Opened 10 years ago

Closed 10 years ago

#41915 closed defect (fixed)

gibbslda @0.2 build failed

Reported by: cihanb@… Owned by: humem (humem)
Priority: Normal Milestone:
Component: ports Version: 2.2.1
Keywords: Cc:
Port: gibbslda

Description (last modified by mf2k (Frank Schima))

Trying to build gibbslda fails with the following message. 

Error: org.macports.build for port gibbslda returned: command execution failed
Please see the log file for port gibbslda for details:
    /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_gibbslda/gibbslda/main.log

The gibbslda/main.log file indicates the following error: 

:info:build 12 errors generated.
:info:build make[1]: *** [utils.o] Error 1
:info:build make[1]: *** Waiting for unfinished jobs....
:info:build 1 warning generated.
:info:build 1 warning generated.
:info:build make[1]: Leaving directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_gibbslda/gibbslda/work/GibbsLDA++-0.2/src'
:info:build make: *** [all] Error 2
:info:build make: Leaving directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_gibbslda/gibbslda/work/GibbsLDA++-0.2'
:info:build Command failed:  cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_gibbslda/gibbslda/work/GibbsLDA++-0.2" && /usr/bin/make -j4 -w all CC="/usr/bin/clang++ -Os -arch x86_64" 
:info:build Exit code: 2
:error:build org.macports.build for port gibbslda returned: command execution failed
:debug:build Error code: CHILDSTATUS 2320 2
:debug:build Backtrace: command execution failed
    while executing
"system -nice 0 $fullcmdstring"
    ("eval" body line 1)
    invoked from within
"eval system $notty $nice \$fullcmdstring"
    invoked from within
"command_exec build"
    (procedure "portbuild::build_main" line 8)
    invoked from within
"$procedure $targetname"
:info:build Warning: targets not executed for gibbslda: org.macports.activate org.macports.build org.macports.destroot org.macports.install
:notice:build Please see the log file for port gibbslda for details:
    /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_gibbslda/gibbslda/main.log

Change History (6)

comment:1 Changed 10 years ago by cihanb@…

When I tried to download and compile this package myself, I ran into a similar issue:

utils.cpp:69:14: error: use of undeclared identifier 'atof'; did you mean 'stof'?

alpha = atof(argv[++i]);

~ stof

I don't know what's causing this. This seems to be related to a VNC bug that was just resolved.

comment:2 Changed 10 years ago by cihanb@…

When I added the following line to source code src/utils.cpp

#include <cstdlib>

I was able to compile the package on my own - without using macports.

Thanks.

comment:3 Changed 10 years ago by mf2k (Frank Schima)

Description: modified (diff)

comment:4 Changed 10 years ago by mf2k (Frank Schima)

Owner: changed from macports-tickets@… to hum@…
Port: gibbslda added

In the future, please use WikiFormatting, fill in the Port field and Cc the port maintainers (port info --maintainers gibbslda). Attach the complete main.log file after cleaning the port and trying again.

comment:5 Changed 10 years ago by cihanb@…

I don't know how to edit the Port field and the CC fields. When I click 'modify', it sends me to the comment box.

I already compiled this by editing the source code for my own purposes. I'm just trying to help the community.

I'm also unfamiliar with WikiFormatting and unwilling to sift through tedious documentation for a simple bug report.

Here I'm copying and pasting the entire log after cleaning the port. Hopefully the formatting will be ok. 

version:1
:debug:clean gibbslda has no conflicts
:debug:main Executing org.macports.main (gibbslda)
:debug:main changing euid/egid - current euid: 0 - current egid: 0
:debug:main egid changed to: 501
:debug:main euid changed to: 502
:debug:archivefetch archivefetch phase started at Fri Dec 27 10:48:38 EET 2013
:msg:archivefetch --->  Fetching archive for gibbslda
:debug:archivefetch Executing org.macports.archivefetch (gibbslda)
:debug:archivefetch euid/egid changed to: 0/0
:debug:archivefetch chowned /opt/local/var/macports/incoming to macports
:debug:archivefetch euid/egid changed to: 502/501
:info:archivefetch --->  gibbslda-0.2_0.darwin_13.x86_64.tbz2 doesn't seem to exist in /opt/local/var/macports/incoming/verified
:msg:archivefetch --->  Attempting to fetch gibbslda-0.2_0.darwin_13.x86_64.tbz2 from http://mse.uk.packages.macports.org/sites/packages.macports.org/gibbslda
:debug:archivefetch Fetching archive failed:: The requested URL returned error: 404 Not Found
:msg:archivefetch --->  Attempting to fetch gibbslda-0.2_0.darwin_13.x86_64.tbz2 from http://lil.fr.packages.macports.org/gibbslda
:debug:archivefetch Fetching archive failed:: The requested URL returned error: 404 Not Found
:msg:archivefetch --->  Attempting to fetch gibbslda-0.2_0.darwin_13.x86_64.tbz2 from http://packages.macports.org/gibbslda
:debug:archivefetch Fetching archive failed:: The requested URL returned error: 404 Not Found
:debug:archivefetch Privilege de-escalation not attempted as not running as root.
:debug:fetch fetch phase started at Fri Dec 27 10:48:43 EET 2013
:notice:fetch --->  Fetching distfiles for gibbslda
:debug:fetch Executing org.macports.fetch (gibbslda)
:debug:fetch Privilege de-escalation not attempted as not running as root.
:debug:checksum checksum phase started at Fri Dec 27 10:48:43 EET 2013
:notice:checksum --->  Verifying checksums for gibbslda
:debug:checksum Executing org.macports.checksum (gibbslda)
:info:checksum --->  Checksumming GibbsLDA++-0.2.tar.gz
:debug:checksum Correct (rmd160) checksum for GibbsLDA++-0.2.tar.gz
:debug:checksum Correct (sha256) checksum for GibbsLDA++-0.2.tar.gz
:debug:checksum Privilege de-escalation not attempted as not running as root.
:debug:extract extract phase started at Fri Dec 27 10:48:43 EET 2013
:notice:extract --->  Extracting gibbslda
:debug:extract Executing org.macports.extract (gibbslda)
:info:extract --->  Extracting GibbsLDA++-0.2.tar.gz
:debug:extract setting option extract.args to '/opt/local/var/macports/distfiles/gibbslda/GibbsLDA++-0.2.tar.gz'
:debug:extract Environment: CPATH='/opt/local/include' CC_PRINT_OPTIONS_FILE='/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_gibbslda/gibbslda/work/.CC_PRINT_OPTIONS' LIBRARY_PATH='/opt/local/lib' CC_PRINT_OPTIONS='YES' MACOSX_DEPLOYMENT_TARGET='10.9'
:debug:extract Assembled command: 'cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_gibbslda/gibbslda/work" && /usr/bin/gzip -dc '/opt/local/var/macports/distfiles/gibbslda/GibbsLDA++-0.2.tar.gz' | /usr/bin/tar -xf -'
:debug:extract Executing command line:  cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_gibbslda/gibbslda/work" && /usr/bin/gzip -dc '/opt/local/var/macports/distfiles/gibbslda/GibbsLDA++-0.2.tar.gz' | /usr/bin/tar -xf - 
:debug:extract euid/egid changed to: 0/0
:debug:extract chowned /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_gibbslda/gibbslda/work to macports
:debug:extract euid/egid changed to: 502/501
:debug:extract Executing proc-post-org.macports.extract-extract-0
:info:extract make -C src/ -f Makefile clean
:info:extract rm strtokenizer.o dataset.o utils.o model.o 
:info:extract rm lda
:debug:extract Privilege de-escalation not attempted as not running as root.
:debug:patch patch phase started at Fri Dec 27 10:48:44 EET 2013
:debug:patch Executing org.macports.patch (gibbslda)
:debug:patch Privilege de-escalation not attempted as not running as root.
:debug:configure configure phase started at Fri Dec 27 10:48:44 EET 2013
:notice:configure --->  Configuring gibbslda
:debug:configure Using compiler 'Xcode Clang'
:debug:configure Executing org.macports.configure (gibbslda)
:debug:configure Privilege de-escalation not attempted as not running as root.
:debug:build build phase started at Fri Dec 27 10:48:44 EET 2013
:notice:build --->  Building gibbslda
:debug:build Executing org.macports.build (gibbslda)
:debug:build Environment: CPATH='/opt/local/include' CC_PRINT_OPTIONS_FILE='/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_gibbslda/gibbslda/work/.CC_PRINT_OPTIONS' LIBRARY_PATH='/opt/local/lib' CC_PRINT_OPTIONS='YES' MACOSX_DEPLOYMENT_TARGET='10.9'
:debug:build Assembled command: 'cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_gibbslda/gibbslda/work/GibbsLDA++-0.2" && /usr/bin/make -j4 -w all CC="/usr/bin/clang++ -Os -arch x86_64"'
:debug:build Executing command line:  cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_gibbslda/gibbslda/work/GibbsLDA++-0.2" && /usr/bin/make -j4 -w all CC="/usr/bin/clang++ -Os -arch x86_64" 
:info:build make: Entering directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_gibbslda/gibbslda/work/GibbsLDA++-0.2'
:info:build make -C src/ -f Makefile all
:info:build make[1]: Entering directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_gibbslda/gibbslda/work/GibbsLDA++-0.2/src'
:info:build /usr/bin/clang++ -Os -arch x86_64 -c -o strtokenizer.o strtokenizer.cpp
:info:build /usr/bin/clang++ -Os -arch x86_64 -c -o dataset.o dataset.cpp
:info:build /usr/bin/clang++ -Os -arch x86_64 -c -o utils.o utils.cpp
:info:build /usr/bin/clang++ -Os -arch x86_64 -c -o model.o model.cpp
:info:build dataset.cppmodel.cpp:40:27:240:: warning: 49: warning: format specifies type 'int' but the argument has type 'const_pointer' (aka 'const char *') [-Wformat]
:info:build format specifies type 'int' but the argument has type 'size_type' (aka 'unsigned long') [-Wformat]
:info:build     fprintf(fout, "%d\n", pword2id->size());
:info:build                    ~~     ^~~~~~~~~~~~~~~~
:info:build                    %lu
:info:build         printf("Cannot open file %d to load model!\n", filename.c_str());
:info:build                                  ~~                    ^~~~~~~~~~~~~~~~
:info:build                                  %s
:info:build utils.cpp:69:14: error: use of undeclared identifier 'atof'; did you mean 'stof'?
:info:build             alpha = atof(argv[++i]);        
:info:build                     ^~~~
:info:build                     stof
:info:build /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/string:3995:13: note: 'stof' declared here
:info:build float       stof (const string& __str, size_t* __idx = 0);
:info:build             ^
:info:build utils.cpp:72:13: error: use of undeclared identifier 'atof'; did you mean 'stof'?
:info:build             beta = atof(argv[++i]);         
:info:build                    ^~~~
:info:build                    stof
:info:build /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/string:3995:13: note: 'stof' declared here
:info:build float       stof (const string& __str, size_t* __idx = 0);
:info:build             ^
:info:build utils.cpp:75:10: error: use of undeclared identifier 'atoi'; did you mean 'stoi'?
:info:build             K = atoi(argv[++i]);            
:info:build                 ^~~~
:info:build                 stoi
:info:build /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/string:3989:20: note: 'stoi' declared here
:info:build int                stoi  (const string& __str, size_t* __idx = 0, int __base = 10);
:info:build                    ^
:info:build utils.cpp:78:15: error: use of undeclared identifier 'atoi'; did you mean 'stoi'?
:info:build             niters = atoi(argv[++i]);       
:info:build                      ^~~~
:info:build                      stoi
:info:build /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/string:3989:20: note: 'stoi' declared here
:info:build int                stoi  (const string& __str, size_t* __idx = 0, int __base = 10);
:info:build                    ^
:info:build utils.cpp:81:17: error: use of undeclared identifier 'atoi'; did you mean 'stoi'?
:info:build             savestep = atoi(argv[++i]);
:info:build                        ^~~~
:info:build                        stoi
:info:build /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/string:3989:20: note: 'stoi' declared here
:info:build int                stoi  (const string& __str, size_t* __idx = 0, int __base = 10);
:info:build                    ^
:info:build utils.cpp:84:15: error: use of undeclared identifier 'atoi'; did you mean 'stoi'?
:info:build             twords = atoi(argv[++i]);
:info:build                      ^~~~
:info:build                      stoi
:info:build /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/string:3989:20: note: 'stoi' declared here
:info:build int                stoi  (const string& __str, size_t* __idx = 0, int __base = 10);
:info:build                    ^
:info:build utils.cpp:270:22: error: use of undeclared identifier 'atof'; did you mean 'stof'?
:info:build             pmodel->alpha = atof(optval.c_str());
:info:build                             ^~~~
:info:build                             stof
:info:build /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/string:3995:13: note: 'stof' declared here
:info:build float       stof (const string& __str, size_t* __idx = 0);
:info:build             ^
:info:build utils.cpp:273:21: error: use of undeclared identifier 'atof'; did you mean 'stof'?
:info:build             pmodel->beta = atof(optval.c_str());
:info:build                            ^~~~
:info:build                            stof
:info:build /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/string:3995:13: note: 'stof' declared here
:info:build float       stof (const string& __str, size_t* __idx = 0);
:info:build             ^
:info:build utils.cpp:276:18: error: use of undeclared identifier 'atoi'; did you mean 'stoi'?
:info:build             pmodel->K = atoi(optval.c_str());
:info:build                         ^~~~
:info:build                         stoi
:info:build /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/string:3989:20: note: 'stoi' declared here
:info:build int                stoi  (const string& __str, size_t* __idx = 0, int __base = 10);
:info:build                    ^
:info:build utils.cpp:279:18: error: use of undeclared identifier 'atoi'; did you mean 'stoi'?
:info:build             pmodel->M = atoi(optval.c_str());
:info:build                         ^~~~
:info:build                         stoi
:info:build /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/string:3989:20: note: 'stoi' declared here
:info:build int                stoi  (const string& __str, size_t* __idx = 0, int __base = 10);
:info:build                    ^
:info:build utils.cpp:282:18: error: use of undeclared identifier 'atoi'; did you mean 'stoi'?
:info:build             pmodel->V = atoi(optval.c_str());
:info:build                         ^~~~
:info:build                         stoi
:info:build /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/string:3989:20: note: 'stoi' declared here
:info:build int                stoi  (const string& __str, size_t* __idx = 0, int __base = 10);
:info:build                    ^
:info:build utils.cpp:285:22: error: use of undeclared identifier 'atoi'; did you mean 'stoi'?
:info:build             pmodel->liter = atoi(optval.c_str());
:info:build                             ^~~~
:info:build                             stoi
:info:build /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/string:3989:20: note: 'stoi' declared here
:info:build int                stoi  (const string& __str, size_t* __idx = 0, int __base = 10);
:info:build                    ^
:info:build 12 errors generated.
:info:build make[1]: *** [utils.o] Error 1
:info:build make[1]: *** Waiting for unfinished jobs....
:info:build 1 warning generated.
:info:build 1 warning generated.
:info:build make[1]: Leaving directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_gibbslda/gibbslda/work/GibbsLDA++-0.2/src'
:info:build make: *** [all] Error 2
:info:build make: Leaving directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_gibbslda/gibbslda/work/GibbsLDA++-0.2'
:info:build Command failed:  cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_gibbslda/gibbslda/work/GibbsLDA++-0.2" && /usr/bin/make -j4 -w all CC="/usr/bin/clang++ -Os -arch x86_64" 
:info:build Exit code: 2
:error:build org.macports.build for port gibbslda returned: command execution failed
:debug:build Error code: CHILDSTATUS 15706 2
:debug:build Backtrace: command execution failed
    while executing
"system -nice 0 $fullcmdstring"
    ("eval" body line 1)
    invoked from within
"eval system $notty $nice \$fullcmdstring"
    invoked from within
"command_exec build"
    (procedure "portbuild::build_main" line 8)
    invoked from within
"$procedure $targetname"
:info:build Warning: targets not executed for gibbslda: org.macports.activate org.macports.build org.macports.destroot org.macports.install
:notice:build Please see the log file for port gibbslda for details:
    /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_gibbslda/gibbslda/main.log

comment:6 Changed 10 years ago by humem (humem)

Resolution: → fixed
Status: new → closed

Thank you very much for your report. I made a patch and committed in r115213.

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