[MacPorts] #36415: hdfeos5 @1.13r2 Configure failure
#36415: hdfeos5 @1.13r2 Configure failure ---------------------+-------------------------------- Reporter: uthyr@… | Owner: macports-tickets@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.1.2 Keywords: | Port: ncarg hdfeos5 ---------------------+-------------------------------- Hi, system info: Xserve hardware, running Mac OS X Server 10.6.8, with all Software Update patches applied. my primary command that led to this configure failure was: "sudo port install ncarg +gcc45". I explicitly install the following ports in the following order, to build a foundation for a few packages along with ncarg/ncl: wget +ssl[[BR]] db46[[BR]] gcc45[[BR]] python27 (followed by the python_select command)[[BR]] ghostscript[[BR]] gv +letter[[BR]] ImageMagick +q16[[BR]] gsl +gcc45[[BR]] hdf5-18 +cxx +gcc45 (have also tried this with "hdf5-18 +cxx +gcc45 +szip")[[BR]] hdf4 +gcc45[[BR]] netcdf +dap +netcdf4 +hdf4[[BR]] netcdf-fortran +gcc45[[BR]] nco[[BR]] ncarg +gcc45 in building the dependencies for ncarg, I now repeatedly get the "configure failure" for hdfeos5. I've tried "sudo port clean hdfeos5", then "sudo port install hdfeos5" and also "sudo port install hdfeos5 +szip". all attempts fail currently. Installation of this same group of packages worked recently, I believe it was last week, on my Lion machine. My list of outdated ports on the Lion machine show upgrades available for: automake 1.12.2_0 < 1.12.4_0 [[BR]] bison 2.6_0 < 2.6.2_0 [[BR]] cairo 1.12.2_0 < 1.12.2_1 [[BR]] cctools 822_2 < 829_1 [[BR]] cctools-headers 822_2 < 829_0 [[BR]] curl 7.26.0_0 < 7.27.0_1 [[BR]] curl-ca-bundle 7.26.0_1 < 7.27.0_0 [[BR]] fftw-3 3.3.2_0 < 3.3.2_1 [[BR]] gcc45 4.5.4_1 < 4.5.4_6 [[BR]] gcc_select 0.1_6 < 0.1_7 [[BR]] gdal 1.9.0_3 < 1.9.1_1 [[BR]] ghostscript 9.05_2 < 9.06_1 [[BR]] gmp 5.0.4_1 < 5.0.5_0 [[BR]] gsl 1.15_1 < 1.15_2 [[BR]] hdf4 4.2.7_0 < 4.2.7_1 [[BR]] hdf5-18 1.8.9_0 < 1.8.9_2 [[BR]] ImageMagick 6.7.8-3_0 < 6.7.9-0_2[[BR]] lcms2 2.3_0 < 2.4_0 [[BR]] ld64 128.2_4 < 133.3_3 [[BR]] lftp 4.3.5_0 < 4.3.8_0 [[BR]] libmpc 1.0_0 < 1.0.1_0 [[BR]] libpng 1.4.12_0 < 1.5.12_0 [[BR]] libtool 2.4.2_2 < 2.4.2_3 [[BR]] libxml2 2.7.8_0 < 2.8.0_0 [[BR]] llvm-3.1 3.1_1 < 3.1_3 [[BR]] mesa 8.0.4_0 < 8.0.4_1 [[BR]] ncarg 6.0.0_5 < 6.0.0_10 [[BR]] nco 4.2.0_0 < 4.2.1_1 [[BR]] netcdf-fortran 4.2_4 < 4.2_5 [[BR]] netpbm 10.59.00_0 < 10.59.00_1 [[BR]] pkgconfig 0.27_0 < 0.27.1_1 [[BR]] sqlite3 3.7.13_0 < 3.7.14_1 [[BR]] tcl 8.5.11_0 < 8.5.12_1 [[BR]] webp 0.1.3_0 < 0.2.0_1[[BR]] wget 1.13.4_0 < 1.14_0[[BR]] wgrib2 1.9.6a_0 < 1.9.6a_3 The only change I've made in the package requests since the Lion install last week (or so) is that hdf5-18 did not have "+cxx" as a default then. At that time, hdfeos5 @1.13r2 configured, built and installed fine. please check, and thanks for all your work with these packages! -- Ticket URL: <https://trac.macports.org/ticket/36415> MacPorts <http://www.macports.org/> Ports system for Mac OS
#36415: hdfeos5 @1.13r2 Configure failure ----------------------------+----------------------- Reporter: uthyr@… | Owner: takeshi@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.1.2 Resolution: | Keywords: Port: ncarg hdfeos5 | ----------------------------+----------------------- Changes (by ryandesign@…): * owner: macports-tickets@… => takeshi@… Comment: Please attach the main.log from the failed installation. -- Ticket URL: <https://trac.macports.org/ticket/36415#comment:1> MacPorts <http://www.macports.org/> Ports system for Mac OS
#36415: hdfeos5 @1.13r2 Configure failure ----------------------------+----------------------- Reporter: uthyr@… | Owner: takeshi@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.1.2 Resolution: | Keywords: Port: ncarg hdfeos5 | ----------------------------+----------------------- Comment (by uthyr@…): Replying to [comment:1 ryandesign@…]:
Please attach the main.log from the failed installation. now attached - thanks!
-- Ticket URL: <https://trac.macports.org/ticket/36415#comment:2> MacPorts <http://www.macports.org/> Ports system for Mac OS
#36415: hdfeos5 @1.13r2 Configure failure ----------------------------+----------------------- Reporter: uthyr@… | Owner: takeshi@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.1.2 Resolution: | Keywords: Port: ncarg hdfeos5 | ----------------------------+----------------------- Comment (by gnwiii@…): The relevant section of hdfeos5.main.log is: {{{ 455 :info:configure checking for gcc... /opt/local/bin/h5cc 456 :info:configure checking for C compiler default output file name... 457 :info:configure configure: error: C compiler cannot create executables 458 :info:configure See `config.log' for more details. }}} You might want to look at h5cc to see why it is failing. -- Ticket URL: <https://trac.macports.org/ticket/36415#comment:3> MacPorts <http://www.macports.org/> Ports system for Mac OS
#36415: hdfeos5 @1.13r2 Configure failure ----------------------------+----------------------- Reporter: uthyr@… | Owner: takeshi@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.1.2 Resolution: | Keywords: Port: ncarg hdfeos5 | ----------------------------+----------------------- Comment (by takeshi@…): Could you upload config.log of hdfeos5? -- Ticket URL: <https://trac.macports.org/ticket/36415#comment:4> MacPorts <http://www.macports.org/> Ports system for Mac OS
#36415: hdfeos5 @1.13r2 Configure failure ----------------------------+----------------------- Reporter: uthyr@… | Owner: takeshi@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.1.2 Resolution: | Keywords: Port: ncarg hdfeos5 | ----------------------------+----------------------- Comment (by uthyr@…): Replying to [comment:4 takeshi@…]:
Could you upload config.log of hdfeos5?
sorry for the delay. hdfeos5 config.log now uploaded. -- Ticket URL: <https://trac.macports.org/ticket/36415#comment:5> MacPorts <http://www.macports.org/> Ports system for Mac OS
#36415: hdfeos5 @1.13r2 Configure failure ----------------------------+----------------------- Reporter: uthyr@… | Owner: takeshi@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.1.2 Resolution: | Keywords: Port: ncarg hdfeos5 | ----------------------------+----------------------- Comment (by uthyr@…): I just looked at the hdfeos web page ([http://hdfeos.org/software/hdfeos.php]), and found a mention of indicating that hdfeos5 requires use of the hdf5 version 1.6 API. The hdf5-18 port is installed, and I was wondering if the CFLAGS definition for "H5_USE_16_API" was being used for hdfeos5... here is the potentially relevant text from the hdfeos web page: "The first step is to execute configure script included in the package. One option is required as a parameter to configure: CC. '''If HDF5 is 1.8 or higher, one needs to define H5_USE_16_API preprocessor macro as CFLAGS. This is because HDF-EOS5 uses HDF5 1.6 API and this is not compatible with HDF5 1.8 API.''' If HDF5 was built with SZIP, another option --with-szlib is required. The following is an example when HDF5 1.8 is built with SZIP." and the sample code block immediately following on the web page is: {{{ $ ./configure \ CC=<hdf5_path>/bin/h5cc \ CFLAGS=-DH5_USE_16_API \ --with-szlib=<szip_path> }}} -- Ticket URL: <https://trac.macports.org/ticket/36415#comment:6> MacPorts <http://www.macports.org/> Ports system for Mac OS
#36415: hdfeos5 @1.13r2 Configure failure ----------------------------+----------------------- Reporter: uthyr@… | Owner: takeshi@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.1.2 Resolution: | Keywords: Port: ncarg hdfeos5 | ----------------------------+----------------------- Comment (by takeshi@…): We have configure.cflags-append -DH5_USE_16_API in Portfile. I looked at config.log. h5cc calls MacPorts' gcc-mp-4.5. Can your gcc- mp-4.5 or h5cc compile hello, world? I have XServe running Snow Leopard Server at work it uses the default gcc-4.2 h5cc is just a shell script. {{{ CCBASE="/usr/bin/gcc-4.2" CLINKERBASE="/usr/bin/gcc-4.2" }}} -- Ticket URL: <https://trac.macports.org/ticket/36415#comment:7> MacPorts <http://www.macports.org/> Ports system for Mac OS
#36415: hdfeos5 @1.13r2 Configure failure ----------------------------+----------------------- Reporter: uthyr@… | Owner: takeshi@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.1.2 Resolution: | Keywords: Port: ncarg hdfeos5 | ----------------------------+----------------------- Comment (by jmr@…): The problem seems to be that it calls h5cc with -arch x86_64, when h5cc is backed by a non-apple gcc. -- Ticket URL: <https://trac.macports.org/ticket/36415#comment:8> MacPorts <http://www.macports.org/> Ports system for Mac OS
#36415: hdfeos5 @1.13r2 Configure failure ----------------------------+----------------------- Reporter: uthyr@… | Owner: takeshi@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.1.2 Resolution: | Keywords: Port: ncarg hdfeos5 | ----------------------------+----------------------- Comment (by uthyr@…): I had this same issue on one of our Mac Pro computers, running 10.6.8, with Xcode 3.6.2 installed. same problem, with h5cc calling /opt/local/bin/gcc-mp-4.5, apparently unable to compile executables. To me this is odd, as 2 of my 8 Mac Pros went through the process of "selfupdate", and "upgrade outdated" without any hitches or changes to package files, while 1 of the 8 exhibited the problem I've found on one of my Xserve computers. on the problematic Mac Pro, I modified the lines in /opt/local/bin/h5cc to: {{{ CCBASE="/usr/bin/gcc-4.2" CLINKERBASE="/usr/bin/gcc-4.2" }}} This did not solve the issue. I then modified them further, to: {{{ CCBASE="/Developer/usr/bin/gcc-4.2" CLINKERBASE="/Developer/usr/bin/gcc-4.2" }}} and then the hdfeos5 package compiled and installed completely! MacPorts found 4 broken ports (wgrib2, ImageMagick, vis5d, and ncarg), which it then repaired. There was an issue with the ncarg install, which was resolved after running the "port clean ncarg" command. However, when I applied a similar procedure on my Xserve, trying both the paths for gcc-4.2 (with and without the /Developer prefix), I had no success. I will be proceeding though the other 5 Mac Pros, and gathering more statistics on my issues with this port. thanks, Roy -- Ticket URL: <https://trac.macports.org/ticket/36415#comment:9> MacPorts <http://www.macports.org/> Ports system for Mac OS
#36415: hdfeos5 @1.13r2 Configure failure ----------------------------+----------------------- Reporter: uthyr@… | Owner: takeshi@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.1.2 Resolution: | Keywords: Port: ncarg hdfeos5 | ----------------------------+----------------------- Comment (by uthyr@…): Replying to [comment:9 uthyr@…]:
However, when I applied a similar procedure on my Xserve, trying both the paths for gcc-4.2 (with and without the /Developer prefix), I had no success.
aha - the problem now on the Xserve was that I hadn't specified that hdfeos5 be built with szip, and it was specified for hdf5! once I specified {{{ sudo port install hdfeos5 +szip }}} the hdfeos5 package built completely! so, it appears the solution for my issues were that I needed to use the Developer gcc-4.2 compiler to compile hdfeos5 on some of my 10.6.8 computers. I believe this ticket may be closed, as I think I can get the rest of my Mac Pros and Xserve updated now. thank you all for your assistance, Roy -- Ticket URL: <https://trac.macports.org/ticket/36415#comment:10> MacPorts <http://www.macports.org/> Ports system for Mac OS
#36415: hdfeos5 @1.13r2 Configure failure ----------------------------+----------------------- Reporter: uthyr@… | Owner: takeshi@… Type: defect | Status: closed Priority: Normal | Milestone: Component: ports | Version: 2.1.2 Resolution: fixed | Keywords: Port: ncarg hdfeos5 | ----------------------------+----------------------- Changes (by takeshi@…): * status: new => closed * resolution: => fixed Comment: I was able to reproduce the problem. I fixed it by unsetting archflags. Committed in r101449. -- Ticket URL: <https://trac.macports.org/ticket/36415#comment:11> MacPorts <http://www.macports.org/> Ports system for Mac OS
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