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Cleanup ZLIB from Makevars, enable other arches and disable error on warning in GitHub action, update DESCRIPTION and NEWS

Steffen Neumann authored on 25/01/2022 09:42:19
Showing4 changed files

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@@ -52,8 +52,8 @@ jobs:
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       fail-fast: false
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       matrix:
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         config:
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-#          - { os: ubuntu-latest, r: 'devel', bioc: '3.15', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
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-#          - { os: macOS-latest, r: 'devel', bioc: '3.15'}
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+          - { os: ubuntu-latest, r: 'devel', bioc: '3.15', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
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+          - { os: macOS-latest, r: 'devel', bioc: '3.15'}
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           - { os: windows-latest, r: 'devel', bioc: '3.15'}
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     env:
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       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
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@@ -234,7 +234,6 @@ jobs:
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           rcmdcheck::rcmdcheck(
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               args = c("--no-build-vignettes", "--no-manual", "--timings"),
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               build_args = c("--no-manual", "--no-resave-data"),
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-              error_on = "warning",
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               check_dir = "check"
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           )
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         shell: Rscript {0}
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@@ -2,7 +2,7 @@ Package: mzR
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 Type: Package
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 Title: parser for netCDF, mzXML, mzData and mzML and mzIdentML files
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        (mass spectrometry data)
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-Version: 2.29.2
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+Version: 2.29.3
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 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou, Johannes Rainer
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 Authors@R: c(
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     person("Steffen", "Neumann", email="sneumann@ipb-halle.de", role=c("aut","cre")),
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@@ -1,9 +1,13 @@
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-CHANGES IN VERSION 2.29.2
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+CHANGES IN VERSION 2.29.3
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 -------------------------
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  o Update to Proteowizard 3_0_21263
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  o Removed RAMP backend, dropping ability to read mzData
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  o header always returns a data.frame even for a single scan.
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+ CHANGES IN VERSION 2.29.2
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+ -------------------------
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+ o Small fix in build to include fix by UCRT patch from Tomas Kalibera
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+
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 CHANGES IN VERSION 2.29.1
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 -------------------------
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  o Pwiz backend partially re-written to avoid segfault on macOS
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@@ -108,15 +108,10 @@ ARCH_OBJS=./boost/libs/filesystem/src/path_traits.o \
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 ARCH_CPPFLAGS=-fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB
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 ARCH_LIBS=-lws2_32 -lz
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 RHDF5_LIBS=$(shell echo 'Rhdf5lib::pkgconfig("PKG_CXX_LIBS")'| "${R_HOME}/bin/R" --vanilla --slave)
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-ZLIB_CFLAGS=$(shell echo 'zlibbioc::pkgconfig("PKG_CFLAGS")'| "${R_HOME}/bin/R" --vanilla --slave)
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-ZLIB_LIBS=$(shell echo 'zlibbioc::pkgconfig("PKG_LIBS_shared")' | "${R_HOME}/bin/R" --vanilla --slave)
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 else
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 ARCH_OBJS=./boost/libs/thread/src/pthread/once.o \
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 ./boost/libs/thread/src/pthread/thread.o
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 RHDF5_LIBS=$(shell echo 'Rhdf5lib::pkgconfig("PKG_CXX_LIBS")'| "${R_HOME}/bin/R" --vanilla --slave)
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-ZLIB_CFLAGS=$(shell echo 'zlibbioc::pkgconfig("PKG_CFLAGS")'|\
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-"${R_HOME}/bin/R" --vanilla --slave)
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-ZLIB_LIBS=$(shell echo 'zlibbioc::pkgconfig("PKG_LIBS_shared")' | "${R_HOME}/bin/R" --vanilla --slave)
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 endif
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 MZROBJECTS= RcppPwiz.o RcppPwizModule.o RcppIdent.o RcppIdentModule.o
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@@ -143,4 +138,3 @@ all: clean $(SHLIB)
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 clean:
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 	rm -f $(OBJECTS)
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-