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${worksrcpath}/src/Makevars.in + } + reinplace "s|@PKG_LIBS@|-L${prefix}/lib -lopenbabel|" ${worksrcpath}/src/Makevars.in } depends_test-append port:R-BiocManager \ @@ -34,6 +44,7 @@ depends_test-append port:R-BiocManager \ port:R-ChemmineR \ port:R-knitr \ port:R-knitrBootstrap \ + port:R-rmarkdown \ port:R-RUnit test.run yes diff --git a/R/R-ChemmineOB/files/patch-fix-flags.diff b/R/R-ChemmineOB/files/patch-fix-flags.diff index f44206166432a..0e1d16645285b 100644 --- a/R/R-ChemmineOB/files/patch-fix-flags.diff +++ b/R/R-ChemmineOB/files/patch-fix-flags.diff @@ -1,12 +1,10 @@ --- src/Makevars.in 2023-10-25 02:13:48.000000000 +0800 +++ src/Makevars.in 2023-10-27 04:21:49.000000000 +0800 -@@ -6,5 +6,7 @@ +@@ -6,5 +6,5 @@ # endif #endif -PKG_CPPFLAGS = -I/usr/include/openbabel3 -I/usr/include/eigen3 -DUSE_BOOST -DHAVE_EIGEN -I/usr/local/include/eigen3 -I/usr/local/include/openbabel3 @OPENBABEL_CFLAGS@ -PKG_LIBS = -L/usr/local/lib/openbabel3 @OPENBABEL_LIBS@ -+PKG_CPPFLAGS = -DUSE_BOOST 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https://github.com/Bioconductor/SparseArray/issues/9 +if {[string match *clang* ${configure.compiler}]} { + patchfiles-append \ + patch-disable-openmp.diff +} + +variant tests description "Enable testing" { + depends_test-append \ + port:R-BiocStyle \ port:R-DelayedArray \ port:R-knitr \ port:R-rmarkdown \ port:R-testthat -test.run yes + test.run yes +} diff --git a/R/R-SparseArray/files/patch-disable-openmp.diff b/R/R-SparseArray/files/patch-disable-openmp.diff new file mode 100644 index 0000000000000..fd00832f1a3a7 --- /dev/null +++ b/R/R-SparseArray/files/patch-disable-openmp.diff @@ -0,0 +1,45 @@ +--- src/Makevars 2024-05-01 08:54:02.000000000 +0800 ++++ src/Makevars 2024-05-05 04:55:32.000000000 +0800 +@@ -1,2 +1,2 @@ +-PKG_CFLAGS = $(SHLIB_OPENMP_CFLAGS) +-PKG_LIBS = $(SHLIB_OPENMP_CFLAGS) ++PKG_CFLAGS = ++PKG_LIBS = + +--- src/thread_control.c 2024-05-01 08:54:02.000000000 +0800 ++++ src/thread_control.c 2024-05-05 04:57:12.000000000 +0800 +@@ -3,14 +3,14 @@ + 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\ + port:R-testthat + + # Tests pass, one example from vignettes fails. + test.run yes +} diff --git a/R/R-Structstrings/files/patch-no-tRNAscanImport.diff b/R/R-Structstrings/files/patch-no-tRNAscanImport.diff new file mode 100644 index 0000000000000..a9a56f2d48856 --- /dev/null +++ b/R/R-Structstrings/files/patch-no-tRNAscanImport.diff @@ -0,0 +1,11 @@ +--- DESCRIPTION 2024-05-02 07:40:27.000000000 +0800 ++++ DESCRIPTION 2024-05-05 05:08:04.000000000 +0800 +@@ -24,7 +24,7 @@ + LinkingTo: IRanges, S4Vectors + Imports: methods, BiocGenerics, XVector, stringr, stringi, crayon, + grDevices +-Suggests: testthat, knitr, rmarkdown, tRNAscanImport, BiocStyle ++Suggests: testthat, knitr, rmarkdown, BiocStyle + VignetteBuilder: knitr + RoxygenNote: 7.3.1 + Collate: 'Structstrings.R' 'AllGenerics.R' diff --git a/R/R-SummarizedExperiment/Portfile b/R/R-SummarizedExperiment/Portfile index 00522139f8e6a..3c8a5b96dd2b2 100644 --- a/R/R-SummarizedExperiment/Portfile +++ 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