Back to Multiple platform build/check report for BioC 3.18: simplified long |
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This page was generated on 2024-04-17 11:38:14 -0400 (Wed, 17 Apr 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4676 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4414 |
merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4437 |
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 1922/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Daniel Jones
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.1 Monterey / x86_64 | ERROR | ERROR | skipped | skipped | |||||||||
kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
To the developers/maintainers of the seqbias package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/seqbias.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: seqbias |
Version: 1.50.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL seqbias |
StartedAt: 2024-04-15 15:13:46 -0400 (Mon, 15 Apr 2024) |
EndedAt: 2024-04-15 15:13:58 -0400 (Mon, 15 Apr 2024) |
EllapsedTime: 11.7 seconds |
RetCode: 1 |
Status: ERROR |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL seqbias ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’ * installing *source* package ‘seqbias’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ $SEQBIAS_OBJ is [common.o miscmath.o pos_table.o kmer_matrix.o logger.o motif.o seqbias.o sequencing_bias.o twobitseq.o] $YAML_CPP_OBJ is [aliasmanager.o conversion.o directives.o emitfromevents.o emitter.o emitterstate.o emitterutils.o exp.o iterator.o nodebuilder.o node.o nodeownership.o null.o ostream.o parser.o regex.o scanner.o scanscalar.o scantag.o scantoken.o simplekey.o singledocparser.o stream.o tag.o] clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/zlibbioc/include' -I/opt/R/x86_64/include -Wall -Wextra -I. -fPIC -falign-functions=64 -Wall -g -O2 -c common.c -o common.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/zlibbioc/include' -I/opt/R/x86_64/include -Wall -Wextra -I. -fPIC -falign-functions=64 -Wall -g -O2 -c miscmath.c -o miscmath.o miscmath.c:21:12: warning: 'finite' is deprecated: first deprecated in macOS 10.9 - Use `isfinite((double)x)` instead. [-Wdeprecated-declarations] return finite(a) && 0.0 <= a && a <= 1.0; ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/math.h:752:12: note: 'finite' has been explicitly marked deprecated here extern int finite(double) ^ miscmath.c:47:9: warning: 'finite' is deprecated: first deprecated in macOS 10.9 - Use `isfinite((double)x)` instead. [-Wdeprecated-declarations] if (finite(u)) return x + log1p(-exp(u)); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/math.h:752:12: note: 'finite' has been explicitly marked deprecated here extern int finite(double) ^ 2 warnings generated. clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/zlibbioc/include' -I/opt/R/x86_64/include -Wall -Wextra -I. -fPIC -falign-functions=64 -Wall -g -O2 -c pos_table.c -o pos_table.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/zlibbioc/include' -I/opt/R/x86_64/include -Wall -Wextra -I. -fPIC -falign-functions=64 -Wall -g -O2 -c kmer_matrix.cpp -o kmer_matrix.o In file included from kmer_matrix.cpp:8: In file included from ./kmer_matrix.hpp:13: In file included from ./yaml-cpp/yaml.h:9: ./yaml-cpp/parser.h:45:8: error: no template named 'auto_ptr' in namespace 'std' std::auto_ptr<Scanner> m_pScanner; ~~~~~^ ./yaml-cpp/parser.h:46:8: error: no template named 'auto_ptr' in namespace 'std' std::auto_ptr<Directives> m_pDirectives; ~~~~~^ In file included from kmer_matrix.cpp:8: In file included from ./kmer_matrix.hpp:13: In file included from ./yaml-cpp/yaml.h:10: In file included from ./yaml-cpp/node.h:12: ./yaml-cpp/iterator.h:20:17: error: no template named 'auto_ptr' in namespace 'std' Iterator(std::auto_ptr<IterPriv> pData); ~~~~~^ ./yaml-cpp/iterator.h:36:8: error: no template named 'auto_ptr' in namespace 'std' std::auto_ptr<IterPriv> m_pData; ~~~~~^ In file included from kmer_matrix.cpp:8: In file included from ./kmer_matrix.hpp:13: In file included from ./yaml-cpp/yaml.h:10: ./yaml-cpp/node.h:43:8: error: no template named 'auto_ptr' in namespace 'std' std::auto_ptr<Node> Clone() const; ~~~~~^ ./yaml-cpp/node.h:115:8: error: no template named 'auto_ptr' in namespace 'std' std::auto_ptr<NodeOwnership> m_pOwnership; ~~~~~^ In file included from kmer_matrix.cpp:8: In file included from ./kmer_matrix.hpp:13: In file included from ./yaml-cpp/yaml.h:13: ./yaml-cpp/emitter.h:98:8: error: no template named 'auto_ptr' in namespace 'std' std::auto_ptr <EmitterState> m_pState; ~~~~~^ 7 errors generated. make: *** [kmer_matrix.o] Error 1 ERROR: compilation failed for package ‘seqbias’ * removing ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/seqbias’