BUILD BIN results for sRACIPE on kjohnson3
To the developers/maintainers of the sRACIPE package:
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|
raw results
Summary
Command output
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### Running command:
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### rm -rf sRACIPE.buildbin-libdir && mkdir sRACIPE.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh sRACIPE_2.3.2.tar.gz /Library/Frameworks/R.framework/Resources/bin/R sRACIPE.buildbin-libdir
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=sRACIPE.buildbin-libdir sRACIPE_2.3.2.tar.gz'
>>>>>>>
* installing *source* package ‘sRACIPE’ ...
** this is package ‘sRACIPE’ version ‘2.3.2’
** 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 -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 -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 generateThresholds.cpp -o generateThresholds.o
generateThresholds.cpp:43:41: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
43 | size_t interactionsNumber[numberGene][interactionTypes];
| ^~~~~~~~~~~~~~~~
generateThresholds.cpp:43:41: note: read of non-const variable 'interactionTypes' is not allowed in a constant expression
generateThresholds.cpp:31:10: note: declared here
31 | size_t interactionTypes = static_cast<size_t>(hyperParameters[8]);
| ^
generateThresholds.cpp:43:29: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
43 | size_t interactionsNumber[numberGene][interactionTypes];
| ^~~~~~~~~~
generateThresholds.cpp:43:29: note: read of non-const variable 'numberGene' is not allowed in a constant expression
generateThresholds.cpp:38:10: note: declared here
38 | size_t numberGene=geneInteraction.nrow();
| ^
2 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 header.cpp -o header.o
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 limitcycle.cpp -o limitcycle.o
limitcycle.cpp:33:20: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
33 | double fX2_arr[number_gene]; //fX2_arr saves fX values for degradation part
| ^~~~~~~~~~~
limitcycle.cpp:33:20: note: function parameter 'number_gene' with unknown value cannot be used in a constant expression
limitcycle.cpp:21:26: note: declared here
21 | void cal_fX_E(const int &number_gene,
| ^
limitcycle.cpp:86:20: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
86 | double exprxGeneH1[number_gene]; //array for temp gene expression values
| ^~~~~~~~~~~
limitcycle.cpp:86:20: note: function parameter 'number_gene' with unknown value cannot be used in a constant expression
limitcycle.cpp:73:26: note: declared here
73 | void cal_fX_R(const int &number_gene,
| ^
limitcycle.cpp:87:20: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
87 | double exprxGeneH2[number_gene]; //array for temp gene expression values
| ^~~~~~~~~~~
limitcycle.cpp:87:20: note: function parameter 'number_gene' with unknown value cannot be used in a constant expression
limitcycle.cpp:73:26: note: declared here
73 | void cal_fX_R(const int &number_gene,
| ^
limitcycle.cpp:88:20: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
88 | double exprxGeneH3[number_gene]; //array for temp gene expression values
| ^~~~~~~~~~~
limitcycle.cpp:88:20: note: function parameter 'number_gene' with unknown value cannot be used in a constant expression
limitcycle.cpp:73:26: note: declared here
73 | void cal_fX_R(const int &number_gene,
| ^
limitcycle.cpp:89:20: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
89 | double exprxGeneH4[number_gene]; //array for temp gene expression values
| ^~~~~~~~~~~
limitcycle.cpp:89:20: note: function parameter 'number_gene' with unknown value cannot be used in a constant expression
limitcycle.cpp:73:26: note: declared here
73 | void cal_fX_R(const int &number_gene,
| ^
limitcycle.cpp:329:17: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
329 | int periodT[MaxPeriods]; //saves the periods
| ^~~~~~~~~~
limitcycle.cpp:329:17: note: function parameter 'MaxPeriods' with unknown value cannot be used in a constant expression
limitcycle.cpp:316:24: note: declared here
316 | const int &MaxPeriods,
| ^
limitcycle.cpp:327:9: warning: variable 'countSameMinDist' set but not used [-Wunused-but-set-variable]
327 | int countSameMinDist=0;
| ^
limitcycle.cpp:621:23: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
621 | int LC_period_arr[maxLCs];
| ^~~~~~
limitcycle.cpp:621:23: note: function parameter 'maxLCs' with unknown value cannot be used in a constant expression
limitcycle.cpp:610:25: note: declared here
610 | const int &maxLCs,
| ^
8 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 simulateGRC.cpp -o simulateGRC.o
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 steppers.cpp -o steppers.o
steppers.cpp:118:21: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
118 | double exprxGeneH[numberGene]; //array for temp gene expression values
| ^~~~~~~~~~
steppers.cpp:118:21: note: function parameter 'numberGene' with unknown value cannot be used in a constant expression
steppers.cpp:93:25: note: declared here
93 | const int &numberGene,
| ^
steppers.cpp:245:21: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
245 | double exprxGeneH[numberGene]; //array for temp gene expression values
| ^~~~~~~~~~
steppers.cpp:245:21: note: function parameter 'numberGene' with unknown value cannot be used in a constant expression
steppers.cpp:219:25: note: declared here
219 | const int &numberGene,
| ^
steppers.cpp:246:20: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
246 | double currNoise[numberGene]; //array for temp gene expression values
| ^~~~~~~~~~
steppers.cpp:246:20: note: function parameter 'numberGene' with unknown value cannot be used in a constant expression
steppers.cpp:219:25: note: declared here
219 | const int &numberGene,
| ^
steppers.cpp:381:20: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
381 | double exprxGeneH1[numberGene]; //array for temp gene expression values
| ^~~~~~~~~~
steppers.cpp:381:20: note: function parameter 'numberGene' with unknown value cannot be used in a constant expression
steppers.cpp:359:25: note: declared here
359 | const int &numberGene,
| ^
steppers.cpp:382:20: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
382 | double exprxGeneH2[numberGene]; //array for temp gene expression values
| ^~~~~~~~~~
steppers.cpp:382:20: note: function parameter 'numberGene' with unknown value cannot be used in a constant expression
steppers.cpp:359:25: note: declared here
359 | const int &numberGene,
| ^
steppers.cpp:383:20: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
383 | double exprxGeneH3[numberGene]; //array for temp gene expression values
| ^~~~~~~~~~
steppers.cpp:383:20: note: function parameter 'numberGene' with unknown value cannot be used in a constant expression
steppers.cpp:359:25: note: declared here
359 | const int &numberGene,
| ^
steppers.cpp:384:20: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
384 | double exprxGeneH4[numberGene]; //array for temp gene expression values
| ^~~~~~~~~~
steppers.cpp:384:20: note: function parameter 'numberGene' with unknown value cannot be used in a constant expression
steppers.cpp:359:25: note: declared here
359 | const int &numberGene,
| ^
steppers.cpp:669:21: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
669 | double exprxGeneH[numberGene]; //array for temp gene expression values
| ^~~~~~~~~~
steppers.cpp:669:21: note: function parameter 'numberGene' with unknown value cannot be used in a constant expression
steppers.cpp:648:26: note: declared here
648 | const int &numberGene,
| ^
steppers.cpp:670:22: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
670 | double exprxGeneH1[numberGene]; //array for temp gene expression values
| ^~~~~~~~~~
steppers.cpp:670:22: note: function parameter 'numberGene' with unknown value cannot be used in a constant expression
steppers.cpp:648:26: note: declared here
648 | const int &numberGene,
| ^
steppers.cpp:671:22: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
671 | double exprxGeneH2[numberGene]; //array for temp gene expression values
| ^~~~~~~~~~
steppers.cpp:671:22: note: function parameter 'numberGene' with unknown value cannot be used in a constant expression
steppers.cpp:648:26: note: declared here
648 | const int &numberGene,
| ^
steppers.cpp:672:22: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
672 | double exprxGeneH3[numberGene]; //array for temp gene expression values
| ^~~~~~~~~~
steppers.cpp:672:22: note: function parameter 'numberGene' with unknown value cannot be used in a constant expression
steppers.cpp:648:26: note: declared here
648 | const int &numberGene,
| ^
steppers.cpp:673:22: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
673 | double exprxGeneH4[numberGene]; //array for temp gene expression values
| ^~~~~~~~~~
steppers.cpp:673:22: note: function parameter 'numberGene' with unknown value cannot be used in a constant expression
steppers.cpp:648:26: note: declared here
648 | const int &numberGene,
| ^
steppers.cpp:674:22: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
674 | double exprxGeneH5[numberGene]; //array for temp gene expression values
| ^~~~~~~~~~
steppers.cpp:674:22: note: function parameter 'numberGene' with unknown value cannot be used in a constant expression
steppers.cpp:648:26: note: declared here
648 | const int &numberGene,
| ^
steppers.cpp:675:22: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
675 | double exprxGeneH6[numberGene]; //array for temp gene expression values
| ^~~~~~~~~~
steppers.cpp:675:22: note: function parameter 'numberGene' with unknown value cannot be used in a constant expression
steppers.cpp:648:26: note: declared here
648 | const int &numberGene,
| ^
steppers.cpp:676:22: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
676 | double exprxGeneH7[numberGene]; //array for temp gene expression values
| ^~~~~~~~~~
steppers.cpp:676:22: note: function parameter 'numberGene' with unknown value cannot be used in a constant expression
steppers.cpp:648:26: note: declared here
648 | const int &numberGene,
| ^
15 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 steppersConv.cpp -o steppersConv.o
steppersConv.cpp:30:21: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
30 | double exprxGeneH[numberGene]; //array for temp gene expression values
| ^~~~~~~~~~
steppersConv.cpp:30:21: note: function parameter 'numberGene' with unknown value cannot be used in a constant expression
steppersConv.cpp:10:25: note: declared here
10 | const int &numberGene,
| ^
steppersConv.cpp:37:10: warning: variable 'i' set but not used [-Wunused-but-set-variable]
37 | double i=0.0;
| ^
steppersConv.cpp:156:20: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
156 | double exprxGeneH1[numberGene]; //array for temp gene expression values
| ^~~~~~~~~~
steppersConv.cpp:156:20: note: function parameter 'numberGene' with unknown value cannot be used in a constant expression
steppersConv.cpp:136:25: note: declared here
136 | const int &numberGene,
| ^
steppersConv.cpp:157:20: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
157 | double exprxGeneH2[numberGene]; //array for temp gene expression values
| ^~~~~~~~~~
steppersConv.cpp:157:20: note: function parameter 'numberGene' with unknown value cannot be used in a constant expression
steppersConv.cpp:136:25: note: declared here
136 | const int &numberGene,
| ^
steppersConv.cpp:158:20: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
158 | double exprxGeneH3[numberGene]; //array for temp gene expression values
| ^~~~~~~~~~
steppersConv.cpp:158:20: note: function parameter 'numberGene' with unknown value cannot be used in a constant expression
steppersConv.cpp:136:25: note: declared here
136 | const int &numberGene,
| ^
steppersConv.cpp:159:20: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
159 | double exprxGeneH4[numberGene]; //array for temp gene expression values
| ^~~~~~~~~~
steppersConv.cpp:159:20: note: function parameter 'numberGene' with unknown value cannot be used in a constant expression
steppersConv.cpp:136:25: note: declared here
136 | const int &numberGene,
| ^
steppersConv.cpp:170:8: warning: variable 'i' set but not used [-Wunused-but-set-variable]
170 | double i=0.0;
| ^
steppersConv.cpp:396:21: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
396 | double exprxGeneH[numberGene]; //array for temp gene expression values
| ^~~~~~~~~~
steppersConv.cpp:396:21: note: function parameter 'numberGene' with unknown value cannot be used in a constant expression
steppersConv.cpp:376:26: note: declared here
376 | const int &numberGene,
| ^
steppersConv.cpp:397:22: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
397 | double exprxGeneH1[numberGene]; //array for temp gene expression values
| ^~~~~~~~~~
steppersConv.cpp:397:22: note: function parameter 'numberGene' with unknown value cannot be used in a constant expression
steppersConv.cpp:376:26: note: declared here
376 | const int &numberGene,
| ^
steppersConv.cpp:398:22: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
398 | double exprxGeneH2[numberGene]; //array for temp gene expression values
| ^~~~~~~~~~
steppersConv.cpp:398:22: note: function parameter 'numberGene' with unknown value cannot be used in a constant expression
steppersConv.cpp:376:26: note: declared here
376 | const int &numberGene,
| ^
steppersConv.cpp:399:22: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
399 | double exprxGeneH3[numberGene]; //array for temp gene expression values
| ^~~~~~~~~~
steppersConv.cpp:399:22: note: function parameter 'numberGene' with unknown value cannot be used in a constant expression
steppersConv.cpp:376:26: note: declared here
376 | const int &numberGene,
| ^
steppersConv.cpp:400:22: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
400 | double exprxGeneH4[numberGene]; //array for temp gene expression values
| ^~~~~~~~~~
steppersConv.cpp:400:22: note: function parameter 'numberGene' with unknown value cannot be used in a constant expression
steppersConv.cpp:376:26: note: declared here
376 | const int &numberGene,
| ^
steppersConv.cpp:401:22: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
401 | double exprxGeneH5[numberGene]; //array for temp gene expression values
| ^~~~~~~~~~
steppersConv.cpp:401:22: note: function parameter 'numberGene' with unknown value cannot be used in a constant expression
steppersConv.cpp:376:26: note: declared here
376 | const int &numberGene,
| ^
steppersConv.cpp:402:22: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
402 | double exprxGeneH6[numberGene]; //array for temp gene expression values
| ^~~~~~~~~~
steppersConv.cpp:402:22: note: function parameter 'numberGene' with unknown value cannot be used in a constant expression
steppersConv.cpp:376:26: note: declared here
376 | const int &numberGene,
| ^
steppersConv.cpp:403:22: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
403 | double exprxGeneH7[numberGene]; //array for temp gene expression values
| ^~~~~~~~~~
steppersConv.cpp:403:22: note: function parameter 'numberGene' with unknown value cannot be used in a constant expression
steppersConv.cpp:376:26: note: declared here
376 | const int &numberGene,
| ^
steppersConv.cpp:422:10: warning: variable 'i' set but not used [-Wunused-but-set-variable]
422 | double i=0.0;
| ^
16 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 sRACIPE.so RcppExports.o generateThresholds.o header.o limitcycle.o simulateGRC.o steppers.o steppersConv.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Users/biocbuild/bbs-3.23-bioc/meat/sRACIPE.buildbin-libdir/00LOCK-sRACIPE/00new/sRACIPE/libs
** R
** data
*** moving datasets to lazyload DB
** 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 (sRACIPE)
>>>>>>>
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR sRACIPE.buildbin-libdir/sRACIPE/libs/sRACIPE.so
>>>>>>>
>>>>>>> Paths before fix:
sRACIPE.buildbin-libdir/sRACIPE/libs/sRACIPE.so:
sRACIPE.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!
