Bug 741626 (packmol)
Summary: | Review Request: packmol - Packing optimization for molecular dynamics simulations | ||
---|---|---|---|
Product: | [Fedora] Fedora | Reporter: | Susi Lehtola <susi.lehtola> |
Component: | Package Review | Assignee: | Martin Gieseking <martin.gieseking> |
Status: | CLOSED ERRATA | QA Contact: | Fedora Extras Quality Assurance <extras-qa> |
Severity: | medium | Docs Contact: | |
Priority: | medium | ||
Version: | rawhide | CC: | alex, marbolangos, martin.gieseking, notting, package-review, pingou, tomspur |
Target Milestone: | --- | Flags: | martin.gieseking:
fedora-review+
gwync: fedora-cvs+ |
Target Release: | --- | ||
Hardware: | All | ||
OS: | Linux | ||
Whiteboard: | |||
Fixed In Version: | packmol-1.1.2.023-1.el6 | Doc Type: | Bug Fix |
Doc Text: | Story Points: | --- | |
Clone Of: | Environment: | ||
Last Closed: | 2012-01-31 21:56:47 UTC | Type: | --- |
Regression: | --- | Mount Type: | --- |
Documentation: | --- | CRM: | |
Verified Versions: | Category: | --- | |
oVirt Team: | --- | RHEL 7.3 requirements from Atomic Host: | |
Cloudforms Team: | --- | Target Upstream Version: | |
Embargoed: |
Description
Susi Lehtola
2011-09-27 13:13:09 UTC
*** Bug 531605 has been marked as a duplicate of this bug. *** - The way you build it breaks the debuginfo package: extracting debug info from /home/tom/rpmbuild/BUILDROOT/packmol-1.1.1.258-1.fc15.x86_64/usr/bin/packmol cpio: packmol/ser/gencan.i: Cannot stat: No such file or directory cpio: packmol/ser/molpa.i: Cannot stat: No such file or directory cpio: packmol/ser/sizes.i: Cannot stat: No such file or directory The files are in packmol/*.i directly. Is there a CMake possibility to put them into the ser directory instead? Running "mv *.i ser/" after building works, but looks rather hackish... - Why are GPLv3 headers -> GPL+? I'd expect GPLv3+ (or GPLv3only) here: (minimal) version = version in COPYING. It would be best to ask upstream to clarify it. (In reply to comment #2) > Is there a CMake possibility to put them into the ser directory instead? > Running "mv *.i ser/" after building works, but looks rather hackish... Maybe. But these are include files... > - Why are GPLv3 headers -> GPL+? > I'd expect GPLv3+ (or GPLv3only) here: > (minimal) version = version in COPYING. > > It would be best to ask upstream to clarify it. .. where do you see gplv3 headers? (In reply to comment #3) > (In reply to comment #2) > > Is there a CMake possibility to put them into the ser directory instead? > > Running "mv *.i ser/" after building works, but looks rather hackish... > > Maybe. But these are include files... How about a complete cp then? e.g. mkdir ser; cd ser cp ../* . %cmake... etc cd .. Do you intend to build both serial and parallel versions? How do you want to name them? par/ppackmol would only be a script that calls packmol with OMP_THREADS With copying around anything from above, it would be possible to install par/packmol as ppackmol and get a backtrace of the segfault with abrt. > > - Why are GPLv3 headers -> GPL+? > > I'd expect GPLv3+ (or GPLv3only) here: > > (minimal) version = version in COPYING. > > > > It would be best to ask upstream to clarify it. > > .. where do you see gplv3 headers? GPL+ for me is any GPL version, that exists and that will come in the future. When adding a GPLv3 COPYING, I either want to have the program licensed under GPLv3 or GPLv3+, but not with GPLv2. But I'm not a lawyer, so asking upstream to clarify it is the best way to be sure. (In reply to comment #4) > (In reply to comment #3) > > (In reply to comment #2) > > > Is there a CMake possibility to put them into the ser directory instead? > > > Running "mv *.i ser/" after building works, but looks rather hackish... > > > > Maybe. But these are include files... > > How about a complete cp then? > e.g. > mkdir ser; cd ser > cp ../* . > %cmake... etc > cd .. I'll copy the inc files. My reason for writing the CMake scripts was to get out-of-tree builds to work, and also make SMP make work correctly. > Do you intend to build both serial and parallel versions? > How do you want to name them? > par/ppackmol would only be a script that calls packmol with OMP_THREADS > > With copying around anything from above, it would be possible to install > par/packmol as ppackmol and get a backtrace of the segfault with abrt. I might in the future. Packmol allocates everything statically (gah!), since it has been written in Fortran 77 (double gah! - Fortran 90 is a *lot* better in every aspect). The segfault is due to the stack memory limit being broken. I don't see a need for a wrapper script. > > > - Why are GPLv3 headers -> GPL+? > > > I'd expect GPLv3+ (or GPLv3only) here: > > > (minimal) version = version in COPYING. > > > > > > It would be best to ask upstream to clarify it. > > > > .. where do you see gplv3 headers? > > GPL+ for me is any GPL version, that exists and that will come in the future. > > When adding a GPLv3 COPYING, I either want to have the program licensed under > GPLv3 or GPLv3+, but not with GPLv2. But I'm not a lawyer, so asking upstream > to clarify it is the best way to be sure. Please read https://fedoraproject.org/wiki/Licensing:FAQ#How_do_I_figure_out_what_version_of_the_GPL.2FLGPL_my_package_is_under.3F I have asked the author to add license boilerplates already a couple of weeks ago, and to port the code to allocate the memory dynamically. I take this one. The package looks good to me -- I just recommend to explicitly remove cenmass.o in %prep in order to prevent linking this object file. Also, upstream has released a new version of packmol. Maybe you'd like to update the package. The license headers are still missing but there's a file LICENSE present now which refers to GPLv2 only while COPYING still contains the GPLv3 license text. Upstream should definitely fix this. The license tag GPL+ is nonetheless correct, though. $ rpmlint *.rpm packmol.src: W: spelling-error %description -l en_US lamellar -> Carmella, Mallarme, Marcella packmol.src:58: W: macro-in-comment %{buildroot} packmol.src:58: W: macro-in-comment %{_bindir} packmol.src:68: W: macro-in-comment %{_bindir} packmol.src: W: invalid-url Source0: http://packmol.googlecode.com/files/packmol-1.1.1.258.tar.gz HTTP Error 404: Not Found packmol.x86_64: W: spelling-error %description -l en_US lamellar -> Carmella, Mallarme, Marcella packmol.x86_64: W: no-manual-page-for-binary packmol packmol.x86_64: W: no-manual-page-for-binary packmol_solvate 3 packages and 0 specfiles checked; 0 errors, 8 warnings. The above warnings can safely be ignored: - macros in comments are expected - invalid url warning is false positive - spelling errors are false positive - no manual pages available for the binaries --------------------------------- key: [+] OK [.] OK, not applicable [X] needs work --------------------------------- [+] MUST: The package must be named according to the Package Naming Guidelines. [+] MUST: The spec file name must match the base package %{name}. [+] MUST: The package must meet the Packaging Guidelines. [+] MUST: The package must be licensed with a Fedora approved license. - GPLv3 license text present - no copyright information in sources => GPL+ [+] MUST: The License field in the package spec file must match the actual license. [+] MUST: The file containing the text of the license(s) for the package must be included in %doc. [+] MUST: The spec file must be written in American English. [+] MUST: The spec file for the package MUST be legible. [+] MUST: The sources used to build the package must match the upstream source. $ md5sum packmol-1.1.1.258.tar.gz* d1b12036b94f48c92595e9c4d3180009 packmol-1.1.1.258.tar.gz d1b12036b94f48c92595e9c4d3180009 packmol-1.1.1.258.tar.gz.upstream [+] MUST: The package MUST successfully compile and build into binary rpms on at least one primary architecture. [.] MUST: If the package does not successfully compile, build or work on an architecture, ... [+] MUST: All build dependencies must be listed in BuildRequires. [+] MUST: When compiling C, C++, or Fortran files, %{optflags} must be applied. [.] MUST: The spec file MUST handle locales properly. [.] MUST: Packages storing shared library files (not just symlinks) must call ldconfig in %post and %postun. [+] MUST: Packages must NOT bundle copies of system libraries. [.] MUST: If the package is designed to be relocatable, ... [+] MUST: A package must own all directories that it creates. [+] MUST: A Fedora package must not list a file more than once in %files. [+] MUST: Permissions on files must be set properly. [+] MUST: Each package must consistently use macros. [+] MUST: The package must contain code, or permissable content. [.] MUST: Large documentation files must go in a -doc subpackage. [+] MUST: Files in %doc must not affect the runtime of the application. [.] MUST: Header files must be in a -devel package. [.] MUST: Static libraries must be in a -static package. [.] MUST: If a package contains library files with a suffix (e.g. libfoo.so.1.1), then library files that end in .so (without suffix) must go in a -devel package. [.] MUST: devel packages must require the base package using a fully versioned dependency. [+] MUST: Packages must NOT contain any .la libtool archives. [.] MUST: Packages containing GUI applications must include a %{name}.desktop file, and that file must be properly installed with desktop-file-install in the %install section. If you feel that your packaged GUI application does not need a .desktop file, you must put a comment in the spec file with your explanation. [+] MUST: Packages must not own files or directories already owned by other packages. [+] MUST: All filenames in rpm packages must be valid UTF-8. EPEL <= 5 only: [+] MUST: The spec file must contain a valid BuildRoot field. [+] MUST: At the beginning of %install, each package MUST run rm -rf %{buildroot}. [+] MUST: Each package must have a %clean section, which contains rm -rf %{buildroot}. [.] MUST: Packages containing pkgconfig(.pc) files must 'Requires: pkgconfig' [.] SHOULD: If the source package does not include license text(s) as a separate file from upstream, the packager SHOULD query upstream to include it. [+] SHOULD: Timestamps of files should be preserved. [+] SHOULD: The reviewer should test that the package builds in mock. [+] SHOULD: The reviewer should test that the package functions as described. [.] SHOULD: If scriptlets are used, those scriptlets must be sane. [.] SHOULD: Usually, subpackages other than devel should require the base package using a fully versioned dependency. [.] SHOULD: pkgconfig(.pc) files should be placed in a -devel pkg. [.] SHOULD: If the package has file dependencies outside of /etc, /bin, /sbin, /usr/bin, or /usr/sbin consider requiring the package which provides the file instead of the file itself. [X] SHOULD: Your package should contain man pages for binaries/scripts. - maybe you can ask upstream to think about adding manpages for the executables (In reply to comment #6) > I take this one. The package looks good to me -- I just recommend to explicitly > remove cenmass.o in %prep in order to prevent linking this object file. Done. > Also, upstream has released a new version of packmol. Maybe you'd like to > update the package. The license headers are still missing but there's a file > LICENSE present now which refers to GPLv2 only while COPYING still contains the > GPLv3 license text. Upstream should definitely fix this. The license tag GPL+ > is nonetheless correct, though. Done; but the correct license tag is now GPLv2. http://theory.physics.helsinki.fi/~jzlehtol/rpms/packmol.spec http://theory.physics.helsinki.fi/~jzlehtol/rpms/packmol-1.1.2.017-1.fc16.src.rpm (In reply to comment #7) > Done; but the correct license tag is now GPLv2. Yes, of course. I think, you can drop COPYING as long as it doesn't match the license of the package. Anyway, the package looks good now. ---------------- Package APPROVED ---------------- Sure. Thanks for the review! New Package SCM Request ======================= Package Name: packmol Short Description: Packing optimization for molecular dynamics simulations Owners: jussilehtola Branches: F-15 F-16 InitialCC: Git done (by process-git-requests). Upstream has added license headers and fixed LICENSE. The license tag has been changed accordingly to GPLv2+. packmol-1.1.2.023-1.fc15 has been submitted as an update for Fedora 15. https://admin.fedoraproject.org/updates/packmol-1.1.2.023-1.fc15 packmol-1.1.2.023-1.fc16 has been submitted as an update for Fedora 16. https://admin.fedoraproject.org/updates/packmol-1.1.2.023-1.fc16 packmol-1.1.2.023-1.fc15 has been pushed to the Fedora 15 testing repository. Hi, Is it possible to build it agains CentOs-6 for the epel repo? I tried on a C6 bix and it works: rpmbuild --rebuild packmol-1.1.2.023-1.fc16.src.rpm Installing packmol-1.1.2.023-1.fc16.src.rpm warning: user mockbuild does not exist - using root warning: group mockbuild does not exist - using root warning: user mockbuild does not exist - using root warning: group mockbuild does not exist - using root warning: user mockbuild does not exist - using root warning: group mockbuild does not exist - using root Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.PT5aQU + umask 022 + cd /root/rpmbuild/BUILD + LANG=C + export LANG + unset DISPLAY + cd /root/rpmbuild/BUILD + rm -rf packmol + /bin/tar -xf - + /usr/bin/gzip -dc /root/rpmbuild/SOURCES/packmol-1.1.2.023.tar.gz + STATUS=0 + '[' 0 -ne 0 ']' + cd packmol + /bin/chmod -Rf a+rX,u+w,g-w,o-w . + cp -a /root/rpmbuild/SOURCES/packmol-CMakeLists.txt CMakeLists.txt + find . -name '*.o' -delete + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.0yG8KE + umask 022 + cd /root/rpmbuild/BUILD + cd packmol + LANG=C + export LANG + unset DISPLAY + export FC=gfortran + FC=gfortran + mkdir ser + cd ser + CFLAGS='-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic' + export CFLAGS + CXXFLAGS='-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic' + export CXXFLAGS + FFLAGS='-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic' + export FFLAGS + /usr/bin/cmake -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_PREFIX:PATH=/usr -DCMAKE_INSTALL_LIBDIR:PATH=/usr/lib64 -DINCLUDE_INSTALL_DIR:PATH=/usr/include -DLIB_INSTALL_DIR:PATH=/usr/lib64 -DSYSCONF_INSTALL_DIR:PATH=/etc -DSHARE_INSTALL_PREFIX:PATH=/usr/share -DLIB_SUFFIX=64 -DBUILD_SHARED_LIBS:BOOL=ON -DUSE_OPENMP=OFF .. -- The Fortran compiler identification is GNU -- Check for working Fortran compiler: /usr/bin/gfortran -- Check for working Fortran compiler: /usr/bin/gfortran -- works -- Detecting Fortran compiler ABI info -- Detecting Fortran compiler ABI info - done -- Checking whether /usr/bin/gfortran supports Fortran 90 -- Checking whether /usr/bin/gfortran supports Fortran 90 -- yes -- The C compiler identification is GNU -- The CXX compiler identification is GNU -- Check for working C compiler: /usr/bin/gcc -- Check for working C compiler: /usr/bin/gcc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Configuring done -- Generating done CMake Warning: The variable, 'BUILD_SHARED_LIBS', specified manually, was not used during the generation. CMake Warning: The variable, 'CMAKE_INSTALL_LIBDIR', specified manually, was not used during the generation. CMake Warning: The variable, 'INCLUDE_INSTALL_DIR', specified manually, was not used during the generation. CMake Warning: The variable, 'LIB_INSTALL_DIR', specified manually, was not used during the generation. CMake Warning: The variable, 'LIB_SUFFIX', specified manually, was not used during the generation. CMake Warning: The variable, 'SHARE_INSTALL_PREFIX', specified manually, was not used during the generation. CMake Warning: The variable, 'SYSCONF_INSTALL_DIR', specified manually, was not used during the generation. -- Build files have been written to: /root/rpmbuild/BUILD/packmol/ser + make -j8 /usr/bin/cmake -H/root/rpmbuild/BUILD/packmol -B/root/rpmbuild/BUILD/packmol/ser --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /root/rpmbuild/BUILD/packmol/ser/CMakeFiles /root/rpmbuild/BUILD/packmol/ser/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[1]: Entering directory `/root/rpmbuild/BUILD/packmol/ser' make -f CMakeFiles/packmol.dir/build.make CMakeFiles/packmol.dir/depend make[2]: Entering directory `/root/rpmbuild/BUILD/packmol/ser' cd /root/rpmbuild/BUILD/packmol/ser && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /root/rpmbuild/BUILD/packmol /root/rpmbuild/BUILD/packmol /root/rpmbuild/BUILD/packmol/ser /root/rpmbuild/BUILD/packmol/ser /root/rpmbuild/BUILD/packmol/ser/CMakeFiles/packmol.dir/DependInfo.cmake --color= Scanning dependencies of target packmol make[2]: Leaving directory `/root/rpmbuild/BUILD/packmol/ser' make -f CMakeFiles/packmol.dir/build.make CMakeFiles/packmol.dir/requires make[2]: Entering directory `/root/rpmbuild/BUILD/packmol/ser' make[2]: Nothing to be done for `CMakeFiles/packmol.dir/requires'. make[2]: Leaving directory `/root/rpmbuild/BUILD/packmol/ser' make -f CMakeFiles/packmol.dir/build.make CMakeFiles/packmol.dir/build make[2]: Entering directory `/root/rpmbuild/BUILD/packmol/ser' /usr/bin/cmake -E cmake_progress_report /root/rpmbuild/BUILD/packmol/ser/CMakeFiles 1 [ 10%] /usr/bin/cmake -E cmake_progress_report /root/rpmbuild/BUILD/packmol/ser/CMakeFiles 2 /usr/bin/cmake -E cmake_progress_report /root/rpmbuild/BUILD/packmol/ser/CMakeFiles 3 Building Fortran object CMakeFiles/packmol.dir/cenmass.f.o [ 20%] [ 30%] /usr/bin/gfortran -o CMakeFiles/packmol.dir/cenmass.f.o -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -Wall -O2 -c /root/rpmbuild/BUILD/packmol/cenmass.f /usr/bin/cmake -E cmake_progress_report /root/rpmbuild/BUILD/packmol/ser/CMakeFiles 4 Building Fortran object CMakeFiles/packmol.dir/gencan.f.o /usr/bin/gfortran -o CMakeFiles/packmol.dir/gencan.f.o -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -Wall -O2 -c /root/rpmbuild/BUILD/packmol/gencan.f Building Fortran object CMakeFiles/packmol.dir/initial.f.o /usr/bin/gfortran -o CMakeFiles/packmol.dir/initial.f.o -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -Wall -O2 -c /root/rpmbuild/BUILD/packmol/initial.f [ 40%] /usr/bin/cmake -E cmake_progress_report /root/rpmbuild/BUILD/packmol/ser/CMakeFiles 5 /usr/bin/cmake -E cmake_progress_report /root/rpmbuild/BUILD/packmol/ser/CMakeFiles 6 [ 50%] Warning: Nonconforming tab character in column 1 of line 2355 [ 60%] Building Fortran object CMakeFiles/packmol.dir/io.f.o /root/rpmbuild/BUILD/packmol/gencan.f:56.36: subroutine evalal(n,x,m,lambda,rho,f,flag) 1 Warning: Unused dummy argument 'lambda' at (1) /root/rpmbuild/BUILD/packmol/gencan.f:56.40: subroutine evalal(n,x,m,lambda,rho,f,flag) 1 Warning: Unused dummy argument 'rho' at (1) /root/rpmbuild/BUILD/packmol/gencan.f:114.37: subroutine evalnal(n,x,m,lambda,rho,g,flag) 1 Warning: Unused dummy argument 'lambda' at (1) /root/rpmbuild/BUILD/packmol/gencan.f:114.41: subroutine evalnal(n,x,m,lambda,rho,g,flag) 1 Warning: Unused dummy argument 'rho' at (1) /root/rpmbuild/BUILD/packmol/gencan.f:177.25: subroutine evalhd(n) 1 Warning: Unused dummy argument 'n' at (1) /usr/bin/gfortran -o CMakeFiles/packmol.dir/io.f.o -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -Wall -O2 -c /root/rpmbuild/BUILD/packmol/io.f /usr/bin/cmake -E cmake_progress_report /root/rpmbuild/BUILD/packmol/ser/CMakeFiles 7 /usr/bin/cmake -E cmake_progress_report /root/rpmbuild/BUILD/packmol/ser/CMakeFiles 8 Building Fortran object CMakeFiles/packmol.dir/fgcommon.f.o /usr/bin/gfortran -o CMakeFiles/packmol.dir/fgcommon.f.o -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -Wall -O2 -c /root/rpmbuild/BUILD/packmol/fgcommon.f [ 80%] [ 80%] Building Fortran object CMakeFiles/packmol.dir/packmolnew.f.o /usr/bin/gfortran -o CMakeFiles/packmol.dir/packmolnew.f.o -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -Wall -O2 -c /root/rpmbuild/BUILD/packmol/packmolnew.f Building Fortran object CMakeFiles/packmol.dir/polartocart.f.o Building Fortran object CMakeFiles/packmol.dir/heuristics.f.o /usr/bin/gfortran -o CMakeFiles/packmol.dir/polartocart.f.o -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -Wall -O2 -c /root/rpmbuild/BUILD/packmol/polartocart.f /usr/bin/gfortran -o CMakeFiles/packmol.dir/heuristics.f.o -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -Wall -O2 -c /root/rpmbuild/BUILD/packmol/heuristics.f /root/rpmbuild/BUILD/packmol/polartocart.f:65.72: xcart(icart,1) = xbar + xcoor*v1(1) + ycoor*v2(1) + zcoor*v3(1) 1 Warning: Line truncated at (1) /root/rpmbuild/BUILD/packmol/polartocart.f:66.72: xcart(icart,2) = ybar + xcoor*v1(2) + ycoor*v2(2) + zcoor*v3(2) 1 Warning: Line truncated at (1) /root/rpmbuild/BUILD/packmol/polartocart.f:67.72: xcart(icart,3) = zbar + xcoor*v1(3) + ycoor*v2(3) + zcoor*v3(3) 1 Warning: Line truncated at (1) /root/rpmbuild/BUILD/packmol/io.f:213.2: 25 write(*,*)' ERROR: Output file not (correctly?) specified. ' 1 Warning: Label 25 at (1) defined but not used /root/rpmbuild/BUILD/packmol/initial.f:527.39: + precision,isem) 1 Warning: Unused dummy argument 'isem' at (1) /root/rpmbuild/BUILD/packmol/initial.f:526.59: subroutine restmol(itype,ilubar,n,x,fx,solve,movefrac, 1 Warning: Unused dummy argument 'movefrac' at (1) /root/rpmbuild/BUILD/packmol/initial.f:527.34: + precision,isem) 1 Warning: Unused dummy argument 'precision' at (1) /root/rpmbuild/BUILD/packmol/gencan.f:2611.5: 1003 format(6X,I6,T22,D17.6,T43,D17.6) 1 Warning: Label 1003 at (1) defined but not used /root/rpmbuild/BUILD/packmol/gencan.f:2622.40: +steabs,epsrel,epsabs,infrel,infabs) 1 Warning: Unused dummy argument 'infabs' at (1) /root/rpmbuild/BUILD/packmol/gencan.f:2622.33: +steabs,epsrel,epsabs,infrel,infabs) 1 Warning: Unused dummy argument 'infrel' at (1) /root/rpmbuild/BUILD/packmol/gencan.f:2622.12: +steabs,epsrel,epsabs,infrel,infabs) 1 Warning: Unused dummy argument 'steabs' at (1) /root/rpmbuild/BUILD/packmol/gencan.f:2621.71: +fmin,maxfc,iprint,fcnt,inform,xtrial,d,gamma,sigma1,sigma2,sterel, 1 Warning: Unused dummy argument 'sterel' at (1) /usr/bin/cmake -E cmake_progress_report /root/rpmbuild/BUILD/packmol/ser/CMakeFiles 9 /usr/bin/cmake -E cmake_progress_report /root/rpmbuild/BUILD/packmol/ser/CMakeFiles 10 [100%] [100%] /root/rpmbuild/BUILD/packmol/fgcommon.f: In function 'feasyseq': /root/rpmbuild/BUILD/packmol/fgcommon.f:612: warning: 'flast' may be used uninitialized in this function Building Fortran object CMakeFiles/packmol.dir/geasy.f.o Building Fortran object CMakeFiles/packmol.dir/feasy.f.o /usr/bin/gfortran -o CMakeFiles/packmol.dir/feasy.f.o -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -Wall -O2 -c /root/rpmbuild/BUILD/packmol/feasy.f /usr/bin/gfortran -o CMakeFiles/packmol.dir/geasy.f.o -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -Wall -O2 -c /root/rpmbuild/BUILD/packmol/geasy.f /root/rpmbuild/BUILD/packmol/gencan.f:3018.19: +epsabs,infrel,infabs) 1 Warning: Unused dummy argument 'infrel' at (1) /root/rpmbuild/BUILD/packmol/packmolnew.f: In function 'packmol': /root/rpmbuild/BUILD/packmol/packmolnew.f:55: warning: 'iirest' may be used uninitialized in this function /root/rpmbuild/BUILD/packmol/gencan.f:3856.61: +sigma1,sigma2,sterel,steabs,epsrel,epsabs,infrel,infabs) 1 Warning: Unused dummy argument 'infabs' at (1) /root/rpmbuild/BUILD/packmol/gencan.f:3856.54: +sigma1,sigma2,sterel,steabs,epsrel,epsabs,infrel,infabs) 1 Warning: Unused dummy argument 'infrel' at (1) /root/rpmbuild/BUILD/packmol/gencan.f:5216.19: +steabs,inform) 1 Warning: Unused dummy argument 'inform' at (1) /root/rpmbuild/BUILD/packmol/gencan.f:5215.52: subroutine calchd(nind,ind,x,d,g,n,xc,m,lambda,rho,hd,xtmp,sterel, 1 Warning: Unused dummy argument 'lambda' at (1) /root/rpmbuild/BUILD/packmol/gencan.f:5215.56: subroutine calchd(nind,ind,x,d,g,n,xc,m,lambda,rho,hd,xtmp,sterel, 1 Warning: Unused dummy argument 'rho' at (1) /root/rpmbuild/BUILD/packmol/gencan.f:5216.12: +steabs,inform) 1 Warning: Unused dummy argument 'steabs' at (1) /root/rpmbuild/BUILD/packmol/gencan.f:5215.71: subroutine calchd(nind,ind,x,d,g,n,xc,m,lambda,rho,hd,xtmp,sterel, 1 Warning: Unused dummy argument 'sterel' at (1) /root/rpmbuild/BUILD/packmol/gencan.f:5215.64: subroutine calchd(nind,ind,x,d,g,n,xc,m,lambda,rho,hd,xtmp,sterel, 1 Warning: Unused dummy argument 'xtmp' at (1) /root/rpmbuild/BUILD/packmol/gencan.f:5699.5: 110 IF (DABS(DX(I)).LE.XMAX) GO TO 115 1 Warning: Label 110 at (1) defined but not used /root/rpmbuild/BUILD/packmol/gencan.f:5698.5: 70 IF (DABS(DX(I)).GT.CUTLO) GO TO 75 1 Warning: Label 70 at (1) defined but not used /root/rpmbuild/BUILD/packmol/gencan.f:5691.5: 50 IF (DX(I).EQ.ZERO) GO TO 200 1 Warning: Label 50 at (1) defined but not used /root/rpmbuild/BUILD/packmol/gencan.f:5689.5: 30 IF (DABS(DX(I)).GT.CUTLO) GO TO 85 1 Warning: Label 30 at (1) defined but not used /root/rpmbuild/BUILD/packmol/io.f: In function 'setrnum': /root/rpmbuild/BUILD/packmol/io.f:732: warning: 'ireslast' may be used uninitialized in this function /root/rpmbuild/BUILD/packmol/gencan.f: In function 'cg': /root/rpmbuild/BUILD/packmol/gencan.f:3272: warning: 'alpha' may be used uninitialized in this function /root/rpmbuild/BUILD/packmol/gencan.f:3272: warning: 'amax1' may be used uninitialized in this function /root/rpmbuild/BUILD/packmol/gencan.f:3272: warning: 'amax1n' may be used uninitialized in this function /root/rpmbuild/BUILD/packmol/gencan.f:3273: warning: 'dnorm2' may be used uninitialized in this function /root/rpmbuild/BUILD/packmol/gencan.f:3273: warning: 'dtr' may be used uninitialized in this function /root/rpmbuild/BUILD/packmol/gencan.f:3274: warning: 'dtw' may be used uninitialized in this function /root/rpmbuild/BUILD/packmol/gencan.f:3271: warning: 'rbdnegaind' may be used uninitialized in this function /root/rpmbuild/BUILD/packmol/gencan.f:3271: warning: 'rbdnegatype' may be used uninitialized in this function /root/rpmbuild/BUILD/packmol/gencan.f:3271: warning: 'rbdposaind' may be used uninitialized in this function /root/rpmbuild/BUILD/packmol/gencan.f:3271: warning: 'rbdposatype' may be used uninitialized in this function /root/rpmbuild/BUILD/packmol/gencan.f:3275: warning: 'rnorm2prev' may be used uninitialized in this function /root/rpmbuild/BUILD/packmol/gencan.f: In function 'gencan': /root/rpmbuild/BUILD/packmol/gencan.f:1729: warning: 'sts' may be used uninitialized in this function /root/rpmbuild/BUILD/packmol/gencan.f:1729: warning: 'sty' may be used uninitialized in this function Linking Fortran executable packmol /usr/bin/cmake -E cmake_link_script CMakeFiles/packmol.dir/link.txt --verbose=1 /usr/bin/gfortran -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -Wall -O2 CMakeFiles/packmol.dir/cenmass.f.o CMakeFiles/packmol.dir/gencan.f.o CMakeFiles/packmol.dir/initial.f.o CMakeFiles/packmol.dir/io.f.o CMakeFiles/packmol.dir/fgcommon.f.o CMakeFiles/packmol.dir/packmolnew.f.o CMakeFiles/packmol.dir/polartocart.f.o CMakeFiles/packmol.dir/heuristics.f.o CMakeFiles/packmol.dir/feasy.f.o CMakeFiles/packmol.dir/geasy.f.o -o packmol -rdynamic make[2]: Leaving directory `/root/rpmbuild/BUILD/packmol/ser' /usr/bin/cmake -E cmake_progress_report /root/rpmbuild/BUILD/packmol/ser/CMakeFiles 1 2 3 4 5 6 7 8 9 10 [100%] Built target packmol make[1]: Leaving directory `/root/rpmbuild/BUILD/packmol/ser' /usr/bin/cmake -E cmake_progress_start /root/rpmbuild/BUILD/packmol/ser/CMakeFiles 0 + cd .. + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.sktY2F + umask 022 + cd /root/rpmbuild/BUILD + '[' /root/rpmbuild/BUILDROOT/packmol-1.1.2.023-1.fc16.x86_64 '!=' / ']' + rm -rf /root/rpmbuild/BUILDROOT/packmol-1.1.2.023-1.fc16.x86_64 ++ dirname /root/rpmbuild/BUILDROOT/packmol-1.1.2.023-1.fc16.x86_64 + mkdir -p /root/rpmbuild/BUILDROOT + mkdir /root/rpmbuild/BUILDROOT/packmol-1.1.2.023-1.fc16.x86_64 + cd packmol + LANG=C + export LANG + unset DISPLAY + rm -rf /root/rpmbuild/BUILDROOT/packmol-1.1.2.023-1.fc16.x86_64 + install -D -p -m 755 ser/packmol /root/rpmbuild/BUILDROOT/packmol-1.1.2.023-1.fc16.x86_64/usr/bin/packmol + install -D -p -m 755 solvate.tcl /root/rpmbuild/BUILDROOT/packmol-1.1.2.023-1.fc16.x86_64/usr/bin/packmol_solvate + /usr/lib/rpm/find-debuginfo.sh --strict-build-id /root/rpmbuild/BUILD/packmol extracting debug info from /root/rpmbuild/BUILDROOT/packmol-1.1.2.023-1.fc16.x86_64/usr/bin/packmol cpio: packmol/ser/gencan.i: Cannot stat: No such file or directory cpio: packmol/ser/molpa.i: Cannot stat: No such file or directory cpio: packmol/ser/sizes.i: Cannot stat: No such file or directory 699 blocks + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/redhat/brp-compress + /usr/lib/rpm/redhat/brp-strip-static-archive /usr/bin/strip + /usr/lib/rpm/redhat/brp-strip-comment-note /usr/bin/strip /usr/bin/objdump + /usr/lib/rpm/brp-python-bytecompile + /usr/lib/rpm/redhat/brp-python-hardlink + /usr/lib/rpm/redhat/brp-java-repack-jars Processing files: packmol-1.1.2.023-1.el6.x86_64 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.FVKRBJ + umask 022 + cd /root/rpmbuild/BUILD + cd packmol + DOCDIR=/root/rpmbuild/BUILDROOT/packmol-1.1.2.023-1.fc16.x86_64/usr/share/doc/packmol-1.1.2.023 + export DOCDIR + rm -rf /root/rpmbuild/BUILDROOT/packmol-1.1.2.023-1.fc16.x86_64/usr/share/doc/packmol-1.1.2.023 + /bin/mkdir -p /root/rpmbuild/BUILDROOT/packmol-1.1.2.023-1.fc16.x86_64/usr/share/doc/packmol-1.1.2.023 + cp -pr AUTHORS LICENSE COPYING /root/rpmbuild/BUILDROOT/packmol-1.1.2.023-1.fc16.x86_64/usr/share/doc/packmol-1.1.2.023 + exit 0 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: /usr/bin/tclsh libc.so.6()(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.4)(64bit) libgcc_s.so.1()(64bit) libgfortran.so.3()(64bit) libgfortran.so.3(GFORTRAN_1.0)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(64bit) rtld(GNU_HASH) Processing files: packmol-debuginfo-1.1.2.023-1.el6.x86_64 Checking for unpackaged file(s): /usr/lib/rpm/check-files /root/rpmbuild/BUILDROOT/packmol-1.1.2.023-1.fc16.x86_64 Wrote: /root/rpmbuild/RPMS/x86_64/packmol-1.1.2.023-1.el6.x86_64.rpm Wrote: /root/rpmbuild/RPMS/x86_64/packmol-debuginfo-1.1.2.023-1.el6.x86_64.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.dTGsGV + umask 022 + cd /root/rpmbuild/BUILD + cd packmol + rm -rf /root/rpmbuild/BUILDROOT/packmol-1.1.2.023-1.fc16.x86_64 + exit 0 Executing(--clean): /bin/sh -e /var/tmp/rpm-tmp.RFSmWZ + umask 022 + cd /root/rpmbuild/BUILD + rm -rf packmol + exit 0 Very well. Package Change Request ====================== Package Name: packmol New Branches: el6 Owners: jussilehtola InitialCC: Git done (by process-git-requests). packmol-1.1.2.023-1.el6 has been submitted as an update for Fedora EPEL 6. https://admin.fedoraproject.org/updates/packmol-1.1.2.023-1.el6 packmol-1.1.2.023-1.fc15 has been pushed to the Fedora 15 stable repository. packmol-1.1.2.023-1.fc16 has been pushed to the Fedora 16 stable repository. packmol-1.1.2.023-1.el6 has been pushed to the Fedora EPEL 6 stable repository. |