| Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-12-04 12:01 -0500 (Thu, 04 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4878 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4624 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4669 |
| 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 1050/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| immApex 1.4.1 (landing page) Nick Borcherding
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | ERROR | OK | ERROR | |||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | ERROR | OK | ERROR | OK | |||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | ERROR | OK | ERROR | ||||||||||
|
To the developers/maintainers of the immApex package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/immApex.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: immApex |
| Version: 1.4.1 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL immApex |
| StartedAt: 2025-12-01 16:15:22 -0500 (Mon, 01 Dec 2025) |
| EndedAt: 2025-12-01 16:16:22 -0500 (Mon, 01 Dec 2025) |
| EllapsedTime: 59.2 seconds |
| RetCode: 1 |
| Status: ERROR |
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL immApex
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘immApex’ ...
** this is package ‘immApex’ version ‘1.4.1’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++17
using SDK: ‘MacOSX11.3.1.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/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++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c calculateMotif.cpp -o calculateMotif.o
calculateMotif.cpp:44:7: warning: variable 'nthreads' set but not used [-Wunused-but-set-variable]
int nthreads = std::max(1, nthreads_requested);
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c fastEditEdges.cpp -o fastEditEdges.o
fastEditEdges.cpp:265:7: warning: unused variable 'nthreads' [-Wunused-variable]
int nthreads = 1;
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o immApex.so RcppExports.o calculateMotif.o encodeSequences.o fastEditEdges.o -F/Library/Frameworks/R.framework/.. -framework R
ld: warning: ignoring file encodeSequences.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64
installing to /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-immApex/00new/immApex/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
Error: package or namespace load failed for ‘immApex’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-immApex/00new/immApex/libs/immApex.so':
dlopen(/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-immApex/00new/immApex/libs/immApex.so, 0x0006): symbol not found in flat namespace (__Z19encodeSequences_cppRKN4Rcpp6VectorILi16ENS_15PreserveStorageEEENSt3__112basic_stringIcNS5_11char_traitsIcEENS5_9allocatorIcEEEES2_NS_8NullableINS_6MatrixILi14ES1_EEEEcSB_ii)
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/immApex’