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BUILD BIN report for ChemmineR on merida1

This page was generated on 2021-05-05 12:13:53 -0400 (Wed, 05 May 2021).

To the developers/maintainers of the ChemmineR package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 276/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChemmineR 3.42.2  (landing page)
Thomas Girke
Snapshot Date: 2021-05-04 14:50:13 -0400 (Tue, 04 May 2021)
URL: https://git.bioconductor.org/packages/ChemmineR
Branch: RELEASE_3_12
Last Commit: d1536d5
Last Changed Date: 2021-02-25 13:09:29 -0400 (Thu, 25 Feb 2021)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    ERROR    OK  
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository

Summary

Package: ChemmineR
Version: 3.42.2
Command: rm -rf ChemmineR.buildbin-libdir && mkdir ChemmineR.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh ChemmineR_3.42.2.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R ChemmineR.buildbin-libdir
StartedAt: 2021-05-05 08:35:35 -0400 (Wed, 05 May 2021)
EndedAt: 2021-05-05 08:36:28 -0400 (Wed, 05 May 2021)
EllapsedTime: 53.0 seconds
RetCode: 0
Status:   OK  
PackageFile: ChemmineR_3.42.2.tgz
PackageFileSize: 2.23 MiB

Command output

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###
### Running command:
###
###   rm -rf ChemmineR.buildbin-libdir && mkdir ChemmineR.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh ChemmineR_3.42.2.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R ChemmineR.buildbin-libdir
###
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=ChemmineR.buildbin-libdir ChemmineR_3.42.2.tar.gz'
>>>>>>> 

* installing *source* package ‘ChemmineR’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I/usr/local/include  -DNO_MAIN -DNO_DEBUG -fPIC  -Wall -g -O2  -c DisjointSets.cpp -o DisjointSets.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I/usr/local/include  -DNO_MAIN -DNO_DEBUG -fPIC  -Wall -g -O2  -c cluster.cc -o cluster.o
cluster.cc:49:13: warning: unused function 'prepare_neighbors' [-Wunused-function]
void static prepare_neighbors(const char* nbr_file, int skip, int p)
            ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I/usr/local/include  -DNO_MAIN -DNO_DEBUG -fPIC  -Wall -g -O2  -c cstrsplit.cc -o cstrsplit.o
In file included from cstrsplit.cc:2:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I/usr/local/include  -DNO_MAIN -DNO_DEBUG -fPIC  -Wall -g -O2  -c desc.cc -o desc.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I/usr/local/include  -DNO_MAIN -DNO_DEBUG -fPIC  -Wall -g -O2  -c fingerprints.cc -o fingerprints.o
In file included from fingerprints.cc:12:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I/usr/local/include  -DNO_MAIN -DNO_DEBUG -fPIC  -Wall -g -O2  -c formats.cc -o formats.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I/usr/local/include  -DNO_MAIN -DNO_DEBUG -fPIC  -Wall -g -O2  -c molecule.cc -o molecule.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I/usr/local/include  -DNO_MAIN -DNO_DEBUG -fPIC  -Wall -g -O2  -c r_wrap.cc -o r_wrap.o
r_wrap.cc:563:7: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
      register size_t l = 0;
      ^~~~~~~~~
r_wrap.cc:564:7: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
      register size_t r = iter->size - 1;
      ^~~~~~~~~
r_wrap.cc:567:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
        register size_t i = (l + r) >> 1; 
        ^~~~~~~~~
r_wrap.cc:570:4: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
          register int compare = strcmp(name, iname);
          ^~~~~~~~~
r_wrap.cc:614:7: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
      register size_t i = 0;
      ^~~~~~~~~
r_wrap.cc:633:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  register const unsigned char *u = (unsigned char *) ptr;
  ^~~~~~~~~
r_wrap.cc:634:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  register const unsigned char *eu =  u + sz;
  ^~~~~~~~~
r_wrap.cc:636:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
    register unsigned char uu = *u;
    ^~~~~~~~~
r_wrap.cc:648:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  register unsigned char *u = (unsigned char *) ptr;
  ^~~~~~~~~
r_wrap.cc:649:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  register const unsigned char *eu = u + sz;
  ^~~~~~~~~
r_wrap.cc:651:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
    register char d = *(c++);
    ^~~~~~~~~
r_wrap.cc:652:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
    register unsigned char uu;
    ^~~~~~~~~
r_wrap.cc:1689:14: warning: explicitly assigning value of variable of type 'void *' to itself [-Wself-assign]
  clientdata = clientdata;
  ~~~~~~~~~~ ^ ~~~~~~~~~~
13 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I/usr/local/include  -DNO_MAIN -DNO_DEBUG -fPIC  -Wall -g -O2  -c script.cc -o script.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I/usr/local/include  -DNO_MAIN -DNO_DEBUG -fPIC  -Wall -g -O2  -c similarity.cc -o similarity.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o ChemmineR.so DisjointSets.o cluster.o cstrsplit.o desc.o fingerprints.o formats.o molecule.o r_wrap.o script.o similarity.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.12-bioc/meat/ChemmineR.buildbin-libdir/00LOCK-ChemmineR/00new/ChemmineR/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** 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 (ChemmineR)


>>>>>>> 
>>>>>>> FIXING LINKS FOR ChemmineR.buildbin-libdir/ChemmineR/libs/ChemmineR.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libgcc_s.1.dylib" "ChemmineR.buildbin-libdir/ChemmineR/libs/ChemmineR.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libgfortran.5.dylib" "ChemmineR.buildbin-libdir/ChemmineR/libs/ChemmineR.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libquadmath.0.dylib" "ChemmineR.buildbin-libdir/ChemmineR/libs/ChemmineR.so"