Hello, My Bioconductor Package ‘LymphoSeq’ received the following build error<http://bioconductor.org/checkResults/3.5/bioc-LATEST/LymphoSeq/veracruz2-buildsrc.html> on veracruz2:
ERROR: dependency ‘msa’ is not available for package ‘LymphoSeq’ Indeed, ‘msa’ is one of my package dependencies. The package was built under the latest version of MacOS on my computer and I have never see this error before. I am wondering if this problem is related to this thread. Will my package not be pushed to the release version because of this error? Thank you, David On Apr 14, 2017, at 12:50 PM, Martin Morgan <martin.mor...@roswellpark.org<mailto:martin.mor...@roswellpark.org>> wrote: On 04/07/2017 11:26 AM, Ulrich Bodenhofer wrote: Hi, The devel version of our package 'msa' currently does not compile on veracruz2 (R 3.4.0 alpha under OS X 10.11.6 El Capitan), but it seems to work on toluca2 (R-devel on OS X 10.9.5 Mavericks). I also checked on my Mac at home (R 3.3.3 under macOS 10.12.3 Sierra using the very latest version of Xcode), and it also compiles without any problems. The error stems from a conflicting definition of the math functions 'log2' and 'log10' in the source code of the ClustalOmega library which is integrated into 'msa' (the same error appears for the inline definition of 'log10'): hhalign/util-C.h:53:14: error: 'log2' is missing exception specification 'throw()' inline float log2(float x) {return (x<=0? (float)(-100000):1.442695041*log(x));} Any ideas? 'log2' and 'log10' are defined in the standard math library. The definitions work well on Linux along with '#include <cmath>' , while Windows requires '#include <math.h>'. So far, '#include <cmath>' also worked on Mac OS, but it seems that now, on veracruz2, neither one nor the other works. Any thoughts? Is this something I should care about or is there something exotic about veracruz2 such that I can simply ignore this issue? I guess the minimal reproducible example is $ cat log2.cpp #include <cmath> // or <math.h> inline float log2(float x) {return (x<=0? (float)(-100000):1.442695041*log(x));} $ R CMD SHLIB log2.cpp clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/opt/X11/include -fPIC -Wall -g -O2 -c log2.cpp -o log2.o log2.cpp:3:14: error: 'log2' is missing exception specification 'throw()' inline float log2(float x) {return (x<=0? (float)(-100000):1.442695041*... ^ throw() /usr/local/clang+llvm-4.0.0-x86_64-apple-darwin/bin/../include/c++/v1/math.h:1221:46: note: previous declaration is here inline _LIBCPP_INLINE_VISIBILITY float log2(float __lcpp_x) _NOEX... ^ 1 error generated. make: *** [log2.o] Error 1 It could be that final changes in the compiler used by R to build mac binaries could change, but at this point I think it would be prudent to implement a work-around; veracruz2 will be our main macOS builder for the release, and if the package is not building on it then the package will not be available to macOS users. I am not enough of a C++ programmer to be able to give concrete advice on how the problem should be addressed; maybe others on the list have insight...? Martin Thanks a lot in advance and best regards, Ulrich _______________________________________________ Bioc-devel@r-project.org<mailto:Bioc-devel@r-project.org> mailing list https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=HjFin7ZZwuYWdlO8wvE3KmoPwjRiq-bV_UKHWdKLLP4&m=q0lYA_4-5lp09oKeciuTpv2FDm4ZddBJHxUO8yw2Tys&s=jeKQlveT4DG2tLfM8ykFwfCXpfvgOHoAQDuZ_1hjVVY&e= This email message may contain legally privileged and/or...{{dropped:2}} _______________________________________________ Bioc-devel@r-project.org<mailto:Bioc-devel@r-project.org> mailing list https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=HjFin7ZZwuYWdlO8wvE3KmoPwjRiq-bV_UKHWdKLLP4&m=q0lYA_4-5lp09oKeciuTpv2FDm4ZddBJHxUO8yw2Tys&s=jeKQlveT4DG2tLfM8ykFwfCXpfvgOHoAQDuZ_1hjVVY&e= [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel