Zheng Wei
| Snapshot Date: 2026-03-22 13:40 -0400 (Sun, 22 Mar 2026) |
| git_url: https://git.bioconductor.org/packages/esATAC |
| git_branch: devel |
| git_last_commit: f884d0f |
| git_last_commit_date: 2026-03-22 02:26:00 -0400 (Sun, 22 Mar 2026) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-03-23 11:35 -0400 (Mon, 23 Mar 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2026-03-05 r89546) -- "Unsuffered Consequences" | 4868 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2026-03-20 r89666) -- "Unsuffered Consequences" | 4548 |
| 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 703/2368 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| esATAC 1.33.1 (landing page) Zheng Wei
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | ERROR | |||||||||
| See other builds for esATAC in R Universe. | ||||||||||||||
|
To the developers/maintainers of the esATAC package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/esATAC.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. |
| Package: esATAC |
| Version: 1.33.1 |
| Command: rm -rf esATAC.buildbin-libdir && mkdir esATAC.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh esATAC_1.33.1.tar.gz /Library/Frameworks/R.framework/Resources/bin/R esATAC.buildbin-libdir |
| StartedAt: 2026-03-22 22:49:48 -0400 (Sun, 22 Mar 2026) |
| EndedAt: 2026-03-22 22:50:28 -0400 (Sun, 22 Mar 2026) |
| EllapsedTime: 40.7 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### rm -rf esATAC.buildbin-libdir && mkdir esATAC.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh esATAC_1.33.1.tar.gz /Library/Frameworks/R.framework/Resources/bin/R esATAC.buildbin-libdir
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=esATAC.buildbin-libdir esATAC_1.33.1.tar.gz'
>>>>>>>
Warning: SystemRequirements specified C++11: support has been removed
* installing *source* package ‘esATAC’ ...
** this is package ‘esATAC’ version ‘1.33.1’
** using staged installation
** libs
specified C++11
using C++ compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’
using SDK: ‘MacOSX26.2.sdk’
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNDEBUG -DPLF_SYS_LINUX -DR_EVN_FLAG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c BedLine.cpp -o BedLine.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNDEBUG -DPLF_SYS_LINUX -DR_EVN_FLAG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c BedUtils.cpp -o BedUtils.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNDEBUG -DPLF_SYS_LINUX -DR_EVN_FLAG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ChrDivi.cpp -o ChrDivi.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNDEBUG -DPLF_SYS_LINUX -DR_EVN_FLAG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c CutCountPre.cpp -o CutCountPre.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNDEBUG -DPLF_SYS_LINUX -DR_EVN_FLAG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c CutSiteCount.cpp -o CutSiteCount.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNDEBUG -DPLF_SYS_LINUX -DR_EVN_FLAG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c LibComplexQC.cpp -o LibComplexQC.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNDEBUG -DPLF_SYS_LINUX -DR_EVN_FLAG -I'/Library/Frameworks/R.framework/Versions/4.6/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 -DNDEBUG -DPLF_SYS_LINUX -DR_EVN_FLAG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SortBed.cpp -o SortBed.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNDEBUG -DPLF_SYS_LINUX -DR_EVN_FLAG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c rcpp_wrapper.cpp -o rcpp_wrapper.o
rcpp_wrapper.cpp:334:7: warning: variable 'tmp_k' set but not used [-Wunused-but-set-variable]
334 | int tmp_k;
| ^
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNDEBUG -DPLF_SYS_LINUX -DR_EVN_FLAG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c renamer.cpp -o renamer.o
renamer.cpp:9:15: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
9 | char line[BUFFER_LENGTH];
| ^~~~~~~~~~~~~
renamer.cpp:9:15: note: implicit use of 'this' pointer is only allowed within the evaluation of a call to a 'constexpr' member function
renamer.cpp:23:15: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
23 | char line[BUFFER_LENGTH];
| ^~~~~~~~~~~~~
renamer.cpp:23:15: note: implicit use of 'this' pointer is only allowed within the evaluation of a call to a 'constexpr' member function
renamer.cpp:41:15: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
41 | char line[BUFFER_LENGTH];
| ^~~~~~~~~~~~~
renamer.cpp:41:15: note: implicit use of 'this' pointer is only allowed within the evaluation of a call to a 'constexpr' member function
3 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNDEBUG -DPLF_SYS_LINUX -DR_EVN_FLAG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c sam2bed.cc -o sam2bed.o
sam2bed.cc:125:16: warning: unused variable 'xspm' [-Wunused-variable]
125 | regmatch_t xspm[1];
| ^~~~
sam2bed.cc:294:16: warning: unused variable 'xspm' [-Wunused-variable]
294 | regmatch_t xspm[1];
| ^~~~
2 warnings generated.
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 esATAC.so BedLine.o BedUtils.o ChrDivi.o CutCountPre.o CutSiteCount.o LibComplexQC.o RcppExports.o SortBed.o rcpp_wrapper.o renamer.o sam2bed.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Users/biocbuild/bbs-3.23-bioc/meat/esATAC.buildbin-libdir/00LOCK-esATAC/00new/esATAC/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 (esATAC)
>>>>>>>
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR esATAC.buildbin-libdir/esATAC/libs/esATAC.so
>>>>>>>
>>>>>>> Paths before fix:
esATAC.buildbin-libdir/esATAC/libs/esATAC.so:
esATAC.so (compatibility version 0.0.0, current version 0.0.0)
/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libR.dylib (compatibility version 4.6.0, current version 4.6.0)
/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 2000.67.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1356.0.0)
>>>>>>> Fix with install_name_tool:
ERROR: R installation problem: File /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/lib/libR.dylib not found!