[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
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