Bug#1135462: marked as done (r-bioc-hdf5array: FTBFS: h5mread_startscounts.c:405:29: error: implicit declaration of function 'DATAPTR'; did you mean 'DATAPTR_RO'? [-Wimplicit-function-declaration])

Debian Bug Tracking System Tue, 06 Oct 2026 21:43:34 -0700

Your message dated Wed, 7 Oct 2026 13:40:45 +0900
with message-id <[email protected]>
and subject line Re: r-bioc-hdf5array: FTBFS: h5mread_startscounts.c:405:29: 
error: implicit declaration of function 'DATAPTR'; did you mean 'DATAPTR_RO'? 
[-Wimplicit-function-declaration]
has caused the Debian Bug report #1135462,
regarding r-bioc-hdf5array: FTBFS: h5mread_startscounts.c:405:29: error: 
implicit declaration of function 'DATAPTR'; did you mean 'DATAPTR_RO'? 
[-Wimplicit-function-declaration]
to be marked as done.


This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.

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-- 
1135462: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1135462
Debian Bug Tracking System
Contact [email protected] with problems

--- Begin Message ---

Package: src:r-bioc-hdf5array
Version: 1.34.0-3
Severity: serious
Tags: ftbfs forky sid

Dear maintainer:

During a rebuild of all packages in unstable, this package failed to build.

Below you will find the last part of the build log (probably the most
relevant part, but not necessarily). If required, the full build log
is available here:

https://people.debian.org/~sanvila/build-logs/202605/

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 cannot 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-hdf5array, so that this is still
visible in the BTS web page for this package.

Thanks.

--------------------------------------------------------------------------------
[...]
 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-bioc-hdf5array/ -O--buildsystem=R
I: R Package: HDF5Array Version: 1.34.0
I: Building using R version 4.6.0-2
I: R API version: r-api-4.0
I: Using built-time from d/changelog: Fri, 13 Mar 2026 16:36:46 +0900
        mkdir -p /<<PKGBUILDDIR>>/debian/r-bioc-hdf5array/usr/lib/R/site-library
        R CMD INSTALL -l 
/<<PKGBUILDDIR>>/debian/r-bioc-hdf5array/usr/lib/R/site-library --clean . 
--built-timestamp="'Fri, 13 Mar 2026 16:36:46 +0900'"
* installing *source* package âHDF5Arrayâ ...
** this is package âHDF5Arrayâ version â1.34.0â
file âsrc/Makevarsâ has the wrong MD5 checksum
** using staged installation
** libs
using C compiler: âx86_64-linux-gnu-gcc (Debian 15.2.0-17) 15.2.0â
make[1]: Entering directory '/<<PKGBUILDDIR>>/src'
x86_64-linux-gnu-gcc -I"/usr/share/R/include" -DNDEBUG  
-I'/usr/lib/R/site-library/S4Vectors/include' 
-I'/usr/lib/R/site-library/Rhdf5lib/include'     -fpic  -g -O2 
-ffile-prefix-map=/build/reproducible-path/r-base-4.6.0=. 
-fstack-protector-strong -fstack-clash-protection -Wformat 
-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2  -c 
S4Vectors_stubs.c -o S4Vectors_stubs.o
x86_64-linux-gnu-gcc -I"/usr/share/R/include" -DNDEBUG  
-I'/usr/lib/R/site-library/S4Vectors/include' 
-I'/usr/lib/R/site-library/Rhdf5lib/include'     -fpic  -g -O2 
-ffile-prefix-map=/build/reproducible-path/r-base-4.6.0=. 
-fstack-protector-strong -fstack-clash-protection -Wformat 
-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2  -c 
H5File.c -o H5File.o
x86_64-linux-gnu-gcc -I"/usr/share/R/include" -DNDEBUG  
-I'/usr/lib/R/site-library/S4Vectors/include' 
-I'/usr/lib/R/site-library/Rhdf5lib/include'     -fpic  -g -O2 
-ffile-prefix-map=/build/reproducible-path/r-base-4.6.0=. 
-fstack-protector-strong -fstack-clash-protection -Wformat 
-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2  -c 
global_errmsg_buf.c -o global_errmsg_buf.o
x86_64-linux-gnu-gcc -I"/usr/share/R/include" -DNDEBUG  
-I'/usr/lib/R/site-library/S4Vectors/include' 
-I'/usr/lib/R/site-library/Rhdf5lib/include'     -fpic  -g -O2 
-ffile-prefix-map=/build/reproducible-path/r-base-4.6.0=. 
-fstack-protector-strong -fstack-clash-protection -Wformat 
-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2  -c 
H5DSetDescriptor.c -o H5DSetDescriptor.o
H5DSetDescriptor.c: In function âC_show_H5DSetDescriptor_xpâ:
H5DSetDescriptor.c:1192:30: warning: format â%lluâ expects argument of type 
âlong long unsigned intâ, but argument 2 has type âhsize_tâ {aka 
âlong unsigned intâ} [-Wformat=]
 1192 |                 Rprintf(" %llu", h5dset->h5dim[h5along]);
      |                           ~~~^   ~~~~~~~~~~~~~~~~~~~~~~
      |                              |                |
      |                              |                hsize_t {aka long 
unsigned int}
      |                              long long unsigned int
      |                           %lu
H5DSetDescriptor.c:1202:38: warning: format â%lluâ expects argument of type 
âlong long unsigned intâ, but argument 2 has type âhsize_tâ {aka 
âlong unsigned intâ} [-Wformat=]
 1202 |                         Rprintf(" %llu",
      |                                   ~~~^
      |                                      |
      |                                      long long unsigned int
      |                                   %lu
 1203 |                                 h5dset->h5chunkdim[h5along]);
      |                                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                                   |
      |                                                   hsize_t {aka long 
unsigned int}
x86_64-linux-gnu-gcc -I"/usr/share/R/include" -DNDEBUG  
-I'/usr/lib/R/site-library/S4Vectors/include' 
-I'/usr/lib/R/site-library/Rhdf5lib/include'     -fpic  -g -O2 
-ffile-prefix-map=/build/reproducible-path/r-base-4.6.0=. 
-fstack-protector-strong -fstack-clash-protection -Wformat 
-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2  -c 
h5dimscales.c -o h5dimscales.o
x86_64-linux-gnu-gcc -I"/usr/share/R/include" -DNDEBUG  
-I'/usr/lib/R/site-library/S4Vectors/include' 
-I'/usr/lib/R/site-library/Rhdf5lib/include'     -fpic  -g -O2 
-ffile-prefix-map=/build/reproducible-path/r-base-4.6.0=. 
-fstack-protector-strong -fstack-clash-protection -Wformat 
-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2  -c 
uaselection.c -o uaselection.o
x86_64-linux-gnu-gcc -I"/usr/share/R/include" -DNDEBUG  
-I'/usr/lib/R/site-library/S4Vectors/include' 
-I'/usr/lib/R/site-library/Rhdf5lib/include'     -fpic  -g -O2 
-ffile-prefix-map=/build/reproducible-path/r-base-4.6.0=. 
-fstack-protector-strong -fstack-clash-protection -Wformat 
-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2  -c 
h5mread_helpers.c -o h5mread_helpers.o
x86_64-linux-gnu-gcc -I"/usr/share/R/include" -DNDEBUG  
-I'/usr/lib/R/site-library/S4Vectors/include' 
-I'/usr/lib/R/site-library/Rhdf5lib/include'     -fpic  -g -O2 
-ffile-prefix-map=/build/reproducible-path/r-base-4.6.0=. 
-fstack-protector-strong -fstack-clash-protection -Wformat 
-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2  -c 
h5mread_startscounts.c -o h5mread_startscounts.o
h5mread_startscounts.c: In function â_h5mread_startscountsâ:
h5mread_startscounts.c:405:29: error: implicit declaration of function 
âDATAPTRâ; did you mean âDATAPTR_ROâ? [-Wimplicit-function-declaration]
  405 |                 void *mem = DATAPTR(ans);
      |                             ^~~~~~~
      |                             DATAPTR_RO
h5mread_startscounts.c:405:29: error: initialization of âvoid *â from 
âintâ makes pointer from integer without a cast [-Wint-conversion]
make[1]: *** [/usr/lib/R/etc/Makeconf:190: h5mread_startscounts.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 âHDF5Arrayâ
* removing 
â/<<PKGBUILDDIR>>/debian/r-bioc-hdf5array/usr/lib/R/site-library/HDF5Arrayâ
dh_auto_install: error: R CMD INSTALL -l 
/<<PKGBUILDDIR>>/debian/r-bioc-hdf5array/usr/lib/R/site-library --clean . 
--built-timestamp="'Fri, 13 Mar 2026 16:36:46 +0900'" returned exit code 1
make: *** [debian/rules:4: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess failed with exit 
status 2
--------------------------------------------------------------------------------

--- End Message ---

--- Begin Message ---

Version: 1.40.0-1

Hi Santiago, it was fixed in the version uploaded after you made yourreport.


Have a nice day,

Charles

On Fri, 01 May 2026 23:14:37 +0000 Santiago Vila <[email protected]> wrote:

Package: src:r-bioc-hdf5array
Version: 1.34.0-3
Severity: serious
Tags: ftbfs forky sid

Dear maintainer:

During a rebuild of all packages in unstable, this package failed to build.

Below you will find the last part of the build log (probably the most
relevant part, but not necessarily). If required, the full build log
is available here:

https://people.debian.org/~sanvila/build-logs/202605/

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 cannot 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-hdf5array, so that this is still
visible in the BTS web page for this package.

Thanks.

--------------------------------------------------------------------------------
[...]
 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-bioc-hdf5array/ -O--buildsystem=R
I: R Package: HDF5Array Version: 1.34.0
I: Building using R version 4.6.0-2
I: R API version: r-api-4.0
I: Using built-time from d/changelog: Fri, 13 Mar 2026 16:36:46 +0900
        mkdir -p /<<PKGBUILDDIR>>/debian/r-bioc-hdf5array/usr/lib/R/site-library
        R CMD INSTALL -l /<<PKGBUILDDIR>>/debian/r-bioc-hdf5array/usr/lib/R/site-library 
--clean . --built-timestamp="'Fri, 13 Mar 2026 16:36:46 +0900'"
* installing *source* package ‘HDF5Array’ ...
** this is package ‘HDF5Array’ version ‘1.34.0’
file ‘src/Makevars’ has the wrong MD5 checksum
** using staged installation
** libs
using C compiler: ‘x86_64-linux-gnu-gcc (Debian 15.2.0-17) 15.2.0’
make[1]: Entering directory '/<<PKGBUILDDIR>>/src'
x86_64-linux-gnu-gcc -I"/usr/share/R/include" -DNDEBUG  
-I'/usr/lib/R/site-library/S4Vectors/include' 
-I'/usr/lib/R/site-library/Rhdf5lib/include'     -fpic  -g -O2 
-ffile-prefix-map=/build/reproducible-path/r-base-4.6.0=. -fstack-protector-strong 
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time 
-D_FORTIFY_SOURCE=2  -c S4Vectors_stubs.c -o S4Vectors_stubs.o


--
Charles Plessy - - ~ ~ ~ ~ ~ ~~~~ ~ ~ ~ ~ ~ - - [email protected]
Okinawa  Institute  of  Science  and  Technology  Graduate  University
Senior staff scientist ~~ Luscombe Unit ~~ https://groups.oist.jp/grsu
Toots from work - ~~ ~~~~ ~~ - https://fediscience.org/@charles_plessy

--- End Message ---

Bug#1135462: marked as done (r-bioc-hdf5array: FTBFS: h5mread_startscounts.c:405:29: error: implicit declaration of function 'DATAPTR'; did you mean 'DATAPTR_RO'? [-Wimplicit-function-declaration])

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