Back to Mac ARM64 build report for BioC 3.18
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This page was generated on 2024-03-28 11:32:27 -0400 (Thu, 28 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson1macOS 13.6.1 Venturaarm644.3.3 (2024-02-29) -- "Angel Food Cake" 4376
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Package 1552/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PING 2.46.0  (landing page)
Renan Sauteraud
Snapshot Date: 2024-03-26 09:00:03 -0400 (Tue, 26 Mar 2024)
git_url: https://git.bioconductor.org/packages/PING
git_branch: RELEASE_3_18
git_last_commit: 49706e2
git_last_commit_date: 2023-10-24 09:49:31 -0400 (Tue, 24 Oct 2023)
kjohnson1macOS 13.6.1 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

BUILD BIN results for PING on kjohnson1


To the developers/maintainers of the PING package:
- 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: PING
Version: 2.46.0
Command: rm -rf PING.buildbin-libdir && mkdir PING.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh PING_2.46.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R PING.buildbin-libdir
StartedAt: 2024-03-28 09:21:28 -0400 (Thu, 28 Mar 2024)
EndedAt: 2024-03-28 09:23:02 -0400 (Thu, 28 Mar 2024)
EllapsedTime: 93.5 seconds
RetCode: 0
Status:   OK  
PackageFile: PING_2.46.0.tgz
PackageFileSize: 5.511 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf PING.buildbin-libdir && mkdir PING.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh PING_2.46.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R PING.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=PING.buildbin-libdir PING_2.46.0.tar.gz'
>>>>>>> 

* installing *source* package ‘PING’ ...
** using staged installation
checking for pkg-config... /opt/R/arm64/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for GSL... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c init.c -o init.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c ping.c -o ping.o
ping.c:145:7: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  if( REAL(VECTOR_ELT(paraPrior, 5))[0]>0 & REAL(VECTOR_ELT(paraEM, 0))[0]==0) // automatically decide minK and maxKK for histone data, when minK=0
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                                          &&
ping.c:145:7: note: cast one or both operands to int to silence this warning
ping.c:321:10: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
      if(abs(REAL(yF)[i]-mu[k]+delta[k]/2.)/sqrt(sF[k])<calpha)
         ^
ping.c:321:10: note: use function 'fabs' instead
      if(abs(REAL(yF)[i]-mu[k]+delta[k]/2.)/sqrt(sF[k])<calpha)
         ^~~
         fabs
ping.c:329:10: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
      if(abs(REAL(yR)[i]-mu[k]-delta[k]/2.)/sqrt(sR[k])<calpha)
         ^
ping.c:329:10: note: use function 'fabs' instead
      if(abs(REAL(yR)[i]-mu[k]-delta[k]/2.)/sqrt(sR[k])<calpha)
         ^~~
         fabs
ping.c:345:12: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
        if(abs(REAL(cF)[i]-mu[k]+delta[k]/2.)/sqrt(sF[k])<calpha)
           ^
ping.c:345:12: note: use function 'fabs' instead
        if(abs(REAL(cF)[i]-mu[k]+delta[k]/2.)/sqrt(sF[k])<calpha)
           ^~~
           fabs
ping.c:353:12: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
        if(abs(REAL(cR)[i]-mu[k]-delta[k]/2.)/sqrt(sR[k])<calpha)
           ^
ping.c:353:12: note: use function 'fabs' instead
        if(abs(REAL(cR)[i]-mu[k]-delta[k]/2.)/sqrt(sR[k])<calpha)
           ^~~
           fabs
ping.c:1536:9: warning: variable 'chiSum' set but not used [-Wunused-but-set-variable]
        double chiSum = 0, etaF, etaR, dd, cc;
               ^
ping.c:3408:10: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
      if((gsl_matrix_get(Index,kMerge,k)==1) | (gsl_matrix_get(Index,kMerge+1,k)==1))
         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                                             ||
ping.c:3408:10: note: cast one or both operands to int to silence this warning
ping.c:3280:20: warning: variable 'tstatMax' set but not used [-Wunused-but-set-variable]
  double tstat=0.0,tstatMax=0.0;
                   ^
8 warnings generated.
clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o PING.so init.o ping.o -L/opt/R/arm64/lib -lgsl -lgslcblas -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/PING.buildbin-libdir/00LOCK-PING/00new/PING/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 (PING)


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

>>>>>>> Paths before fix:
PING.buildbin-libdir/PING/libs/PING.so:
	PING.so (compatibility version 0.0.0, current version 0.0.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)
	/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.3)
	/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)

>>>>>>> Fix with install_name_tool:
install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libgcc_s.1.1.dylib" "PING.buildbin-libdir/PING/libs/PING.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libgfortran.5.dylib" "PING.buildbin-libdir/PING/libs/PING.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libquadmath.0.dylib" "PING.buildbin-libdir/PING/libs/PING.so"

>>>>>>> Paths after fix:
PING.buildbin-libdir/PING/libs/PING.so:
	PING.so (compatibility version 0.0.0, current version 0.0.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)
	/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.3)
	/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)