Package: NuPoP

Version: 1.34.0

Command: rm -rf NuPoP.buildbin-libdir && mkdir NuPoP.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh NuPoP_1.34.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R NuPoP.buildbin-libdir

StartedAt: 2019-10-16 09:03:30 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 09:03:53 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 22.2 seconds

RetCode: 0

Status:  OK

PackageFile: NuPoP_1.34.0.tgz

PackageFileSize: 2.002 MiB

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### Running command:
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###   rm -rf NuPoP.buildbin-libdir && mkdir NuPoP.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh NuPoP_1.34.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R NuPoP.buildbin-libdir
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=NuPoP.buildbin-libdir NuPoP_1.34.0.tar.gz'
>>>>>>> 

* installing *source* package ‘NuPoP’ ...
** using staged installation
** libs
gfortran  -fPIC  -Wall -g -O2  -c  vtbfb.f90 -o vtbfb.o
vtbfb.f90:13:32:

   character*80 seqName,out1,out2; character*2 tpc
                                1
Warning: Unused variable ‘out2’ declared at (1) [-Wunused-variable]
gfortran  -fPIC  -Wall -g -O2  -c  vtbfbNL4.f90 -o vtbfbNL4.o
vtbfbNL4.f90:257:106:

         if(d>=3) temp=temp*tranL2(w(t-d+1),w(t-d+2),w(t-d+3))*tranL2(c(z-t+1),c(z-t+2),c(z-t+3))/r(t-d+2)   
                                                                                                          1
Warning: Nonconforming tab character at (1) [-Wtabs]
vtbfbNL4.f90:272:13:

       end if 
             1
Warning: Nonconforming tab character at (1) [-Wtabs]
vtbfbNL4.f90:301:107:

         if(d>=3) temp=temp*tranL2(w(t-d+1),w(t-d+2),w(t-d+3))*tranL2(c(z-t+1),c(z-t+2),c(z-t+3))/ra(t-d+2)   
                                                                                                           1
Warning: Nonconforming tab character at (1) [-Wtabs]
vtbfbNL4.f90:314:23:

       tempL=tempL+temp 
                       1
Warning: Nonconforming tab character at (1) [-Wtabs]
vtbfbNL4.f90:335:87:

     if(z-t>=3) rb(t)=rb(t)*tranL2(w(t+1),w(t+2),w(t+3))*tranL2(c(1),c(2),c(3))/rb(t+2)   
                                                                                       1
Warning: Nonconforming tab character at (1) [-Wtabs]
vtbfbNL4.f90:364:105:

         if(d>=3) temp=temp*tranL2(w(t+1),w(t+2),w(t+3))*tranL2(c(z-t-d+1),c(z-t-d+2),c(z-t-d+3))/rb(t+2)   
                                                                                                         1
Warning: Nonconforming tab character at (1) [-Wtabs]
vtbfbNL4.f90:15:32:

   character*80 seqName,out1,out2; character*2 tpc
                                1
Warning: Unused variable ‘out2’ declared at (1) [-Wunused-variable]
clang -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 NuPoP.so vtbfb.o vtbfbNL4.o -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.9-bioc/meat/NuPoP.buildbin-libdir/00LOCK-NuPoP/00new/NuPoP/libs
** R
** 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 (NuPoP)


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

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libgcc_s.1.dylib" "NuPoP.buildbin-libdir/NuPoP/libs//NuPoP.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libgfortran.3.dylib" "NuPoP.buildbin-libdir/NuPoP/libs//NuPoP.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libreadline.5.2.dylib" "NuPoP.buildbin-libdir/NuPoP/libs//NuPoP.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libreadline.dylib" "NuPoP.buildbin-libdir/NuPoP/libs//NuPoP.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libquadmath.0.dylib" "NuPoP.buildbin-libdir/NuPoP/libs//NuPoP.so"
install_name_tool -change "/usr/local/gfortran/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libgfortran.3.dylib" "NuPoP.buildbin-libdir/NuPoP/libs//NuPoP.so"
install_name_tool -change "/usr/local/gfortran/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libquadmath.0.dylib" "NuPoP.buildbin-libdir/NuPoP/libs//NuPoP.so"