[Bioc-devel] new Windows toolchain for R-3.3.0
Kasper Daniel Hansen
kasperdanielhansen at gmail.com
Fri Apr 1 03:59:05 CEST 2016
Let's see what Henrik says, he is a Windows user. I'll look at getting a VM.
Kasper
On Thu, Mar 31, 2016 at 9:31 PM, Dan Tenenbaum <dtenenba at fredhutch.org>
wrote:
> I asked Jim Hester about affxparser and he said:
>
> > affxparser - Looks like they are overriding the WINVAR constant (
> >
> https://github.com/Bioconductor-mirror/affxparser/blob/master/src/R_affx_constants.h#L17
> ),
> > which is causing the windows symbols to be missed. You may want to try
> > commenting that out (plus it feels wrong to be hardcoding that to Windows
> > XP anyway…)
>
>
> However, I did try commenting out the WINVAR constant and that did not
> help.
>
> The headers alone in the directory you asked for are ~8MB zipped. If you
> want to do any real troubleshooting I think you will need a VM.
>
> Dan
>
>
> ----- Original Message -----
> > From: "Kasper Daniel Hansen" <kasperdanielhansen at gmail.com>
> > To: "Dan Tenenbaum" <dtenenba at fredhutch.org>
> > Cc: "bioc-devel" <bioc-devel at r-project.org>
> > Sent: Thursday, March 31, 2016 5:52:36 PM
> > Subject: Re: [Bioc-devel] new Windows toolchain for R-3.3.0
>
> > There are tons of errors with affxparser (as mentioned on the toolchain
> > setup documentation). However, (almost) all of them seems to be errors
> in
> > header files included with mingq. The first one is pasted below, and the
> > error (seems to be) in the minwindef.h header file. Given that this is a
> > new toolchain and that this package compiles fine with clang, I am
> tempted
> > to blame the toolchain. I could try to have a look in the header file
> (not
> > sure if it helps). Could anyone with windows and the new toolchain
> > installed send me all the header files in
> > C:/Rtools/mingw_32/i686-w64-mingw32/include/
> > (should be small)
> >
> > Best,
> > Kasper
> >
> >
> > * installing *source* package 'affxparser' ...
> > ** libs
> > rm -f fusion_sdk/calvin_files/data/src/CDFData.o
> > fusion_sdk/calvin_files/data/src/CDFProbeGroupInformation.o
> > fusion_sdk/calvin_files/data/src/CDFProbeInformation.o
> > fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.o
> > fusion_sdk/calvin_files/data/src/CDFQCProbeInformation.o
> > fusion_sdk/calvin_files/data/src/CDFQCProbeSetInformation.o
> > fusion_sdk/calvin_files/data/src/CELData.o
> > fusion_sdk/calvin_files/data/src/CHPBackgroundZone.o
> > fusion_sdk/calvin_files/data/src/CHPData.o
> > fusion_sdk/calvin_files/data/src/CHPExpressionEntry.o
> > fusion_sdk/calvin_files/data/src/CHPMultiDataData.o
> > fusion_sdk/calvin_files/data/src/CHPTilingData.o
> > fusion_sdk/calvin_files/data/src/CHPQuantificationData.o
> > fusion_sdk/calvin_files/data/src/CHPQuantificationDetectionData.o
> > fusion_sdk/calvin_files/data/src/CHPGenotypeEntry.o
> > fusion_sdk/calvin_files/data/src/CHPUniversalEntry.o
> > fusion_sdk/calvin_files/data/src/ColumnInfo.o
> > fusion_sdk/calvin_files/data/src/DataGroup.o
> > fusion_sdk/calvin_files/data/src/DataGroupHeader.o
> > fusion_sdk/calvin_files/data/src/DataSet.o
> > fusion_sdk/calvin_files/data/src/DataSetHeader.o
> > fusion_sdk/calvin_files/data/src/FileHeader.o
> > fusion_sdk/calvin_files/data/src/GenericData.o
> > fusion_sdk/calvin_files/data/src/GenericDataHeader.o
> > fusion_sdk/calvin_files/exception/src/ExceptionBase.o
> > fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCELDataAdapter.o
> > fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCHPDataAdapter.o
> > fusion_sdk/calvin_files/fusion/src/FusionBPMAPData.o
> > fusion_sdk/calvin_files/fusion/src/FusionCDFData.o
> > fusion_sdk/calvin_files/fusion/src/FusionCDFQCProbeSetNames.o
> > fusion_sdk/calvin_files/fusion/src/FusionCELData.o
> > fusion_sdk/calvin_files/fusion/src/FusionCHPData.o
> > fusion_sdk/calvin_files/fusion/src/FusionProbeSetResults.o
> > fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCELDataAdapter.o
> > fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCHPDataAdapter.o
> > fusion_sdk/calvin_files/fusion/src/FusionCHPLegacyData.o
> > fusion_sdk/calvin_files/fusion/src/FusionCHPMultiDataAccessor.o
> > fusion_sdk/calvin_files/fusion/src/FusionCHPMultiDataData.o
> > fusion_sdk/calvin_files/fusion/src/FusionCHPTilingData.o
> > fusion_sdk/calvin_files/fusion/src/FusionCHPGenericData.o
> > fusion_sdk/calvin_files/fusion/src/FusionCHPQuantificationData.o
> > fusion_sdk/calvin_files/fusion/src/FusionCHPQuantificationDetectionData.o
> > fusion_sdk/calvin_files/parameter/src/ParameterNameValueType.o
> > fusion_sdk/calvin_files/parsers/src/CDFFileReader.o
> > fusion_sdk/calvin_files/parsers/src/CelFileReader.o
> > fusion_sdk/calvin_files/parsers/src/CHPFileReader.o
> > fusion_sdk/calvin_files/parsers/src/CHPMultiDataFileReader.o
> > fusion_sdk/calvin_files/parsers/src/CHPTilingFileReader.o
> > fusion_sdk/calvin_files/parsers/src/CHPQuantificationFileReader.o
> >
> fusion_sdk/calvin_files/parsers/src/CHPQuantificationDetectionFileReader.o
> > fusion_sdk/calvin_files/parsers/src/DataGroupHeaderReader.o
> > fusion_sdk/calvin_files/parsers/src/DataGroupReader.o
> > fusion_sdk/calvin_files/parsers/src/DataSetHeaderReader.o
> > fusion_sdk/calvin_files/parsers/src/DataSetReader.o
> > fusion_sdk/calvin_files/parsers/src/FileHeaderReader.o
> > fusion_sdk/calvin_files/parsers/src/FileInput.o
> > fusion_sdk/calvin_files/parsers/src/GenericDataHeaderReader.o
> > fusion_sdk/calvin_files/parsers/src/GenericFileReader.o
> > fusion_sdk/calvin_files/utils/src/AffymetrixGuid.o
> > fusion_sdk/calvin_files/utils/src/DateTime.o
> > fusion_sdk/calvin_files/utils/src/FileUtils.o
> > fusion_sdk/calvin_files/utils/src/StringUtils.o
> > fusion_sdk/calvin_files/utils/src/checksum.o
> > fusion_sdk/file/BPMAPFileData.o fusion_sdk/file/BPMAPFileWriter.o
> > fusion_sdk/file/CDFFileData.o fusion_sdk/file/CELFileData.o
> > fusion_sdk/file/CHPFileData.o fusion_sdk/file/FileIO.o
> > fusion_sdk/file/FileWriter.o fusion_sdk/file/TsvFile/ClfFile.o
> > fusion_sdk/file/TsvFile/PgfFile.o fusion_sdk/file/TsvFile/TsvFile.o
> > fusion_sdk/util/AffxByteArray.o fusion_sdk/util/AffxConv.o
> > fusion_sdk/util/MsgStream.o fusion_sdk/util/Util.o fusion_sdk/util/Err.o
> > fusion_sdk/util/Fs.o fusion_sdk/util/Verbose.o fusion_sdk/util/RowFile.o
> > fusion_sdk/util/TableFile.o fusion_sdk/util/Convert.o R_affx_cel_parser.o
> > R_affx_cdf_parser.o R_affx_cdf_extras.o R_affx_bpmap_parser.o
> > R_affx_clf_pgf_parser.o R_affx_chp_parser.o
> > C:/Rtools/mingw_32/bin/g++ -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG
> > -I. -Ifusion_sdk/calvin_files/array/src
> -Ifusion_sdk/calvin_files/data/src
> > -Ifusion_sdk/calvin_files/exception/src
> > -Ifusion_sdk/calvin_files/fusion/src
> > -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter
> > -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter
> > -Ifusion_sdk/calvin_files/parameter/src
> > -Ifusion_sdk/calvin_files/parsers/src
> > -Ifusion_sdk/calvin_files/portability/src
> > -Ifusion_sdk/calvin_files/template/src
> -Ifusion_sdk/calvin_files/utils/src
> > -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file
> > -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util
> > -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"c:/local323/include"
> > -O2 -Wall -mtune=core2 -Wno-sign-compare -Wno-unknown-pragmas -c
> > fusion_sdk/calvin_files/data/src/CDFData.cpp -o
> > fusion_sdk/calvin_files/data/src/CDFData.o
> > In file included from
> > fusion_sdk/calvin_files/portability/src/AffymetrixBaseTypes.h:27:0,
> > from
> > fusion_sdk/calvin_files/exception/src/ExceptionBase.h:24,
> > from fusion_sdk/calvin_files/data/src/DataException.h:27,
> > from fusion_sdk/calvin_files/data/src/DataGroup.h:31,
> > from
> > fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.h:32,
> > from fusion_sdk/calvin_files/data/src/CDFData.h:26,
> > from fusion_sdk/calvin_files/data/src/CDFData.cpp:21:
> > ./R_affx_constants.h:17:0: warning: "WINVER" redefined
> > #define WINVER WindowsXP /* for Util.cpp, via TsvFile.cpp */
> > ^
> > In file included from
> > C:/Rtools/mingw_32/i686-w64-mingw32/include/windows.h:9:0,
> > from
> > fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.h:28,
> > from fusion_sdk/calvin_files/data/src/CDFData.h:26,
> > from fusion_sdk/calvin_files/data/src/CDFData.cpp:21:
> > ./_mingw.h:240:0: note: this is the location of the previous definition
> > #define WINVER 0x0502
> > ^
> > In file included from
> > C:/Rtools/mingw_32/i686-w64-mingw32/include/windef.h:8:0,
> > from
> > C:/Rtools/mingw_32/i686-w64-mingw32/include/windows.h:69,
> > from
> > fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.h:28,
> > from fusion_sdk/calvin_files/data/src/CDFData.h:26,
> > from fusion_sdk/calvin_files/data/src/CDFData.cpp:21:
> > C:/Rtools/mingw_32/i686-w64-mingw32/include/minwindef.h:24:29: error:
> > expected initializer before 'ULONG'
> > typedef unsigned __LONG32 ULONG;
> > ^
> > C:/Rtools/mingw_32/i686-w64-mingw32/include/minwindef.h:25:11: error:
> > 'ULONG' does not name a type
> > typedef ULONG *PULONG;
> > ^
> > C:/Rtools/mingw_32/i686-w64-mingw32/include/minwindef.h:124:29: error:
> > expected initializer before 'DWORD'
> > typedef unsigned __LONG32 DWORD;
> > ^
> > C:/Rtools/mingw_32/i686-w64-mingw32/include/minwindef.h:133:11: error:
> > '__LONG32' does not name a type
> > typedef __LONG32 *LPLONG;
> > ^
> > C:/Rtools/mingw_32/i686-w64-mingw32/include/minwindef.h:134:11: error:
> > 'DWORD' does not name a type
> > typedef DWORD *PDWORD;
> > ^
> > C:/Rtools/mingw_32/i686-w64-mingw32/include/minwindef.h:135:11: error:
> > 'DWORD' does not name a type
> > typedef DWORD *LPDWORD;
> >
> >
> > On Thu, Mar 31, 2016 at 1:36 PM, Dan Tenenbaum <dtenenba at fredhutch.org>
> > wrote:
> >
> >> Hello all,
> >>
> >> R is planning to use a new Windows toolchain (known as Rtools33) for the
> >> soon-to-be-released R-3.3.0.
> >> This toolchain will use gcc/g++ 4.9.3 (an upgrade from 4.6.3).
> >>
> >> We expect CRAN packages for Windows using this toolchain in a few days.
> >> We are currently building the devel branch of Bioconductor using the new
> >> toolchain and expect the results later today.
> >>
> >> What this means:
> >>
> >> - If you are using R-3.3.0 on Windows, please update to a recent version
> >> from
> >> https://cran.r-project.org/bin/windows/base/rtest.html .
> >> You should do a completely fresh install (i.e., don't keep packages
> from
> >> a previous install around).
> >> - Set it up to use the new toolchain as follows:
> >>
> >>
> https://github.com/Bioconductor/Bioconductor/blob/master/documentation/new-toolchain-setup.md#setting-up-r-to-use-the-new-toolchain
> >>
> >> There is a binary incompatibility between packages built with the old
> >> toolchain and packages built with the new toolchain (IF the packages or
> >> their system dependencies contain C++ code or bindings).
> >>
> >> At the moment, windows packages are not available for Bioconductor's
> devel
> >> branch. When they become available, later today, they will be packages
> >> built with the new toolchain, and should only be used by a recent
> R-3.3.0
> >> which has been configured to use the new toolchain.
> >>
> >> You also need to set up R to NOT install binary packages (the process
> for
> >> doing this is described at the link above) because the binary packages
> >> provided by CRAN at the moment were built with the old toolchain and are
> >> not compatible.
> >>
> >> Package authors should read
> >>
> >>
> >>
> https://github.com/Bioconductor/Bioconductor/blob/master/documentation/new-toolchain-setup.md
> >>
> >> Which describes how to set up a windows machine to build R packages
> using
> >> the new toolchain.
> >> This page will change over time as we get more packages / system
> >> dependencies to build.
> >>
> >> You can test your packages using this setup.
> >> If you don't have physical access to a windows machine, you can
> download a
> >> virtual machine from Microsoft:
> >>
> >> https://developer.microsoft.com/en-us/microsoft-edge/tools/vms/
> >>
> >> This mailing list (bioc-devel) is the appropriate place for questions
> >> about the new toolchain.
> >>
> >> When the build report from today's build is available, I may send a
> >> follow-up email (either to bioc-devel or specific maintainers) to
> discuss
> >> how to get certain packages to install under the new toolchain.
> >>
> >> Dan
> >>
> >> _______________________________________________
> >> Bioc-devel at r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
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