Sunyoung Shin
| Snapshot Date: 2026-03-20 13:40 -0400 (Fri, 20 Mar 2026) |
| git_url: https://git.bioconductor.org/packages/atSNP |
| git_branch: devel |
| git_last_commit: 0b80e8a |
| git_last_commit_date: 2025-10-29 10:50:02 -0400 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-03-21 11:34 -0400 (Sat, 21 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" | 4866 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2026-03-20 r89666) -- "Unsuffered Consequences" | 4545 |
| 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 119/2368 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| atSNP 1.27.0 (landing page) Sunyoung Shin
| 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 atSNP in R Universe. | ||||||||||||||
|
To the developers/maintainers of the atSNP package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/atSNP.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: atSNP |
| Version: 1.27.0 |
| Command: rm -rf atSNP.buildbin-libdir && mkdir atSNP.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh atSNP_1.27.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R atSNP.buildbin-libdir |
| StartedAt: 2026-03-21 02:16:49 -0400 (Sat, 21 Mar 2026) |
| EndedAt: 2026-03-21 02:17:19 -0400 (Sat, 21 Mar 2026) |
| EllapsedTime: 29.5 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### rm -rf atSNP.buildbin-libdir && mkdir atSNP.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh atSNP_1.27.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R atSNP.buildbin-libdir
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=atSNP.buildbin-libdir atSNP_1.27.0.tar.gz'
>>>>>>>
* installing *source* package ‘atSNP’ ...
** this is package ‘atSNP’ version ‘1.27.0’
** using staged installation
** libs
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 -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 ImportanceSample.cpp -o ImportanceSample.o
ImportanceSample.cpp:77:9: warning: variable 'mean_sample' set but not used [-Wunused-but-set-variable]
77 | double mean_sample = 0;
| ^
ImportanceSample.cpp:78:9: warning: variable 'mean_adj_score' set but not used [-Wunused-but-set-variable]
78 | double mean_adj_score = 0;
| ^
ImportanceSample.cpp:229:19: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
229 | double prob_stat[motif_len];
| ^~~~~~~~~
ImportanceSample.cpp:229:19: note: read of non-const variable 'motif_len' is not allowed in a constant expression
ImportanceSample.cpp:222:6: note: declared here
222 | int motif_len = pwm.nrow();
| ^
ImportanceSample.cpp:309:6: warning: variable 'snp_id' set but not used [-Wunused-but-set-variable]
309 | int snp_id = 0;
| ^
ImportanceSample.cpp:347:14: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
347 | double heap[n_top];
| ^~~~~
ImportanceSample.cpp:347:14: note: read of non-const variable 'n_top' is not allowed in a constant expression
ImportanceSample.cpp:345:6: note: declared here
345 | int n_top = scores.size() * p + 1;
| ^
5 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -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 ImportanceSampleChange.cpp -o ImportanceSampleChange.o
ImportanceSampleChange.cpp:51:15: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
51 | double score[n_sample][4];
| ^~~~~~~~
ImportanceSampleChange.cpp:51:15: note: function parameter 'n_sample' with unknown value cannot be used in a constant expression
ImportanceSampleChange.cpp:16:219: note: declared here
16 | Rcpp::List p_value_change(NumericMatrix pwm, NumericMatrix wei_mat, NumericMatrix adj_mat, NumericVector stat_dist, NumericMatrix trans_mat, NumericVector scores, NumericVector pval_ratio, double score_percentile, int n_sample) {
| ^
ImportanceSampleChange.cpp:49:9: warning: variable 'mean_score' set but not used [-Wunused-but-set-variable]
49 | double mean_score = 0;
| ^
ImportanceSampleChange.cpp:120:17: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
120 | double adj_sum[motif_len];
| ^~~~~~~~~
ImportanceSampleChange.cpp:120:17: note: read of non-const variable 'motif_len' is not allowed in a constant expression
ImportanceSampleChange.cpp:117:6: note: declared here
117 | int motif_len = wei_mat.nrow();
| ^
ImportanceSampleChange.cpp:190:20: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
190 | double prob_start[motif_len];
| ^~~~~~~~~
ImportanceSampleChange.cpp:190:20: note: read of non-const variable 'motif_len' is not allowed in a constant expression
ImportanceSampleChange.cpp:183:6: note: declared here
183 | int motif_len = wei_mat.nrow();
| ^
ImportanceSampleChange.cpp:334:14: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
334 | double heap[n_top];
| ^~~~~
ImportanceSampleChange.cpp:334:14: note: read of non-const variable 'n_top' is not allowed in a constant expression
ImportanceSampleChange.cpp:332:6: note: declared here
332 | int n_top = scores.size() * p + 1;
| ^
5 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -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 ImportanceSampleDiff.cpp -o ImportanceSampleDiff.o
ImportanceSampleDiff.cpp:85:9: warning: variable 'mean_diff' set but not used [-Wunused-but-set-variable]
85 | double mean_diff = 0;
| ^
ImportanceSampleDiff.cpp:213:20: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
213 | double prob_start[motif_len];
| ^~~~~~~~~
ImportanceSampleDiff.cpp:213:20: note: read of non-const variable 'motif_len' is not allowed in a constant expression
ImportanceSampleDiff.cpp:206:6: note: declared here
206 | int motif_len = wei_mat.nrow();
| ^
ImportanceSampleDiff.cpp:338:14: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
338 | double heap[n_top];
| ^~~~~
ImportanceSampleDiff.cpp:338:14: note: read of non-const variable 'n_top' is not allowed in a constant expression
ImportanceSampleDiff.cpp:336:6: note: declared here
336 | int n_top = scores.size() * p + 1;
| ^
3 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -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 MotifScore.cpp -o MotifScore.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 atSNP.so ImportanceSample.o ImportanceSampleChange.o ImportanceSampleDiff.o MotifScore.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Users/biocbuild/bbs-3.23-bioc/meat/atSNP.buildbin-libdir/00LOCK-atSNP/00new/atSNP/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 (atSNP)
>>>>>>>
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR atSNP.buildbin-libdir/atSNP/libs/atSNP.so
>>>>>>>
>>>>>>> Paths before fix:
atSNP.buildbin-libdir/atSNP/libs/atSNP.so:
atSNP.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!