Dear Bioconductor Developers, I recently contributed a package `normR` for calling enrichment and differences in ChIP-seq data (http://bioconductor.org/packages/normr/). To test the functionality of the package, I used `testthat`. All the tests run well when using `testthat::test()`, `R CMD build` or `R CMD check`. However, the `normr` package landing package (http://bioconductor.org/packages/normr/) reports "Test coverage: unknown". I installed `covr` on my local machine and ran `covr::package_coverage()`. It seems to work fine: > normr Coverage: 77.50% > R/NormRCountConfig.R: 50.00% > R/methods.R: 64.32% > src/em.cpp: 79.27% > R/NormRFit.R: 87.33% > src/normr_init.c: 100.00% Is "Test Coverage: unknown" related to the Bioconductor build system not being able to build my package on Linux? (I filed this in an earlier post related to the unavailability of automake-1.14 for Rhtslib 1.5.3 installation) Thank you very much, Johannes Helmuth
[Bioc-devel] normr 0.99.5 Test Coverage "unknown"
3 messages · Johannes Helmuth, Kasper Daniel Hansen
Without knowing the details it seems self-evident to me that the build system can do the coverage report if the package doesn't build. Best, Kasper On Tue, Jul 12, 2016 at 12:29 PM, Johannes Helmuth <helmuth at molgen.mpg.de> wrote:
Dear Bioconductor Developers, I recently contributed a package `normR` for calling enrichment and differences in ChIP-seq data (http://bioconductor.org/packages/normr/). To test the functionality of the package, I used `testthat`. All the tests run well when using `testthat::test()`, `R CMD build` or `R CMD check`. However, the `normr` package landing package ( http://bioconductor.org/packages/normr/) reports "Test coverage: unknown". I installed `covr` on my local machine and ran `covr::package_coverage()`. It seems to work fine:
normr Coverage: 77.50% R/NormRCountConfig.R: 50.00% R/methods.R: 64.32% src/em.cpp: 79.27% R/NormRFit.R: 87.33% src/normr_init.c: 100.00%
Is "Test Coverage: unknown" related to the Bioconductor build system not being able to build my package on Linux? (I filed this in an earlier post related to the unavailability of automake-1.14 for Rhtslib 1.5.3 installation) Thank you very much, Johannes Helmuth
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obviously "cannot do the coverage report" On Tue, Jul 12, 2016 at 12:32 PM, Kasper Daniel Hansen <
kasperdanielhansen at gmail.com> wrote:
Without knowing the details it seems self-evident to me that the build system can do the coverage report if the package doesn't build. Best, Kasper On Tue, Jul 12, 2016 at 12:29 PM, Johannes Helmuth <helmuth at molgen.mpg.de> wrote:
Dear Bioconductor Developers, I recently contributed a package `normR` for calling enrichment and differences in ChIP-seq data (http://bioconductor.org/packages/normr/). To test the functionality of the package, I used `testthat`. All the tests run well when using `testthat::test()`, `R CMD build` or `R CMD check`. However, the `normr` package landing package ( http://bioconductor.org/packages/normr/) reports "Test coverage: unknown". I installed `covr` on my local machine and ran `covr::package_coverage()`. It seems to work fine:
normr Coverage: 77.50% R/NormRCountConfig.R: 50.00% R/methods.R: 64.32% src/em.cpp: 79.27% R/NormRFit.R: 87.33% src/normr_init.c: 100.00%
Is "Test Coverage: unknown" related to the Bioconductor build system not being able to build my package on Linux? (I filed this in an earlier post related to the unavailability of automake-1.14 for Rhtslib 1.5.3 installation) Thank you very much, Johannes Helmuth
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