[Bioc-devel] new Windows toolchain for R-3.3.0

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

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[Bioc-devel] new Windows toolchain for R-3.3.0

Thread (4 messages)