| Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-05-01 11:35:47 -0400 (Wed, 01 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4753 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" | 4518 |
| 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 270/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Thomas D. Sherman
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | ERROR | ERROR | skipped | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK |  | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the CancerInSilico package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CancerInSilico.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: CancerInSilico |
| Version: 2.24.0 |
| Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL CancerInSilico |
| StartedAt: 2024-04-30 21:34:58 -0400 (Tue, 30 Apr 2024) |
| EndedAt: 2024-04-30 21:35:44 -0400 (Tue, 30 Apr 2024) |
| EllapsedTime: 46.3 seconds |
| RetCode: 1 |
| Status: ERROR |
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### Running command:
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### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL CancerInSilico
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* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘CancerInSilico’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c RunModel.cpp -o RunModel.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c CellModels/DrasdoHohmeModel.cpp -o CellModels/DrasdoHohmeModel.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c OffLatticeModel/OffLatticeCell.cpp -o OffLatticeModel/OffLatticeCell.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c OffLatticeModel/OffLatticeCellBasedModel.cpp -o OffLatticeModel/OffLatticeCellBasedModel.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c OffLatticeModel/OffLatticeRadiusSolver.cpp -o OffLatticeModel/OffLatticeRadiusSolver.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c Core/Cell.cpp -o Core/Cell.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c Core/CellBasedModel.cpp -o Core/CellBasedModel.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c Core/CellType.cpp -o Core/CellType.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c Core/Drug.cpp -o Core/Drug.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c Core/Random.cpp -o Core/Random.o
In file included from /home/biocbuild/bbs-3.19-bioc/R/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/biocbuild/bbs-3.19-bioc/R/site-library/BH/include/boost/mpl/arg.hpp:25,
from /home/biocbuild/bbs-3.19-bioc/R/site-library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/biocbuild/bbs-3.19-bioc/R/site-library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /home/biocbuild/bbs-3.19-bioc/R/site-library/BH/include/boost/iterator/iterator_concepts.hpp:10,
from /home/biocbuild/bbs-3.19-bioc/R/site-library/BH/include/boost/range/concepts.hpp:20,
from /home/biocbuild/bbs-3.19-bioc/R/site-library/BH/include/boost/range/size_type.hpp:20,
from /home/biocbuild/bbs-3.19-bioc/R/site-library/BH/include/boost/range/size.hpp:21,
from /home/biocbuild/bbs-3.19-bioc/R/site-library/BH/include/boost/random/hyperexponential_distribution.hpp:29,
from /home/biocbuild/bbs-3.19-bioc/R/site-library/BH/include/boost/random.hpp:70,
from Core/Random.cpp:3:
/home/biocbuild/bbs-3.19-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^~~~~~~~~~~~~~~~~~~
195 | assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
196 | );
| ~
/home/biocbuild/bbs-3.19-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:194:21: note: remove parentheses
194 | failed ************ (Pred::************
| ^~~~~~~~~~~~~~~~~~~
| -
195 | assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
196 | );
| ~
| -
/home/biocbuild/bbs-3.19-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
200 | assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
201 | );
| ~
/home/biocbuild/bbs-3.19-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:199:21: note: remove parentheses
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| -
200 | assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
201 | );
| ~
| -
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c test-runner.cpp -o test-runner.o
In file included from /usr/include/signal.h:328,
from Tests/catch.h:6450,
from test-runner.cpp:2:
Tests/catch.h:6473:33: error: size of array ‘altStackMem’ is not an integral constant-expression
6473 | static char altStackMem[SIGSTKSZ];
| ^~~~~~~~
Tests/catch.h:6524:45: error: size of array ‘altStackMem’ is not an integral constant-expression
6524 | char FatalConditionHandler::altStackMem[SIGSTKSZ] = {};
| ^~~~~~~~
make: *** [/home/biocbuild/bbs-3.19-bioc/R/etc/Makeconf:202: test-runner.o] Error 1
ERROR: compilation failed for package ‘CancerInSilico’
* removing ‘/home/biocbuild/bbs-3.19-bioc/R/site-library/CancerInSilico’