Hi, Following the lead of the R folks, we've started to build and check Bioconductor packages on El Capitan using the compilers that Simon made available here:
https://r.research.att.com/libs/ The cran-usr-local-darwin15.6-20170320.tar.gz tarball contains clang 4.0.0 that is used to compile package C and C++ code. Our latest daily build report can be found here: https://bioconductor.org/checkResults/3.5/bioc-LATEST/ The builder running El Capitan + clang 4.0.0 is veracruz2: veracruz2:~ biocbuild$ clang -v clang version 4.0.0 (tags/RELEASE_400/final) Target: x86_64-apple-darwin15.6.0 Thread model: posix InstalledDir: /usr/local/clang+llvm-4.0.0-x86_64-apple-darwin/bin toluca2 is another builder that has the same specs than veracruz2 but is running Mavericks and uses the clang compiler from Apple's Command Line Developer Tools: toluca2:~ biocbuild$ clang -v Apple LLVM version 6.0 (clang-600.0.57) (based on LLVM 3.5svn) Target: x86_64-apple-darwin13.4.0 Thread model: posix We're observing significantly slower compiling times on veracruz2 compared to toluca2. For example, looking at packages where 'R CMD INSTALL' time is dominated by compilation: 683.0 vs 483.6 seconds for the mzR package (C++ code): https://bioconductor.org/checkResults/3.5/bioc-LATEST/mzR/veracruz2-install.html https://bioconductor.org/checkResults/3.5/bioc-LATEST/mzR/toluca2-install.html 378.3 vs 299.9 seconds for the flowWorkspace package (C++ code): https://bioconductor.org/checkResults/3.5/bioc-LATEST/flowWorkspace/veracruz2-install.html https://bioconductor.org/checkResults/3.5/bioc-LATEST/flowWorkspace/toluca2-install.html 186.3 vs 126.2 seconds for the rTANDEM package (C++ code): https://bioconductor.org/checkResults/3.5/bioc-LATEST/rTANDEM/veracruz2-install.html https://bioconductor.org/checkResults/3.5/bioc-LATEST/rTANDEM/toluca2-install.html 109.4 vs 80.8 seconds for the rhdf5 package (C code): https://bioconductor.org/checkResults/3.5/bioc-LATEST/rhdf5/veracruz2-install.html https://bioconductor.org/checkResults/3.5/bioc-LATEST/rhdf5/toluca2-install.html etc... The slowdown seems pretty consistent with a time_on_veracruz2 / time_on_toluca2 ratio varying between 1.25 and 1.5. In addition to clang 4.0.0 we also have the clang compiler from Apple's Command Line Developer Tools on veracruz2: veracruz2:sandbox biocbuild$ /usr/bin/clang -v Apple LLVM version 8.0.0 (clang-800.0.42.1) Target: x86_64-apple-darwin15.6.0 Thread model: posix InstalledDir: /Library/Developer/CommandLineTools/usr/bin If I switch between the 2 compilers on veracruz2 I observe a similar slowdown i.e. the time_with_clang_4.0.0 / time_with_Apple_clang ratio is about the same as the previous ratios. The only difference this time is the compiler. I was wondering if anybody else observed this or if this a known "issue" with clang 4.0.0. On the other hand the good news is that packages with no native code seem to build and check slightly faster on veracruz2 than on toluca2. For example: https://bioconductor.org/checkResults/3.5/bioc-LATEST/GenomicFeatures/veracruz2-buildsrc.html https://bioconductor.org/checkResults/3.5/bioc-LATEST/GenomicFeatures/toluca2-buildsrc.html https://bioconductor.org/checkResults/3.5/bioc-LATEST/GenomicFeatures/veracruz2-checksrc.html https://bioconductor.org/checkResults/3.5/bioc-LATEST/GenomicFeatures/toluca2-checksrc.html Note that R was compiled with Apple's clang on toluca2 and with clang 4.0.0 on veracruz2. So is the deal that clang 4.0.0 produces more efficient code at the cost of longer compilation times? Cheers, H. -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fredhutch.org Phone: (206) 667-5791 Fax: (206) 667-1319 _______________________________________________ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
