Hello ! I am receiving these messages. We haven't changed anything in the package and all of a sudden we are getting errors to the effect that the "vignette build failed" "because a connect error" I do not know what causes the error (Since we haven't changed anything in the package) and how to recreate it. Can you assist solving the issue ? Thanks! George Weingart PhD Huttenhower Lab Harvard School of Pubilc Health ---------- Forwarded message --------- From: <BBS-noreply at bioconductor.org> Date: Mon, Jun 24, 2019 at 11:36 AM Subject: banocc problems reported in the Multiple platform build/check report for BioC 3.9 To: <george.weingart at gmail.com> [This is an automatically generated email. Please don't reply.] Hi banocc maintainer, According to the Multiple platform build/check report for BioC 3.9, the banocc package has the following problem(s): o ERROR for 'R CMD build' on malbec2. See the details here: https://master.bioconductor.org/checkResults/3.9/bioc-LATEST/banocc/malbec2-buildsrc.html Please take the time to address this by committing and pushing changes to your package at git.bioconductor.org Notes: * This was the status of your package at the time this email was sent to you. Given that the online report is updated daily (in normal conditions) you could see something different when you visit the URL(s) above, especially if you do so several days after you received this email. * It is possible that the problems reported in this report are false positives, either because another package (from CRAN or Bioconductor) breaks your package (if yours depends on it) or because of a Build System problem. If this is the case, then you can ignore this email. * Please check the report again 24h after you've committed your changes to the package and make sure that all the problems have gone. * If you have questions about this report or need help with the maintenance of your package, please use the Bioc-devel mailing list: https://bioconductor.org/help/mailing-list/ (all package maintainers are requested to subscribe to this list) For immediate notification of package build status, please subscribe to your package's RSS feed. Information is at: https://bioconductor.org/developers/rss-feeds/ Thanks for contributing to the Bioconductor project!
[Bioc-devel] Fwd: banocc problems reported in the Multiple platform build/check report for BioC 3.9
2 messages · George Weingart, Vincent Carey
The error reported by the build system is reproducible on my mac running R CMD check on banocc_1.8.0.tar.gz The check error is pretty terse. I turned your vignette into an R script using knitr::purl and ran into
compiled_banocc_model <- rstan::stan_model(model_code =
banocc::banocc_model) DIAGNOSTIC(S) FROM PARSER: Info: integer division implicitly rounds to integer. Found int division: (P * (P - 1)) / 2 Positive values rounded down, negative values rounded up or down in platform-dependent way. *Error in compileCode(f, code, language = language, verbose = verbose) : * * Compilation ERROR, function(s)/method(s) not created! In file included from file15ef4c04043e.cpp:8:* *In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/model/model_header.hpp:4:* *In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math.hpp:4:* *In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:4:* *In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:5:* *In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/core/build_vari_array.hpp:4:* *In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4:* *In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/l* *In addition: Warning message:* *In system(cmd, intern = !verbose) :* * running command '/Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB file15ef4c04043e.cpp 2> file15ef4c04043e.cpp.err.txt' had status 1* Selection: I don't know how to interpret this as I don't make much use of rstan. Even though you have not changed anything in this version of banocc, other software that you rely on may be changing ... perhaps https://github.com/stan-dev/rstan/issues/666 is relevant? On Mon, Jun 24, 2019 at 10:27 PM George Weingart <george.weingart at gmail.com> wrote:
Hello ! I am receiving these messages. We haven't changed anything in the package and all of a sudden we are getting errors to the effect that the "vignette build failed" "because a connect error" I do not know what causes the error (Since we haven't changed anything in the package) and how to recreate it. Can you assist solving the issue ? Thanks! George Weingart PhD Huttenhower Lab Harvard School of Pubilc Health ---------- Forwarded message --------- From: <BBS-noreply at bioconductor.org> Date: Mon, Jun 24, 2019 at 11:36 AM Subject: banocc problems reported in the Multiple platform build/check report for BioC 3.9 To: <george.weingart at gmail.com> [This is an automatically generated email. Please don't reply.] Hi banocc maintainer, According to the Multiple platform build/check report for BioC 3.9, the banocc package has the following problem(s): o ERROR for 'R CMD build' on malbec2. See the details here: https://master.bioconductor.org/checkResults/3.9/bioc-LATEST/banocc/malbec2-buildsrc.html Please take the time to address this by committing and pushing changes to your package at git.bioconductor.org Notes: * This was the status of your package at the time this email was sent to you. Given that the online report is updated daily (in normal conditions) you could see something different when you visit the URL(s) above, especially if you do so several days after you received this email. * It is possible that the problems reported in this report are false positives, either because another package (from CRAN or Bioconductor) breaks your package (if yours depends on it) or because of a Build System problem. If this is the case, then you can ignore this email. * Please check the report again 24h after you've committed your changes to the package and make sure that all the problems have gone. * If you have questions about this report or need help with the maintenance of your package, please use the Bioc-devel mailing list: https://bioconductor.org/help/mailing-list/ (all package maintainers are requested to subscribe to this list) For immediate notification of package build status, please subscribe to your package's RSS feed. Information is at: https://bioconductor.org/developers/rss-feeds/ Thanks for contributing to the Bioconductor project! [[alternative HTML version deleted]]
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