[Phylobase-devl] Fwd: [site-Support][125] mac binary is missing many directories, files

Ben Bolker bolker at zoo.ufl.edu
Tue Mar 11 13:02:11 CET 2008 

   It looks like the warning is related to an issue with
"autoconf" (one of the configuration tools) on Leopard ...
(or rather with the interaction between libtool and autoconf).

http://www.mail-archive.com/autoconf@gnu.org/msg16623.html

I don't think this is the real problem, though.

   Cutting and pasting the log file from a previous message
(I assume this is up to date) in case any one has any bright
ideas.   The only odd/fishy thing I see is that for both
libRcpp and ncl, we get results along the lines of:

make  all-recursive
Making all in ncl
make[2]: Nothing to be done for `all'.

   ???

    Ben


Log file:
* Installing *source* package 'phylobase' ...
checking for C++ compiler default output file name... a.out
checking whether the C++ compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ -arch ppc accepts -g... yes
rm: conftest.dSYM: is a directory
checking how to run the C++ preprocessor... g++ -arch ppc -E
Building libRcpp.a in RcppSrc...
make: Nothing to be done for `all'.
Building libncl.a in ncl...
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... config/install-sh -c -d
checking for gawk... awk
checking whether make sets $(MAKE)... yes
checking how to create a ustar tar archive... gnutar
checking whether ln -s works... yes
checking for a BSD-compatible install... /usr/bin/install -c
checking for g++... g++
checking for C++ compiler default output file name... a.out
checking whether the C++ compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking for style of include used by make... GNU
checking dependency style of g++... gcc3
checking for ranlib... ranlib
checking build system type... i686-apple-darwin9.2.0
checking host system type... i686-apple-darwin9.2.0
checking for gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking dependency style of gcc... gcc3
checking for a sed that does not truncate output... /usr/bin/sed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ld used by gcc... /usr/libexec/gcc/i686-apple-darwin9/4.0.1/ld
checking if the linker (/usr/libexec/gcc/i686-apple-darwin9/4.0.1/ld) is 
GNU ld... no
checking for /usr/libexec/gcc/i686-apple-darwin9/4.0.1/ld option to 
reload object files... -r
checking for BSD-compatible nm... /usr/bin/nm -p
checking how to recognise dependent libraries... pass_all
checking how to run the C preprocessor... gcc -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 dlfcn.h usability... yes
checking dlfcn.h presence... yes
checking for dlfcn.h... yes
checking how to run the C++ preprocessor... g++ -E
checking for g77... no
checking for xlf... no
checking for f77... no
checking for frt... no
checking for pgf77... no
checking for cf77... no
checking for fort77... no
checking for fl32... no
checking for af77... no
checking for xlf90... no
checking for f90... no
checking for pgf90... no
checking for pghpf... no
checking for epcf90... no
checking for gfortran... no
checking for g95... no
checking for xlf95... no
checking for f95... no
checking for fort... no
checking for ifort... no
checking for ifc... no
checking for efc... no
checking for pgf95... no
checking for lf95... no
checking for ftn... no
checking whether we are using the GNU Fortran 77 compiler... no
checking whether  accepts -g... no
checking the maximum length of command line arguments... 196608
checking command to parse /usr/bin/nm -p output from gcc object... rm: 
conftest.dSYM: is a directory
rm: conftest.dSYM: is a directory
rm: conftest.dSYM: is a directory
rm: conftest.dSYM: is a directory
ok
checking for objdir... .libs
checking for ar... ar
checking for ranlib... (cached) ranlib
checking for strip... strip
rm: conftest.dSYM: is a directory
rm: conftest.dSYM: is a directory
checking if gcc static flag  works... rm: conftest.dSYM: is a directory
yes
checking if gcc supports -fno-rtti -fno-exceptions... rm: conftest.dSYM: 
is a directory
no
checking for gcc option to produce PIC... -fno-common
checking if gcc PIC flag -fno-common works... rm: conftest.dSYM: is a 
directory
yes
checking if gcc supports -c -o file.o... rm: conftest.dSYM: is a directory
yes
checking whether the gcc linker 
(/usr/libexec/gcc/i686-apple-darwin9/4.0.1/ld) supports shared 
libraries... yes
checking dynamic linker characteristics... darwin9.2.0 dyld
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
configure: creating libtool
appending configuration tag "CXX" to libtool
rm: conftest.dSYM: is a directory
rm: conftest.dSYM: is a directory
checking for ld used by g++... /usr/libexec/gcc/i686-apple-darwin9/4.0.1/ld
checking if the linker (/usr/libexec/gcc/i686-apple-darwin9/4.0.1/ld) is 
GNU ld... no
checking whether the g++ linker 
(/usr/libexec/gcc/i686-apple-darwin9/4.0.1/ld) supports shared 
libraries... yes
checking for g++ option to produce PIC... -fno-common
checking if g++ PIC flag -fno-common works... rm: conftest.dSYM: is a 
directory
yes
checking if g++ supports -c -o file.o... rm: conftest.dSYM: is a directory
yes
checking whether the g++ linker 
(/usr/libexec/gcc/i686-apple-darwin9/4.0.1/ld) supports shared 
libraries... yes
checking dynamic linker characteristics... darwin9.2.0 dyld
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
appending configuration tag "F77" to libtool
checking for ANSI C header files... (cached) yes
checking float.h usability... yes
checking float.h presence... yes
checking for float.h... yes
checking for stdlib.h... (cached) yes
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for an ANSI C-conforming const... yes
checking for inline... inline
checking whether struct tm is in sys/time.h or time.h... time.h
checking whether time.h and sys/time.h may both be included... yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking for unistd.h... (cached) yes
checking for alarm... yes
checking for working mktime... yes
checking for working strtod... yes
checking for memmove... yes
checking for strchr... yes
checking for strtol... yes
checking for python... /usr/bin/python
checking python module: subprocess... yes
checking whether make sets $(MAKE)... (cached) yes
configure: creating ./config.status
config.status: creating Makefile
config.status: creating ncl/Makefile
config.status: creating config.h
config.status: config.h is unchanged
config.status: executing depfiles commands
make  all-recursive
Making all in ncl
make[2]: Nothing to be done for `all'.
configure: creating ./config.status
config.status: creating src/Makevars
** libs
** arch - ppc
make: `phylobase.so' is up to date.
* DONE (phylobase)



Marguerite Butler wrote:
> Hello,
> 
> The mac binaries are still broken. I have reported this issue to R-forge 
> and checked the log files (you can see it on the R forge package page 
> after logging in as developer).
> 
> There seems to be a problem in the configure script that is not working 
> for the mac binaries. (although it works on my machines, it does not on 
> the r-forge compiler). Does anyone know how to fix this?
> 
> A kind person looked at the build log and noticed this:
> ----
> This was a recurrent message:
> 
> rm: conftest.dSYM: is a directory
> 
> hinting that perhaps there is something strange in your config file?
> ----
> 
> Marguerite
> 
> Begin forwarded message:
> 
>> From: site-support at r-forge.r-project.org
>> Date: March 10, 2008 2:47:40 AM HST
>> To: noreply at r-forge.r-project.org
>> Subject: [site-Support][125] mac binary is missing many directories, 
>> files
>> Reply-To: site-support at r-forge.r-project.org
>>
>> Support item #125, was opened at 2008-03-07 20:26
>> Status: Open
>> Priority: 4
>> Submitted By: Marguerite Butler (mbutler)
>> Assigned to: Stefan Theussl (stefan7th)
>> Summary: mac binary is missing many directories, files
>> Hardware: Macintosh
>> Operating System: MacOS X
>> Severity: blocker
>> URL: 
>> http://r-forge.r-project.org/bin/macosx/universal/contrib/latest/phylobase_0.3.tgz 
>>
>>
>>
>> Initial Comment:
>> Dear Administrators,
>>
>> Thank you for adding the mac binaries!
>>
>> However, it does not work on our package, phylobase. The generated 
>> binaries hold only the /lib directory, and so it does not install 
>> (I've attached it).
>>
>> Oddly, our package codes from source work just fine (passing R CMD 
>> check, build, install, build --binaries).
>>
>> Can you please look into this issue and let us know what you find? Are 
>> you getting errors?
>>
>> Thanks,
>> Marguerite Butler
>> (from phylobase team)
>>
>> ----------------------------------------------------------------------
>>
>>> Comment By: Stefan Theussl (stefan7th)
>> Date: 2008-03-10 13:47
>>
>> Message:
>> gfortran was available but not in the search path. this is fixed and 
>> works for most of the packages now. I'm afraid but it seems that it 
>> does not work for your package. Does it support building universal 
>> binaries? Perhaps there is something wrong with the configure file?
>>
>> Best,
>> Stefan
>>
>> ----------------------------------------------------------------------
>>
>> Comment By: Marguerite Butler (mbutler)
>> Date: 2008-03-09 20:36
>>
>> Message:
>> The build log indicates that it is not finding gfortran. Is there any 
>> plan to add gfortran?  I think this may affect a lot of packages.
>>
>> Thanks,
>> Marguerite
>>
>> ----------------------------------------------------------------------
>>
>> Comment By: Marguerite Butler (mbutler)
>> Date: 2008-03-09 12:52
>>
>> Message:
>> Thanks for your reponse.
>>
>> Is there any way we can find out what is causing the build failure? It 
>> builds fine on my macs.
>>
>> Thanks,
>> Marguerite
>>
>> ----------------------------------------------------------------------
>>
>> Comment By: Stefan Theussl (stefan7th)
>> Date: 2008-03-09 12:42
>>
>> Message:
>> This is an indication that your package has not passed the building 
>> process.
>>
>> currently, we have this suboptimal behavior that there is an empty 
>> package when failing the R CMD INSTALL for building the binary. We 
>> clearly have to change that.
>>
>> Best,
>> Stefan
>>
>> ----------------------------------------------------------------------
>>
>> You can respond by visiting:
>> http://r-forge.r-project.org/tracker/?func=detail&atid=194&aid=125&group_id=34 
>>
> 
> ____________________________________________
> Marguerite A. Butler
> Department of Zoology
> University of Hawaii
> 2538 McCarthy Mall, Edmondson 259
> Honolulu, HI  96822
> 
> Phone: 808-956-4713
> Lab:  808-956-5867
> FAX:   808-956-9812
> Dept: 808-956-8617
> http://www.hawaii.edu/zoology/faculty/butler.html
> http://www2.hawaii.edu/~mbutler
> http://www.hawaii.edu/zoology/
> 
> 
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> Phylobase-devl mailing list
> Phylobase-devl at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/phylobase-devl


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