[Bioc-devel] new Windows toolchain for R-3.3.0
Dan Tenenbaum
dtenenba at fredhutch.org
Fri Apr 1 03:31:10 CEST 2016
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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