvila/build-logs/202504/
About the archive rebuild: The build was made on virtual machines from AWS,
using sbuild and a reduced chroot with only build-essential packages.
If you could not reproduce the bug please contact me privately, as I
am willing to provide ssh access to a virtual machine where the bug is
fully reproducible.
If this is really a bug in one of the build-depends, please use
reassign and add an affects on src:r-cran-genabel, so that this is still
visible in the BTS web page for this package.
Thanks.
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