[R-pkg-team] Bug#1103199: r-bioc-oligo: FTBFS: ParserGzXYS.c:62:11: error: implicit declaration of function 'Calloc'; did you mean 'calloc'? [-Wimplicit-function-declaration]

[Santiago Vila]

Package: src:r-bioc-oligo
Version: 1.70.0+ds-2
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
   debian/rules override_dh_auto_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_install
I: R Package: oligo Version: 1.70.0
I: Building using R version 4.5.0-1
I: R API version: r-api-4.0
I: Using built-time from d/changelog: Mon, 13 Jan 2025 15:18:40 +0100
	mkdir -p /<<BUILDDIR>>/r-bioc-oligo-1.70.0\+ds/debian/r-bioc-oligo/usr/lib/R/site-library
	R CMD INSTALL -l /<<BUILDDIR>>/r-bioc-oligo-1.70.0\+ds/debian/r-bioc-oligo/usr/lib/R/site-library --clean . "--built-timestamp='Mon, 13 Jan 2025 15:18:40 +0100'"
* installing *source* package ‘oligo’ ...
** this is package ‘oligo’ version ‘1.70.0’
files ‘inst/doc/oug.pdf’, ‘inst/scripts/oug.pdf’, ‘inst/scripts/primer.pdf’ are missing
file ‘tests/doRUnit.R’ has the wrong MD5 checksum
** using staged installation
** libs
using C compiler: ‘gcc (Debian 14.2.0-19) 14.2.0’
make[2]: Entering directory '/<<PKGBUILDDIR>>/src'
gcc -std=gnu23 -I"/usr/share/R/include" -DNDEBUG  -I'/usr/lib/R/site-library/preprocessCore/include'     -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 DABG.c -o DABG.o
gcc -std=gnu23 -I"/usr/share/R/include" -DNDEBUG  -I'/usr/lib/R/site-library/preprocessCore/include'     -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 ParserGzXYS.c -o ParserGzXYS.o
ParserGzXYS.c: In function ‘gzxys_header_field’:
ParserGzXYS.c:62:11: error: implicit declaration of function ‘Calloc’; did you mean ‘calloc’? [-Wimplicit-function-declaration]
   62 |   final = Calloc(strlen(result)+1, char);
      |           ^~~~~~
      |           calloc
ParserGzXYS.c:62:36: error: expected expression before ‘char’
   62 |   final = Calloc(strlen(result)+1, char);
      |                                    ^~~~
ParserGzXYS.c: In function ‘R_read_gzxys_files’:
ParserGzXYS.c:147:9: error: implicit declaration of function ‘Free’; did you mean ‘free’? [-Wimplicit-function-declaration]
  147 |         Free(d0);
      |         ^~~~
      |         free
make[2]: *** [/usr/lib/R/etc/Makeconf:202: ParserGzXYS.o] Error 1
make[2]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[2]: Entering directory '/<<PKGBUILDDIR>>/src'
make[2]: Leaving directory '/<<PKGBUILDDIR>>/src'
ERROR: compilation failed for package ‘oligo’
* removing ‘/<<PKGBUILDDIR>>/debian/r-bioc-oligo/usr/lib/R/site-library/oligo’
dh_auto_install: error: R CMD INSTALL -l /<<BUILDDIR>>/r-bioc-oligo-1.70.0\+ds/debian/r-bioc-oligo/usr/lib/R/site-library --clean . "--built-timestamp='Mon, 13 Jan 2025 15:18:40 +0100'" returned exit code 1
make[1]: *** [debian/rules:7: override_dh_auto_install] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:4: binary] Error 2
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-bioc-oligo, so that this is still
visible in the BTS web page for this package.

Thanks.