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 âGenABELâ ...
** this is package âGenABELâ version â1.8-0â
files âsrc/ctest.hâ, âsrc/fexact.câ have the wrong MD5 checksums
** using staged installation
** libs
using C compiler: âgcc (Debian 14.2.0-19) 14.2.0â
using C++ compiler: âg++ (Debian 14.2.0-19) 14.2.0â
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 âSEXPREC* set_all_varnames_R(SEXP, SEXP)â:
AbstractMatrix_R.cpp:171:82: warning: format â%uâ expects argument of type
âunsigned intâ, but argument 2 has type âlong unsigned intâ [-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 âSEXPREC* set_all_obsnames_R(SEXP, SEXP)â:
AbstractMatrix_R.cpp:247:88: warning: format â%uâ expects argument of type
âunsigned intâ, but argument 2 has type âlong unsigned intâ [-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 âSEXPREC*
write_variable_double_FileMatrix_R(SEXP, SEXP, SEXP)â:
AbstractMatrix_R.cpp:392:58: warning: format â%uâ expects argument of type
âunsigned intâ, but argument 2 has type âlong unsigned intâ [-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 âvoid
convert_snp_affymetrix_C(char**, char**, unsigned int*, char**, char**,
unsigned int*, char**, char*, unsigned int*)â:
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 â%iâ expects argument of
type âintâ, but argument 2 has type âlong unsigned intâ [-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 â%iâ expects argument of
type âintâ, but argument 2 has type âlong unsigned intâ [-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 âvoid convert_snp_illumina(char**,
char**, int*, int*, char**, int*)â:
convert_snp_illumina.cpp:113:72: warning: format â%iâ expects argument of
type âintâ, but argument 2 has type âlong unsigned intâ [-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 â%iâ expects argument of
type âintâ, but argument 2 has type âlong unsigned intâ [-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 â%iâ expects argument of
type âintâ, but argument 3 has type âlong unsigned intâ [-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 â%sâ expects a matching
âchar*â argument [-Wformat=]
210 | error ("ran out of memory reading file
'%s' line %li !");
|
~^
|
|
|
char*
convert_snp_illumina.cpp:210:84: warning: format â%liâ expects a matching
âlong intâ argument [-Wformat=]
210 | error ("ran out of memory reading file
'%s' line %li !");
|
~~^
|
|
|
long int
convert_snp_illumina.cpp:213:74: warning: format â%sâ expects a matching
âchar*â argument [-Wformat=]
213 | error ("ran out of memory reading file
'%s' line %li !");
|
~^
|
|
|
char*
convert_snp_illumina.cpp:213:84: warning: format â%liâ expects a matching
âlong intâ 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 âvoid convert_snp_merlin(char**, char**,
char**, int*, int*, char**, int*, int*, int*, int*)â:
convert_snp_merlin.cpp:311:66: warning: format â%sâ expects a matching
âchar*â argument [-Wformat=]
311 | error ("ran out of memory reading file '%s'
line %li !");
| ~^
| |
| char*
convert_snp_merlin.cpp:311:76: warning: format â%liâ expects a matching
âlong intâ argument [-Wformat=]
311 | error ("ran out of memory reading file '%s'
line %li !");
|
~~^
|
|
|
long int
convert_snp_merlin.cpp:314:66: warning: format â%sâ expects a matching
âchar*â argument [-Wformat=]
314 | error ("ran out of memory reading file '%s'
line %li !");
| ~^
| |
| char*
convert_snp_merlin.cpp:314:76: warning: format â%liâ expects a matching
âlong intâ argument [-Wformat=]
314 | error ("ran out of memory reading file '%s'
line %li !");
|
~~^
|
|
|
long int
convert_snp_merlin.cpp:355:51: warning: format â%liâ expects argument of
type âlong intâ, but argument 2 has type âintâ [-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 âvoid
convert_snp_merlin_wslash(char**, char**, char**, int*, int*, char**, int*,
int*, int*, int*)â:
convert_snp_merlin_wslash.cpp:335:66: warning: format â%sâ expects a
matching âchar*â argument [-Wformat=]
335 | error ("ran out of memory reading file '%s'
line %li !");
| ~^
| |
| char*
convert_snp_merlin_wslash.cpp:335:76: warning: format â%liâ expects a
matching âlong intâ argument [-Wformat=]
335 | error ("ran out of memory reading file '%s'
line %li !");
|
~~^
|
|
|
long int
convert_snp_merlin_wslash.cpp:338:66: warning: format â%sâ expects a
matching âchar*â argument [-Wformat=]
338 | error ("ran out of memory reading file '%s'
line %li !");
| ~^
| |
| char*
convert_snp_merlin_wslash.cpp:338:76: warning: format â%liâ expects a
matching âlong intâ argument [-Wformat=]
338 | error ("ran out of memory reading file '%s'
line %li !");
|
~~^
|
|
|
long int
convert_snp_merlin_wslash.cpp:379:51: warning: format â%liâ expects
argument of type âlong intâ, but argument 2 has type âintâ [-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 âvoid convert_snp_tped(char**, char**,
char**, int*, int*, char**, int*)â:
convert_snp_tped.cpp:182:74: warning: format â%sâ expects a matching
âchar*â argument [-Wformat=]
182 | error ("ran out of memory reading file
'%s' line %li !");
|
~^
|
|
|
char*
convert_snp_tped.cpp:182:84: warning: format â%liâ expects a matching
âlong intâ argument [-Wformat=]
182 | error ("ran out of memory reading file
'%s' line %li !");
|
~~^
|
|
|
long int
convert_snp_tped.cpp:185:74: warning: format â%sâ expects a matching
âchar*â argument [-Wformat=]
185 | error ("ran out of memory reading file
'%s' line %li !");
|
~^
|
|
|
char*
convert_snp_tped.cpp:185:84: warning: format â%liâ expects a matching
âlong intâ argument [-Wformat=]
185 | error ("ran out of memory reading file
'%s' line %li !");
|
~~^
|
|
|
long int
convert_snp_tped.cpp:237:42: warning: format â%iâ expects argument of type
âintâ, but argument 2 has type
âstd::vector<std::__cxx11::basic_string<char> >::size_typeâ {aka âlong
unsigned intâ} [-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 âint sprintf(char*, const char*, ...)â,
inlined from âvoid 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)â 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 âint __builtin___sprintf_chk(char*, int, long unsigned int, const
char*, ...)â
In function âint sprintf(char*, const char*, ...)â,
inlined from âvoid 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)â 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 âint __builtin___sprintf_chk(char*, int, long unsigned int, const
char*, ...)â
/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination
pointer [-Wformat-overflow=]
In function âint sprintf(char*, const char*, ...)â,
inlined from âvoid 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)â 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 âfexactâ:
fexact.c:181:37: error: implicit declaration of function âCallocâ; did you
mean âcallocâ? [-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 âdoubleâ
181 | equiv = (double *) Calloc(iwkmax / 2, double); // call
Free(equiv) at the end.
| ^~~~~~
fexact.c:305:17: error: implicit declaration of function âFreeâ; did you
mean âfreeâ? [-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 âGenABELâ
* removing
â/<<PKGBUILDDIR>>/debian/r-cran-genabel/usr/lib/R/site-library/GenABELâ
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.
