Discussion:
Bug#850336: rmpi: FTBFS (Cannot find mpi.h header file)
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Santiago Vila
2017-01-06 01:00:02 UTC
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Package: src:rmpi
Version: 0.6-6-1
Severity: serious

Dear maintainer:

I tried to build this package in stretch with "dpkg-buildpackage -B"
but it failed:

--------------------------------------------------------------------------------
[...]
debian/rules build-arch
CDBS WARNING: simple-patchsys.mk is deprecated since 0.4.85 - please use source format 3.0 (quilt) instead
test -x debian/rules
mkdir -p "."
/usr/bin/make -f debian/rules reverse-config
make[1]: Entering directory '/<<PKGBUILDDIR>>'
CDBS WARNING: simple-patchsys.mk is deprecated since 0.4.85 - please use source format 3.0 (quilt) instead
make[1]: 'reverse-config' is up to date.
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
if [ "debian/stamp-patched" = "reverse-patches" ]; then rm -f debian/stamp-patched; fi
patches:
if [ "debian/stamp-patched" != "reverse-patches" ]; then touch debian/stamp-patched; fi
if [ "debian/stamp-patched" != "reverse-patches" ] ; then \

[... snipped ...]

if test -f /usr/bin/xvfb-run; then \
xvfb-run -a \
R CMD INSTALL -l /<<PKGBUILDDIR>>/debian/r-cran-rmpi/usr/lib/R/site-library --clean \
"--no-test-load" . \
"--built-timestamp=\"Sat, 25 Jun 2016 07:43:11 -0500\"" \
; \
else \
R CMD INSTALL -l /<<PKGBUILDDIR>>/debian/r-cran-rmpi/usr/lib/R/site-library \
--clean "--no-test-load" . \
"--built-timestamp=\"Sat, 25 Jun 2016 07:43:11 -0500\"" \
; \
fi
* installing *source* package 'Rmpi' ...
** package 'Rmpi' successfully unpacked and MD5 sums checked
checking for gcc... gcc -std=gnu99
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -std=gnu99 -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking mpi.h usability... no
checking mpi.h presence... no
checking for mpi.h... no
configure: error: "Cannot find mpi.h header file"
ERROR: configuration failed for package 'Rmpi'
* removing '/<<PKGBUILDDIR>>/debian/r-cran-rmpi/usr/lib/R/site-library/Rmpi'
/usr/share/R/debian/r-cran.mk:98: recipe for target 'R_any_arch' failed
make: *** [R_any_arch] Error 1
dpkg-buildpackage: error: fakeroot debian/rules binary-arch gave error exit status 2
--------------------------------------------------------------------------------

This is just how the build ends, not necessarily the relevant part.

I've put several build logs here:

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

If this is really a bug in one of the build-depends, please use reassign and affects,
so that this is still visible in the page for this package.

The bug should be reproducible with sbuild on a single CPU virtual machine.

Thanks.
Dirk Eddelbuettel
2017-01-06 01:30:01 UTC
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On 6 January 2017 at 00:53, Santiago Vila wrote:
| Package: src:rmpi
| Version: 0.6-6-1
| Severity: serious
|
| Dear maintainer:
|
| I tried to build this package in stretch with "dpkg-buildpackage -B"
| but it failed:
|
| --------------------------------------------------------------------------------
| [...]
| debian/rules build-arch
| CDBS WARNING: simple-patchsys.mk is deprecated since 0.4.85 - please use source format 3.0 (quilt) instead
| test -x debian/rules
| mkdir -p "."
| /usr/bin/make -f debian/rules reverse-config
| make[1]: Entering directory '/<<PKGBUILDDIR>>'
| CDBS WARNING: simple-patchsys.mk is deprecated since 0.4.85 - please use source format 3.0 (quilt) instead
| make[1]: 'reverse-config' is up to date.
| make[1]: Leaving directory '/<<PKGBUILDDIR>>'
| if [ "debian/stamp-patched" = "reverse-patches" ]; then rm -f debian/stamp-patched; fi
| patches:
| if [ "debian/stamp-patched" != "reverse-patches" ]; then touch debian/stamp-patched; fi
| if [ "debian/stamp-patched" != "reverse-patches" ] ; then \
|
| [... snipped ...]
|
| if test -f /usr/bin/xvfb-run; then \
| xvfb-run -a \
| R CMD INSTALL -l /<<PKGBUILDDIR>>/debian/r-cran-rmpi/usr/lib/R/site-library --clean \
| "--no-test-load" . \
| "--built-timestamp=\"Sat, 25 Jun 2016 07:43:11 -0500\"" \
| ; \
| else \
| R CMD INSTALL -l /<<PKGBUILDDIR>>/debian/r-cran-rmpi/usr/lib/R/site-library \
| --clean "--no-test-load" . \
| "--built-timestamp=\"Sat, 25 Jun 2016 07:43:11 -0500\"" \
| ; \
| fi
| * installing *source* package 'Rmpi' ...
| ** package 'Rmpi' successfully unpacked and MD5 sums checked
| checking for gcc... gcc -std=gnu99
| checking whether the C compiler works... yes
| checking for C compiler default output file name... a.out
| checking for suffix of executables...
| checking whether we are cross compiling... no
| checking for suffix of object files... o
| checking whether we are using the GNU C compiler... yes
| checking whether gcc -std=gnu99 accepts -g... yes
| checking for gcc -std=gnu99 option to accept ISO C89... none needed
| checking how to run the C preprocessor... gcc -std=gnu99 -E
| checking for grep that handles long lines and -e... /bin/grep
| checking for egrep... /bin/grep -E
| checking for ANSI C header files... yes
| checking for sys/types.h... yes
| checking for sys/stat.h... yes
| checking for stdlib.h... yes
| checking for string.h... yes
| checking for memory.h... yes
| checking for strings.h... yes
| checking for inttypes.h... yes
| checking for stdint.h... yes
| checking for unistd.h... yes
| checking mpi.h usability... no
| checking mpi.h presence... no
| checking for mpi.h... no
| configure: error: "Cannot find mpi.h header file"
| ERROR: configuration failed for package 'Rmpi'
| * removing '/<<PKGBUILDDIR>>/debian/r-cran-rmpi/usr/lib/R/site-library/Rmpi'
| /usr/share/R/debian/r-cran.mk:98: recipe for target 'R_any_arch' failed
| make: *** [R_any_arch] Error 1
| dpkg-buildpackage: error: fakeroot debian/rules binary-arch gave error exit status 2
| --------------------------------------------------------------------------------
|
| This is just how the build ends, not necessarily the relevant part.
|
| I've put several build logs here:
|
| https://people.debian.org/~sanvila/build-logs/rmpi/
|
| If this is really a bug in one of the build-depends, please use reassign and affects,
| so that this is still visible in the page for this package.
|
| The bug should be reproducible with sbuild on a single CPU virtual machine.

Probably a side effect of the OpenMPI v2 changes. The configure for this is
very much ad-hoc and grown. Could you have a look and test?


if test -z "$MPI_ROOT" ; then
for d in /opt/lib /usr/lib /usr /usr/local/lib /usr/local \
/usr/lib64/mpi/gcc/openmpi; do
if test -f $d/include/mpi.h && test -d $d/lib/openmpi; then
echo "I am here $d and it is OpenMPI"
MPI_ROOT=$d
MPITYPE="OPENMPI"
break
elif test -f $d/include/openmpi/mpi.h && test -d $d/lib/openmpi; then
echo "I am here $d and it is OpenMPI"
MPI_ROOT=$d
MPITYPE="OPENMPI"
MPI_INCLUDE_PATH=$d/include/openmpi
break
elif test -f $d/include/openmpi/mpi.h && test -d $d/lib64/openmpi; then
echo "I am here $d and it is OpenMPI"
MPI_ROOT=$d
MPITYPE="OPENMPI"
MPI_INCLUDE_PATH=$d/include/openmpi
break
elif test -f $d/openmpi/include/mpi.h && test -d $d/openmpi/lib; then
echo "I am here $d/openmpi and it is OpenMPI"
MPI_ROOT=$d/openmpi
MPITYPE="OPENMPI"
MPI_INCLUDE_PATH=$d/include/openmpi
break
elif test -f $d/include/mpi.h && test -d $d/lib64; then
echo "I am here $d and it is OpenMPI"
MPI_ROOT=$d
MPITYPE="OPENMPI"
MPI_INCLUDE_PATH=$d/include
break
elif test -f $d/lam/include/mpi.h && test -f $d/lam/lib/libmpi.so; then
echo "I am here $d/lam and it is LAM"
MPI_ROOT=$d/lam
MPITYPE="LAM"
MPI_INCLUDE_PATH=$d/include/lam
break
elif test -f $d/include/lam/mpi.h && test -f $d/lib/lam/libmpi.so; then
echo "I am here $d and it is LAM"
MPI_ROOT=$d
MPITYPE="LAM"
MPI_INCLUDE_PATH=$d/include/lam
break
elif test -f $d/include/lam/mpi.h && test -f $d/lib64/lam/libmpi.so; then
echo "I am here $d and it is LAM"
MPI_ROOT=$d
MPITYPE="LAM"
MPI_INCLUDE_PATH=$d/include/lam
break
elif test -f $d/mpich/include/mpi.h; then
echo "I am here $d/mpich and it is MPICH"
MPI_ROOT=$d/mpich
MPITYPE="MPICH"
MPI_INCLUDE_PATH=$d/mpich/include
break
elif test -f $d/mpi/include/mpi.h; then
echo "I am here $d/mpi"
MPI_ROOT=$d/mpi
MPI_INCLUDE_PATH=$d/mpi/include
break
elif test -f $d/include/mpi.h; then
echo "I am here $d"
MPI_ROOT=$d
break
fi
done
fi

Similarly for the library.

Dirk
--
http://dirk.eddelbuettel.com | @eddelbuettel | ***@debian.org
Dirk Eddelbuettel
2017-01-06 02:20:01 UTC
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On 6 January 2017 at 02:53, Santiago Vila wrote:
| Hi.
|
| I've triggered rebuilds in reproducible builds

Why? That wasn't what I asked you to do.

| and it also fails there:
|
| https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/rmpi.html

Well, doh. Computers and being deterministic and all that.

Dirk

|
| in both testing and unstable, so it should be easy to reproduce.
| (i.e. please try it for yourself first).
|
| Thanks.
--
http://dirk.eddelbuettel.com | @eddelbuettel | ***@debian.org
Debian Bug Tracking System
2017-01-06 03:10:02 UTC
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Your message dated Fri, 06 Jan 2017 03:07:48 +0000
with message-id <E1cPKse-0002Jk-***@fasolo.debian.org>
and subject line Bug#850336: fixed in rmpi 0.6-6-2
has caused the Debian Bug report #850336,
regarding rmpi: FTBFS (Cannot find mpi.h header file)
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.

(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact ***@bugs.debian.org
immediately.)
--
850336: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=850336
Debian Bug Tracking System
Contact ***@bugs.debian.org with problems
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