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This page was generated on 2025-03-19 11:46 -0400 (Wed, 19 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences" 4742
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" 4545
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4576
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4528
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4459
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 1670/2313HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ramr 1.15.2  (landing page)
Oleksii Nikolaienko
Snapshot Date: 2025-03-18 13:40 -0400 (Tue, 18 Mar 2025)
git_url: https://git.bioconductor.org/packages/ramr
git_branch: devel
git_last_commit: f361f7c
git_last_commit_date: 2025-03-06 10:21:44 -0400 (Thu, 06 Mar 2025)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  

BUILD BIN results for ramr on kjohnson3

To the developers/maintainers of the ramr package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ramr.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: ramr
Version: 1.15.2
Command: rm -rf ramr.buildbin-libdir && mkdir ramr.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh ramr_1.15.2.tar.gz /Library/Frameworks/R.framework/Resources/bin/R ramr.buildbin-libdir
StartedAt: 2025-03-18 22:38:55 -0400 (Tue, 18 Mar 2025)
EndedAt: 2025-03-18 22:39:13 -0400 (Tue, 18 Mar 2025)
EllapsedTime: 18.4 seconds
RetCode: 0
Status:   OK  
PackageFile: ramr_1.15.2.tgz
PackageFileSize: 2.849 MiB

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf ramr.buildbin-libdir && mkdir ramr.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh ramr_1.15.2.tar.gz /Library/Frameworks/R.framework/Resources/bin/R ramr.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=ramr.buildbin-libdir ramr_1.15.2.tar.gz'
>>>>>>> 

* installing *source* package ‘ramr’ ...
** this is package ‘ramr’ version ‘1.15.2’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using C++20
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c rcpp_compute_logp.cpp -o rcpp_compute_logp.o
rcpp_compute_logp.cpp:150:16: warning: unused variable 'nthreads' [-Wunused-variable]
  const size_t nthreads = thr->size() - 1;                                      // 'thr' always starts with 0 and ends with 'nrow'
               ^
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c rcpp_compute_xiqr.cpp -o rcpp_compute_xiqr.o
rcpp_compute_xiqr.cpp:37:16: warning: unused variable 'nthreads' [-Wunused-variable]
  const size_t nthreads = thr->size() - 1;                                      // 'thr' always starts with 0 and ends with 'nrow'
               ^
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c rcpp_create_granges.cpp -o rcpp_create_granges.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c rcpp_filter_threshold.cpp -o rcpp_filter_threshold.o
rcpp_filter_threshold.cpp:32:16: warning: unused variable 'nthreads' [-Wunused-variable]
  const size_t nthreads = thr->size() - 1;                                      // 'thr' always starts with 0 and ends with 'nrow'
               ^
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c rcpp_fit_beta.cpp -o rcpp_fit_beta.o
rcpp_fit_beta.cpp:28:16: warning: unused variable 'nthreads' [-Wunused-variable]
  const size_t nthreads = thr->size() - 1;                                      // 'thr' always starts with 0 and ends with 'nrow'
               ^
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c rcpp_fit_betabinom.cpp -o rcpp_fit_betabinom.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c rcpp_fit_binom.cpp -o rcpp_fit_binom.o
rcpp_fit_binom.cpp:33:16: warning: unused variable 'nthreads' [-Wunused-variable]
  const size_t nthreads = thr->size() - 1;                                      // 'thr' always starts with 0 and ends with 'nrow'
               ^
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c rcpp_generate_random_values.cpp -o rcpp_generate_random_values.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c rcpp_get_iqr.cpp -o rcpp_get_iqr.o
rcpp_get_iqr.cpp:35:16: warning: unused variable 'nthreads' [-Wunused-variable]
  const size_t nthreads = thr->size() - 1;                                      // 'thr' always starts with 0 and ends with 'nrow'
               ^
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c rcpp_get_meanvar.cpp -o rcpp_get_meanvar.o
rcpp_get_meanvar.cpp:62:16: warning: unused variable 'nthreads' [-Wunused-variable]
  const size_t nthreads = thr->size() - 1;                                      // 'thr' always starts with 0 and ends with 'nrow'
               ^
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c rcpp_helper_functions.cpp -o rcpp_helper_functions.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c rcpp_prepare_data.cpp -o rcpp_prepare_data.o
rcpp_prepare_data.cpp:87:16: warning: unused variable 'nthreads' [-Wunused-variable]
  const size_t nthreads = thr->size() - 1;                                      // 'thr' always starts with 0 and ends with 'nrow'
               ^
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c rcpp_test_omp.cpp -o rcpp_test_omp.o
clang++ -arch arm64 -std=gnu++20 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o ramr.so RcppExports.o rcpp_compute_logp.o rcpp_compute_xiqr.o rcpp_create_granges.o rcpp_filter_threshold.o rcpp_fit_beta.o rcpp_fit_betabinom.o rcpp_fit_binom.o rcpp_generate_random_values.o rcpp_get_iqr.o rcpp_get_meanvar.o rcpp_helper_functions.o rcpp_prepare_data.o rcpp_test_omp.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.21-bioc/meat/ramr.buildbin-libdir/00LOCK-ramr/00new/ramr/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 (ramr)


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

>>>>>>> Paths before fix:
ramr.buildbin-libdir/ramr/libs/ramr.so:
	ramr.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.0)
	/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/4.5-arm64/Resources/lib/libgcc_s.1.1.dylib" "ramr.buildbin-libdir/ramr/libs/ramr.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libgfortran.5.dylib" "ramr.buildbin-libdir/ramr/libs/ramr.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libquadmath.0.dylib" "ramr.buildbin-libdir/ramr/libs/ramr.so"

>>>>>>> Paths after fix:
ramr.buildbin-libdir/ramr/libs/ramr.so:
	ramr.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.0)
	/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)