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This page was generated on 2024-06-11 15:41 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4679
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4414
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4441
kjohnson1macOS 13.6.6 Venturaarm644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4394
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 819/2239HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeoDiff 1.11.0  (landing page)
Nicole Ortogero
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/GeoDiff
git_branch: devel
git_last_commit: c1d6199
git_last_commit_date: 2024-04-30 11:38:43 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

BUILD BIN results for GeoDiff on merida1

To the developers/maintainers of the GeoDiff package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GeoDiff.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: GeoDiff
Version: 1.11.0
Command: rm -rf GeoDiff.buildbin-libdir && mkdir GeoDiff.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh GeoDiff_1.11.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R GeoDiff.buildbin-libdir
StartedAt: 2024-06-10 12:40:44 -0400 (Mon, 10 Jun 2024)
EndedAt: 2024-06-10 12:44:27 -0400 (Mon, 10 Jun 2024)
EllapsedTime: 222.5 seconds
RetCode: 0
Status:   OK  
PackageFile: GeoDiff_1.11.0.tgz
PackageFileSize: 4.835 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf GeoDiff.buildbin-libdir && mkdir GeoDiff.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh GeoDiff_1.11.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R GeoDiff.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=GeoDiff.buildbin-libdir GeoDiff_1.11.0.tar.gz'
>>>>>>> 

* installing *source* package ‘GeoDiff’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -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/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/roptim/include' -I/opt/R/x86_64/include     -fPIC  -falign-functions=64 -Wall -g -O2   -c NBthDEOptPara.cpp -o NBthDEOptPara.o
NBthDEOptPara.cpp:34:9: warning: unused variable 'm' [-Wunused-variable]
    int m = y.n_elem;
        ^
NBthDEOptPara.cpp:58:9: warning: unused variable 'm' [-Wunused-variable]
    int m = y.n_elem;
        ^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -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/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/roptim/include' -I/opt/R/x86_64/include     -fPIC  -falign-functions=64 -Wall -g -O2   -c NBthmDEGrad.cpp -o NBthmDEGrad.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -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/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/roptim/include' -I/opt/R/x86_64/include     -fPIC  -falign-functions=64 -Wall -g -O2   -c NBthmDEMH.cpp -o NBthmDEMH.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -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/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/roptim/include' -I/opt/R/x86_64/include     -fPIC  -falign-functions=64 -Wall -g -O2   -c NBthmDEOptPara.cpp -o NBthmDEOptPara.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -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/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/roptim/include' -I/opt/R/x86_64/include     -fPIC  -falign-functions=64 -Wall -g -O2   -c NBthmDEOptU.cpp -o NBthmDEOptU.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -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/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/roptim/include' -I/opt/R/x86_64/include     -fPIC  -falign-functions=64 -Wall -g -O2   -c PoisthNormOptPara.cpp -o PoisthNormOptPara.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -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/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/roptim/include' -I/opt/R/x86_64/include     -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -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/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/roptim/include' -I/opt/R/x86_64/include     -fPIC  -falign-functions=64 -Wall -g -O2   -c dnbinom_mu_vec.cpp -o dnbinom_mu_vec.o
clang++ -arch x86_64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o GeoDiff.so NBthDEOptPara.o NBthmDEGrad.o NBthmDEMH.o NBthmDEOptPara.o NBthmDEOptU.o PoisthNormOptPara.o RcppExports.o dnbinom_mu_vec.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.20-bioc/meat/GeoDiff.buildbin-libdir/00LOCK-GeoDiff/00new/GeoDiff/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 (GeoDiff)


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

>>>>>>> Paths before fix:
GeoDiff.buildbin-libdir/GeoDiff/libs/GeoDiff.so:
	GeoDiff.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRlapack.dylib (compatibility version 4.4.0, current version 4.4.0)
	/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRblas.dylib (compatibility version 0.0.0, current version 0.0.0)
	/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0/libgfortran.5.dylib (compatibility version 6.0.0, current version 6.0.0)
	/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0)
	/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.0)
	/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" "GeoDiff.buildbin-libdir/GeoDiff/libs/GeoDiff.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" "GeoDiff.buildbin-libdir/GeoDiff/libs/GeoDiff.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" "GeoDiff.buildbin-libdir/GeoDiff/libs/GeoDiff.so"
install_name_tool -change "/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libgfortran.5.dylib" "GeoDiff.buildbin-libdir/GeoDiff/libs/GeoDiff.so"
install_name_tool -change "/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libquadmath.0.dylib" "GeoDiff.buildbin-libdir/GeoDiff/libs/GeoDiff.so"

>>>>>>> Paths after fix:
GeoDiff.buildbin-libdir/GeoDiff/libs/GeoDiff.so:
	GeoDiff.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRlapack.dylib (compatibility version 4.4.0, current version 4.4.0)
	/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRblas.dylib (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libgfortran.5.dylib (compatibility version 6.0.0, current version 6.0.0)
	/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0)
	/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.0)
	/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)