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This page was generated on 2024-11-20 12:06 -0500 (Wed, 20 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4481
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4479
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4359
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4539
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 327/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChemmineOB 1.44.0  (landing page)
Thomas Girke
Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024)
git_url: https://git.bioconductor.org/packages/ChemmineOB
git_branch: RELEASE_3_20
git_last_commit: 20cbc10
git_last_commit_date: 2024-10-29 09:47:40 -0500 (Tue, 29 Oct 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  


BUILD BIN results for ChemmineOB on lconway

To the developers/maintainers of the ChemmineOB package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ChemmineOB.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: ChemmineOB
Version: 1.44.0
Command: rm -rf ChemmineOB.buildbin-libdir && mkdir ChemmineOB.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh ChemmineOB_1.44.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R ChemmineOB.buildbin-libdir
StartedAt: 2024-11-20 04:18:41 -0500 (Wed, 20 Nov 2024)
EndedAt: 2024-11-20 04:21:26 -0500 (Wed, 20 Nov 2024)
EllapsedTime: 165.3 seconds
RetCode: 0
Status:   OK  
PackageFile: ChemmineOB_1.44.0.tgz
PackageFileSize: 5.27 MiB

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf ChemmineOB.buildbin-libdir && mkdir ChemmineOB.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh ChemmineOB_1.44.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R ChemmineOB.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=ChemmineOB.buildbin-libdir ChemmineOB_1.44.0.tar.gz'
>>>>>>> 

* installing *source* package ‘ChemmineOB’ ...
** using staged installation
checking for pkg-config... /opt/R/x86_64/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for OPENBABEL... no
checking for OPENBABEL... no
checking for gcc... clang -arch x86_64
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 clang -arch x86_64 accepts -g... yes
checking for clang -arch x86_64 option to accept ISO C89... none needed
checking how to run the C preprocessor... clang -arch x86_64 -E
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/include/openbabel3  -I/usr/include/eigen3  -DUSE_BOOST -DHAVE_EIGEN -D_LIBCPP_ENABLE_CXX17_REMOVED_UNARY_BINARY_FUNCTION  -I/usr/local/include/eigen3 -I/usr/local/include/openbabel3    -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/zlibbioc/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c ChemmineOB.cpp -o ChemmineOB.o
In file included from ChemmineOB.cpp:1576:
/usr/local/include/openbabel3/openbabel/griddata.h:74:12: warning: 'OpenBabel::OBGridData::GetValue' hides overloaded virtual function [-Woverloaded-virtual]
    double GetValue(int i, int j, int k) const;
           ^
/usr/local/include/openbabel3/openbabel/base.h:228:32: note: hidden overloaded virtual function 'OpenBabel::OBGenericData::GetValue' declared here: different number of parameters (0 vs 3)
    virtual const std::string &GetValue()  const
                               ^
In file included from ChemmineOB.cpp:1576:
/usr/local/include/openbabel3/openbabel/griddata.h:76:12: warning: 'OpenBabel::OBGridData::GetValue' hides overloaded virtual function [-Woverloaded-virtual]
    double GetValue (vector3 pos) const;
           ^
/usr/local/include/openbabel3/openbabel/base.h:228:32: note: hidden overloaded virtual function 'OpenBabel::OBGenericData::GetValue' declared here: different number of parameters (0 vs 1)
    virtual const std::string &GetValue()  const
                               ^
In file included from ChemmineOB.cpp:1582:
/usr/local/include/openbabel3/openbabel/reaction.h:99:15: warning: 'OpenBabel::OBReaction::GetTitle' hides overloaded virtual function [-Woverloaded-virtual]
  std::string GetTitle()        const { return _title; }
              ^
/usr/local/include/openbabel3/openbabel/base.h:286:28: note: hidden overloaded virtual function 'OpenBabel::OBBase::GetTitle' declared here: different number of parameters (1 vs 0)
      virtual const char  *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";}
                           ^
In file included from ChemmineOB.cpp:1582:
/usr/local/include/openbabel3/openbabel/reaction.h:101:8: warning: 'OpenBabel::OBReaction::SetTitle' hides overloaded virtual function [-Woverloaded-virtual]
  void SetTitle(const std::string& title) { _title=title; }
       ^
/usr/local/include/openbabel3/openbabel/base.h:287:21: note: hidden overloaded virtual function 'OpenBabel::OBBase::SetTitle' declared here: type mismatch at 1st parameter ('const char *' vs 'const std::string &' (aka 'const basic_string<char, char_traits<char>, allocator<char>> &'))
      virtual void  SetTitle(const char *) {}
                    ^
ChemmineOB.cpp:4160:7: warning: unused variable 'ecode' [-Wunused-variable]
  int ecode = 0; arg1 = (std::ios_base::event) swigarg_arg1; arg2 = (std::ios_base *) &swigarg_arg2; arg3 = (int) swigarg_arg3;
      ^
5 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/include/openbabel3  -I/usr/include/eigen3  -DUSE_BOOST -DHAVE_EIGEN -D_LIBCPP_ENABLE_CXX17_REMOVED_UNARY_BINARY_FUNCTION  -I/usr/local/include/eigen3 -I/usr/local/include/openbabel3    -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/zlibbioc/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c canonical.cpp -o canonical.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o ChemmineOB.so ChemmineOB.o canonical.o -L/usr/local/lib/openbabel3 -lopenbabel -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: dylib (/usr/local/lib/openbabel3/libopenbabel.dylib) was built for newer macOS version (12.0) than being linked (11.0)
installing to /Users/biocbuild/bbs-3.20-bioc/meat/ChemmineOB.buildbin-libdir/00LOCK-ChemmineOB/00new/ChemmineOB/libs
** R
** inst
** byte-compile and prepare package for lazy loading
in method for ‘copyToR’ with signature ‘"_p_std::char_traits<(char)>"’: no definition for class “_p_std::char_traits<(char)>”
in method for ‘copyToR’ with signature ‘"_p_std::pair<(unsigned int,unsigned int)>"’: no definition for class “_p_std::pair<(unsigned int,unsigned int)>”
in method for ‘copyToR’ with signature ‘"_p_OpenBabel::CharPtrLess"’: no definition for class “_p_OpenBabel::CharPtrLess”
in method for ‘copyToR’ with signature ‘"_p_OpenBabel::FptIndexHeader"’: no definition for class “_p_OpenBabel::FptIndexHeader”
in method for ‘copyToR’ with signature ‘"_p_OpenBabel::OBStereo"’: no definition for class “_p_OpenBabel::OBStereo”
in method for ‘copyToR’ with signature ‘"_p_OpenBabel::OBStereoUnit"’: no definition for class “_p_OpenBabel::OBStereoUnit”
in method for ‘copyToR’ with signature ‘"_p_OpenBabel::LineSearchType"’: no definition for class “_p_OpenBabel::LineSearchType”
in method for ‘copyToR’ with signature ‘"_p_OpenBabel::OBTetrahedralConfig"’: no definition for class “_p_OpenBabel::OBTetrahedralConfig”
in method for ‘copyToR’ with signature ‘"_p_OpenBabel::OBCisTransConfig"’: no definition for class “_p_OpenBabel::OBCisTransConfig”
in method for ‘copyToR’ with signature ‘"_p_OpenBabel::OBSquarePlanarConfig"’: no definition for class “_p_OpenBabel::OBSquarePlanarConfig”
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ChemmineOB)


>>>>>>> 
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR ChemmineOB.buildbin-libdir/ChemmineOB/libs/ChemmineOB.so
>>>>>>> 

>>>>>>> Paths before fix:
ChemmineOB.buildbin-libdir/ChemmineOB/libs/ChemmineOB.so:
	ChemmineOB.so (compatibility version 0.0.0, current version 0.0.0)
	/usr/local/opt/open-babel/lib/libopenbabel.7.dylib (compatibility version 7.0.0, current version 7.0.0)
	/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.1)
	/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
	/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)

>>>>>>> Fix with install_name_tool:
install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libgcc_s.1.1.dylib" "ChemmineOB.buildbin-libdir/ChemmineOB/libs/ChemmineOB.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libgfortran.5.dylib" "ChemmineOB.buildbin-libdir/ChemmineOB/libs/ChemmineOB.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libquadmath.0.dylib" "ChemmineOB.buildbin-libdir/ChemmineOB/libs/ChemmineOB.so"

>>>>>>> Paths after fix:
ChemmineOB.buildbin-libdir/ChemmineOB/libs/ChemmineOB.so:
	ChemmineOB.so (compatibility version 0.0.0, current version 0.0.0)
	/usr/local/opt/open-babel/lib/libopenbabel.7.dylib (compatibility version 7.0.0, current version 7.0.0)
	/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.1)
	/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
	/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)