rClr
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Published
20 hours ago •
rdotnet
rdotnet
ubuntu 14.04 error on install (segfault)
Hi,
I am also trying to install rsqlserver and this requires rClr. I am on ubuntu 14.04 using the Xamarin package of mono running R 3.22. In order to get to this step, i also had to install libmonosgen-2.0-dev (otherwise it would complain about "Package monosgen-2 was not found in the pkg-config search path"
$ mono -V
Mono JIT compiler version 4.0.4 (Stable 4.0.4.1/5ab4c0d Tue Aug 25 23:11:51 UTC 2015)
Copyright (C) 2002-2014 Novell, Inc, Xamarin Inc and Contributors. www.mono-project.com
TLS: __thread
SIGSEGV: altstack
Notifications: epoll
Architecture: amd64
Disabled: none
Misc: softdebug
LLVM: supported, not enabled.
GC: sgen
R session
> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.3 LTS
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] devtools_1.9.1
loaded via a namespace (and not attached):
[1] httr_1.0.0 R6_2.1.1 magrittr_1.5 tools_3.2.2 curl_0.9.3
[6] memoise_0.2.1 stringi_1.0-1 knitr_1.11 stringr_1.0.0 digest_0.6.8
Install commands and output, same thing with build_vignettes=FALSE
> library(devtools)
> install_github("jmp75/rClr", build_vignettes=TRUE)
Downloading GitHub repo jmp75/rClr@master
Installing rClr
'/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore CMD \
INSTALL '/tmp/RtmpnoZ4LD/devtools1d5e75fe3e9d/jmp75-rClr-a0cb9b6' \
--library='/home/ubuntu/R/x86_64-pc-linux-gnu-library/3.2' --install-tests
* installing *source* package ‘rClr’ ...
MONO_CFLAGS=-D_REENTRANT -I/usr/lib/pkgconfig/../../include/mono-2.0
GLIB_CFLAGS=-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include
Created ./src/Makevars
** libs
/bin/bash: -c: line 0: syntax error near unexpected token `('
/bin/bash: -c: line 0: `echo **Variable (information only for diagnosis purposes)**'
make: [printarch] Error 1 (ignored)
R_ARCH=
OBJECTS=rClrMono.o
SHLIB_EXT=.so
CC=gcc -std=gnu99
CXX=g++
**END Variable**
g++ -std=c++11 -I/usr/share/R/include -DNDEBUG `pkg-config --cflags monosgen-2 glib-2.0` -g -D MONO_CLR -D MONO_INST -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c rClr.cpp -o rClrMono.o -lsupc++
rClr.cpp: In function ‘CLR_OBJ* rclr_mono_create_object(MonoDomain*, MonoImage*, char*, SEXP)’:
rClr.cpp:79:82: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
MonoMethod * method = rclr_mono_get_method( spTypeClrFacade, "CreateInstance", 2);
^
rClr.cpp: In function ‘CLR_OBJ* rclr_mono_get_current_object_direct()’:
rClr.cpp:140:85: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
MonoMethod * method = rclr_mono_get_method( spTypeClrFacade, "get_CurrentObject", 0);
^
rClr.cpp: In function ‘MonoString* rclr_mono_get_last_clr_exception()’:
rClr.cpp:173:88: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
MonoMethod * method = rclr_mono_get_method(spTypeClrFacade, "get_LastCallException", 0);
^
rClr.cpp: In function ‘SEXPREC* rclr_mono_call_method_with_exception(const char*, CLR_OBJ*, MonoClass*, SEXP, CLR_OBJ*)’:
rClr.cpp:215:104: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
MonoMethod * methodCallInstanceMethod = rclr_mono_get_method( spTypeClrFacade, "CallInstanceMethod", 3);
^
rClr.cpp: In function ‘SEXPREC* make_date_sexp(int, double*)’:
rClr.cpp:486:21: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
char * classname = "Date";
^
rClr.cpp: In function ‘SEXPREC* make_POSIXct_sexp(int, double*)’:
rClr.cpp:493:15: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
classname[0] = "POSIXct"; classname[1] = "POSIXt";
^
rClr.cpp:493:41: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
classname[0] = "POSIXct"; classname[1] = "POSIXt";
^
rClr.cpp:501:46: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
setAttrib(result, make_char_sexp_one("tzone"), make_char_sexp_one("UTC"));
^
rClr.cpp:501:73: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
setAttrib(result, make_char_sexp_one("tzone"), make_char_sexp_one("UTC"));
^
rClr.cpp: In function ‘CLR_OBJ* rclr_convert_element(SEXP)’:
rClr.cpp:1259:125: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
parameter = rclr_mono_call_static_method_tname_directcall("Rclr.ClrFacade", "CreateDateFromREpoch", (void**)(&values), 1);
^
rClr.cpp:1259:125: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
rClr.cpp:1268:127: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
parameter = rclr_mono_call_static_method_tname_directcall("Rclr.ClrFacade", "CreateDateFromRPOSIXct", (void**)(&values), 1);
^
rClr.cpp:1268:127: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
rClr.cpp:1287:145: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
ay = (MonoArray*)rclr_mono_call_static_method_tname_directcall("Rclr.ClrFacade", "CreateDateArrayFromREpoch", (void**)(&monoArray), 1);
^
rClr.cpp:1287:145: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
rClr.cpp:1291:147: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
= (MonoArray*)rclr_mono_call_static_method_tname_directcall("Rclr.ClrFacade", "CreateDateArrayFromRPOSIXct", (void**)(&monoArray), 1);
^
rClr.cpp:1291:147: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
rClr.cpp: In function ‘double* clr_datetimearray_obj_to_r_date_numeric(CLR_OBJ*)’:
rClr.cpp:1532:135: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
eturn clr_datetimearray_obj_to_numeric( datetimearray_ptr, rclr_mono_get_method( spTypeClrFacade, "GetRDateDoubleRepresentations", 1));
^
rClr.cpp: In function ‘double* clr_datetimearray_obj_to_r_posixct_numeric(CLR_OBJ*)’:
rClr.cpp:1536:134: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
return clr_datetimearray_obj_to_numeric( datetimearray_ptr, rclr_mono_get_method( spTypeClrFacade, "GetRDatePosixtcNumericValues", 1));
^
rClr.cpp: In function ‘double* clr_datetime_obj_to_r_date_numeric(CLR_OBJ*)’:
rClr.cpp:1549:123: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
return clr_datetime_obj_to_double( datetime_ptr, rclr_mono_get_method( spTypeClrFacade, "GetRDateDoubleRepresentation", 1));
^
rClr.cpp: In function ‘double* clr_datetime_obj_to_r_posixtc_numeric(CLR_OBJ*)’:
rClr.cpp:1559:122: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
return clr_datetime_obj_to_double( datetime_ptr, rclr_mono_get_method( spTypeClrFacade, "GetRDatePosixtcNumericValue", 1));
^
rClr.cpp: In function ‘SEXPREC* rclr_mono_diagnose_method_parameters(SEXP)’:
rClr.cpp:1753:101: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
MonoMethod * methodCallStaticMethod = rclr_mono_get_method(spTypeClrFacade, "DiagnoseMethodCall", 1);
^
rClr.cpp: In function ‘CLR_OBJ* rclr_mono_call_static_method_tname(char*, char*, void**, int)’:
rClr.cpp:1765:103: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
MonoMethod * methodCallStaticMethod = rclr_mono_get_method(spTypeClrFacade, "CallStaticMethodMono", 3);
^
rClr.cpp: In function ‘CLR_OBJ* rclr_mono_convert_element_rdotnet(SEXP)’:
rClr.cpp:1783:63: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
rclr_mono_get_method(spTypeClrFacade, "CreateSexpWrapper", 1);
^
rClr.cpp: In function ‘CLR_OBJ* rclr_mono_call_static_method_tname_directcall(char*, char*, void**, int)’:
rClr.cpp:1804:82: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
MonoMethod * methodGetType = rclr_mono_get_method( spTypeClrFacade, "GetType", 1);
^
rClr.cpp: In function ‘void rclr_mono_load_assembly(char**)’:
rClr.cpp:1908:76: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
MonoMethod * method = rclr_mono_get_method( spTypeClrFacade, "LoadFrom", 1);
^
# On a CentOS OS, I needed to use the following. The CPP and C flags would otherwise return two options not understood:
# -xHOST -fp-model precise
# @echo ALL_CPPFLAGS=-I/usr/share/R/include -DNDEBUG
# @echo ALL_CFLAGS= `pkg-config --cflags monosgen-2 glib-2.0` -g -D MONO_CLR -D MONO_INST -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g
# g++ -std=c++11 -I/apps/R/3.1.1/lib64/R/include -DNDEBUG -I/usr/local/include `pkg-config --cflags mono-2 glib-2.0` -g -D MONO_CLR -D MONO_INST -fpic -O3 -openmp -c rClr.cpp -o rClrMono.o -lsupc++
#gcc -std=gnu99 -shared -o rClr.so rClrMono.o -L/usr/lib/pkgconfig/../../lib -lmono-2.0 -lm -lrt -ldl -lpthread -lglib-2.0 -L/usr/lib/R/lib -lR
g++ -std=c++11 -shared -Wl,-z,relro -o rClrMono.so rClrMono.o `pkg-config --libs monosgen-2 glib-2.0` -L/usr/lib/R/lib -lR
#g++ -shared -L/usr/lib/R/lib -Wl,-z,relro -o rClr.so rClrMono.o -L/usr/lib/pkgconfig/../../lib -lmono-2.0 -lm -lrt -ldl -lpthread -lglib-2.0 -L/usr/lib/R/lib -lR
"xbuild" rClr_monodev.sln /t:Rebuild /p:Configuration=UnixDebug /p:Platform="Any CPU"
XBuild Engine Version 12.0
Mono, Version 4.0.4.0
Copyright (C) 2005-2013 Various Mono authors
Build started 10/28/2015 4:36:15 PM.
__________________________________________________
Project "/tmp/RtmpnoZ4LD/devtools1d5e75fe3e9d/jmp75-rClr-a0cb9b6/src/rClr_monodev.sln" (Rebuild target(s)):
Target ValidateSolutionConfiguration:
Building solution configuration "UnixDebug|Any CPU".
Target Rebuild:
Project "/tmp/RtmpnoZ4LD/devtools1d5e75fe3e9d/jmp75-rClr-a0cb9b6/src/ClrFacade/ClrFacade.csproj" (Rebuild target(s)):
Target RestorePackages:
Executing: mono --runtime=v4.0.30319 "/tmp/RtmpnoZ4LD/devtools1d5e75fe3e9d/jmp75-rClr-a0cb9b6/src/.nuget/NuGet.exe" install "/tmp/RtmpnoZ4LD/devtools1d5e75fe3e9d/jmp75-rClr-a0cb9b6/src/ClrFacade/packages.config" -source "" -RequireConsent -solutionDir "/tmp/RtmpnoZ4LD/devtools1d5e75fe3e9d/jmp75-rClr-a0cb9b6/src/"
Restoring NuGet packages...
To prevent NuGet from downloading packages during build, open the Visual Studio Options dialog, click on the Package Manager node and uncheck 'Allow NuGet to download missing packages'.
Installing 'DynamicInterop 0.7.4'.
Successfully installed 'DynamicInterop 0.7.4'.
Installing 'R.NET.Community 1.6.5'.
Successfully installed 'R.NET.Community 1.6.5'.
Target PrepareForBuild:
Configuration: Debug Platform: AnyCPU
Created directory "../Debug/"
Created directory "obj/Debug/"
Target ResolveAssemblyReferences:
/usr/lib/mono/4.5/Microsoft.Common.targets: warning : Reference 'DynamicInterop' not resolved
For searchpath {CandidateAssemblyFiles}
Warning: {CandidateAssemblyFiles} not supported currently
For searchpath {HintPathFromItem}
Considered ../packages/DynamicInterop.0.7.3/lib/net40/DynamicInterop.dll, but it does not exist.
For searchpath {TargetFrameworkDirectory}
Considered target framework dir /usr/lib/mono/4.0, assembly named 'DynamicInterop' not found.
For searchpath {PkgConfig}
Considered DynamicInterop, but could not find in any pkg-config files.
For searchpath {GAC}
Considered DynamicInterop, but could not find in the GAC.
For searchpath {RawFileName}
Considered '/tmp/RtmpnoZ4LD/devtools1d5e75fe3e9d/jmp75-rClr-a0cb9b6/src/ClrFacade/DynamicInterop' as a file, but the file does not exist
For searchpath ../Debug/
Considered '/tmp/RtmpnoZ4LD/devtools1d5e75fe3e9d/jmp75-rClr-a0cb9b6/src/Debug/DynamicInterop' as a file, but the file does not exist
Considered '/tmp/RtmpnoZ4LD/devtools1d5e75fe3e9d/jmp75-rClr-a0cb9b6/src/Debug/DynamicInterop.exe' as a file, but the file does not exist
Considered '/tmp/RtmpnoZ4LD/devtools1d5e75fe3e9d/jmp75-rClr-a0cb9b6/src/Debug/DynamicInterop.dll' as a file, but the file does not exist
Target CopyFilesMarkedCopyLocal:
Copying file from '/tmp/RtmpnoZ4LD/devtools1d5e75fe3e9d/jmp75-rClr-a0cb9b6/src/packages/DynamicInterop.0.7.4/lib/net40/DynamicInterop.dll' to '/tmp/RtmpnoZ4LD/devtools1d5e75fe3e9d/jmp75-rClr-a0cb9b6/src/Debug/DynamicInterop.dll'
Copying file from '/tmp/RtmpnoZ4LD/devtools1d5e75fe3e9d/jmp75-rClr-a0cb9b6/src/packages/R.NET.Community.1.6.5/lib/net40/RDotNet.dll' to '/tmp/RtmpnoZ4LD/devtools1d5e75fe3e9d/jmp75-rClr-a0cb9b6/src/Debug/RDotNet.dll'
Copying file from '/tmp/RtmpnoZ4LD/devtools1d5e75fe3e9d/jmp75-rClr-a0cb9b6/src/packages/R.NET.Community.1.6.5/lib/net40/RDotNet.NativeLibrary.dll' to '/tmp/RtmpnoZ4LD/devtools1d5e75fe3e9d/jmp75-rClr-a0cb9b6/src/Debug/RDotNet.NativeLibrary.dll'
Target GenerateSatelliteAssemblies:
No input files were specified for target GenerateSatelliteAssemblies, skipping.
Target CoreCompile:
Tool /usr/lib/mono/4.5/mcs.exe execution started with arguments: /noconfig /debug:full /debug+ /optimize- /out:obj/Debug/ClrFacade.dll ClrFacade.cs DataConverterExtensions.cs HelloWorld.cs IDataConverter.cs PerformanceProfiling.cs Properties/AssemblyInfo.cs RclrBinder.cs RclrUnmanagedDll.cs RDotNetDataConverter.cs RdotnetDataConverterTests.cs ReflectionHelper.cs TestArrayMemoryHandling.cs TestCases.cs TestMethodBinding.cs Tests/RefClasses/BaseAbstractClassOne.cs Tests/RefClasses/InterfaceOne.cs Tests/RefClasses/LevelOneClass.cs Tests/RefClasses/LevelThreeClass.cs Tests/RefClasses/LevelTwoClass.cs Tests/TestUtilities.cs DataConversionHelper.cs obj/Debug/.NETFramework,Version=v4.0.AssemblyAttribute.cs /target:library /define:"DEBUG;TRACE" /nostdlib /reference:../packages/DynamicInterop.0.7.4/lib/net40/DynamicInterop.dll /reference:../packages/R.NET.Community.1.6.5/lib/net40/RDotNet.dll /reference:../packages/R.NET.Community.1.6.5/lib/net40/RDotNet.NativeLibrary.dll /reference:/usr/lib/mono/4.0/System.dll /reference:/usr/lib/mono/4.0/System.Numerics.dll /reference:/usr/lib/mono/4.0/System.Xml.Linq.dll /reference:/usr/lib/mono/4.0/System.Data.DataSetExtensions.dll /reference:/usr/lib/mono/4.0/Microsoft.CSharp.dll /reference:/usr/lib/mono/4.0/System.Data.dll /reference:/usr/lib/mono/4.0/System.Xml.dll /reference:/usr/lib/mono/4.0/System.Core.dll /reference:/usr/lib/mono/4.0/mscorlib.dll /warn:4
TestCases.cs(106,17): warning CS0219: The variable `breakpoint' is assigned but its value is never used
DataConversionHelper.cs(155,21): warning CS0162: Unreachable code detected
DataConversionHelper.cs(168,17): warning CS0162: Unreachable code detected
Target _CopyAppConfigFile:
Copying file from '/tmp/RtmpnoZ4LD/devtools1d5e75fe3e9d/jmp75-rClr-a0cb9b6/src/ClrFacade/app.config' to '/tmp/RtmpnoZ4LD/devtools1d5e75fe3e9d/jmp75-rClr-a0cb9b6/src/Debug/ClrFacade.dll.config'
Target DeployOutputFiles:
Copying file from '/tmp/RtmpnoZ4LD/devtools1d5e75fe3e9d/jmp75-rClr-a0cb9b6/src/ClrFacade/obj/Debug/ClrFacade.dll.mdb' to '/tmp/RtmpnoZ4LD/devtools1d5e75fe3e9d/jmp75-rClr-a0cb9b6/src/Debug/ClrFacade.dll.mdb'
Copying file from '/tmp/RtmpnoZ4LD/devtools1d5e75fe3e9d/jmp75-rClr-a0cb9b6/src/ClrFacade/obj/Debug/ClrFacade.dll' to '/tmp/RtmpnoZ4LD/devtools1d5e75fe3e9d/jmp75-rClr-a0cb9b6/src/Debug/ClrFacade.dll'
Done building project "/tmp/RtmpnoZ4LD/devtools1d5e75fe3e9d/jmp75-rClr-a0cb9b6/src/ClrFacade/ClrFacade.csproj".
Project "/tmp/RtmpnoZ4LD/devtools1d5e75fe3e9d/jmp75-rClr-a0cb9b6/src/RclrTests/TestApp/TestApp.csproj" (Rebuild target(s)):
Target RestorePackages:
Executing: mono --runtime=v4.0.30319 "/tmp/RtmpnoZ4LD/devtools1d5e75fe3e9d/jmp75-rClr-a0cb9b6/src/.nuget/NuGet.exe" install "/tmp/RtmpnoZ4LD/devtools1d5e75fe3e9d/jmp75-rClr-a0cb9b6/src/RclrTests/TestApp/packages.config" -source "" -RequireConsent -solutionDir "/tmp/RtmpnoZ4LD/devtools1d5e75fe3e9d/jmp75-rClr-a0cb9b6/src/"
Restoring NuGet packages...
To prevent NuGet from downloading packages during build, open the Visual Studio Options dialog, click on the Package Manager node and uncheck 'Allow NuGet to download missing packages'.
Installing 'R.NET.Community 1.5.22'.
Successfully installed 'R.NET.Community 1.5.22'.
Target PrepareForBuild:
Configuration: Debug Platform: AnyCPU
Created directory "bin/Debug/"
Created directory "obj/Debug/"
Target CopyFilesMarkedCopyLocal:
Copying file from '/tmp/RtmpnoZ4LD/devtools1d5e75fe3e9d/jmp75-rClr-a0cb9b6/src/packages/R.NET.Community.1.5.22/lib/net40/RDotNet.dll' to '/tmp/RtmpnoZ4LD/devtools1d5e75fe3e9d/jmp75-rClr-a0cb9b6/src/RclrTests/TestApp/bin/Debug/RDotNet.dll'
Copying file from '/tmp/RtmpnoZ4LD/devtools1d5e75fe3e9d/jmp75-rClr-a0cb9b6/src/packages/R.NET.Community.1.5.22/lib/net40/RDotNet.NativeLibrary.dll' to '/tmp/RtmpnoZ4LD/devtools1d5e75fe3e9d/jmp75-rClr-a0cb9b6/src/RclrTests/TestApp/bin/Debug/RDotNet.NativeLibrary.dll'
Copying file from '/tmp/RtmpnoZ4LD/devtools1d5e75fe3e9d/jmp75-rClr-a0cb9b6/src/packages/DynamicInterop.0.7.4/lib/net40/DynamicInterop.dll' to '/tmp/RtmpnoZ4LD/devtools1d5e75fe3e9d/jmp75-rClr-a0cb9b6/src/RclrTests/TestApp/bin/Debug/DynamicInterop.dll'
Copying file from '/tmp/RtmpnoZ4LD/devtools1d5e75fe3e9d/jmp75-rClr-a0cb9b6/src/Debug/ClrFacade.dll' to '/tmp/RtmpnoZ4LD/devtools1d5e75fe3e9d/jmp75-rClr-a0cb9b6/src/RclrTests/TestApp/bin/Debug/ClrFacade.dll'
Copying file from '/tmp/RtmpnoZ4LD/devtools1d5e75fe3e9d/jmp75-rClr-a0cb9b6/src/Debug/ClrFacade.dll.mdb' to '/tmp/RtmpnoZ4LD/devtools1d5e75fe3e9d/jmp75-rClr-a0cb9b6/src/RclrTests/TestApp/bin/Debug/ClrFacade.dll.mdb'
Target GenerateSatelliteAssemblies:
No input files were specified for target GenerateSatelliteAssemblies, skipping.
Target CoreCompile:
Tool /usr/lib/mono/4.5/mcs.exe execution started with arguments: /noconfig /debug:full /debug+ /optimize- /out:obj/Debug/TestApp.exe Program.cs Properties/AssemblyInfo.cs obj/Debug/.NETFramework,Version=v4.0.AssemblyAttribute.cs /target:exe /define:DEBUG /nostdlib /reference:../../packages/R.NET.Community.1.5.22/lib/net40/RDotNet.dll /reference:../../packages/R.NET.Community.1.5.22/lib/net40/RDotNet.NativeLibrary.dll /reference:/usr/lib/mono/4.0/System.dll /reference:/usr/lib/mono/4.0/System.Numerics.dll /reference:../../packages/DynamicInterop.0.7.4/lib/net40/DynamicInterop.dll /reference:/usr/lib/mono/4.0/System.Core.dll /reference:/tmp/RtmpnoZ4LD/devtools1d5e75fe3e9d/jmp75-rClr-a0cb9b6/src/Debug//ClrFacade.dll /reference:/usr/lib/mono/4.0/mscorlib.dll /warn:4
Program.cs(16,17): warning CS0219: The variable `tz' is assigned but its value is never used
Program.cs(23,17): warning CS0219: The variable `yep' is assigned but its value is never used
Target DeployOutputFiles:
Copying file from '/tmp/RtmpnoZ4LD/devtools1d5e75fe3e9d/jmp75-rClr-a0cb9b6/src/RclrTests/TestApp/obj/Debug/TestApp.exe.mdb' to '/tmp/RtmpnoZ4LD/devtools1d5e75fe3e9d/jmp75-rClr-a0cb9b6/src/RclrTests/TestApp/bin/Debug/TestApp.exe.mdb'
Copying file from '/tmp/RtmpnoZ4LD/devtools1d5e75fe3e9d/jmp75-rClr-a0cb9b6/src/RclrTests/TestApp/obj/Debug/TestApp.exe' to '/tmp/RtmpnoZ4LD/devtools1d5e75fe3e9d/jmp75-rClr-a0cb9b6/src/RclrTests/TestApp/bin/Debug/TestApp.exe'
Done building project "/tmp/RtmpnoZ4LD/devtools1d5e75fe3e9d/jmp75-rClr-a0cb9b6/src/RclrTests/TestApp/TestApp.csproj".
Project "/tmp/RtmpnoZ4LD/devtools1d5e75fe3e9d/jmp75-rClr-a0cb9b6/src/RclrTests/RclrTests.csproj" (Rebuild target(s)):
Target RestorePackages:
Executing: mono --runtime=v4.0.30319 "/tmp/RtmpnoZ4LD/devtools1d5e75fe3e9d/jmp75-rClr-a0cb9b6/src/.nuget/NuGet.exe" install "/tmp/RtmpnoZ4LD/devtools1d5e75fe3e9d/jmp75-rClr-a0cb9b6/src/RclrTests/packages.config" -source "" -RequireConsent -solutionDir "/tmp/RtmpnoZ4LD/devtools1d5e75fe3e9d/jmp75-rClr-a0cb9b6/src/"
Restoring NuGet packages...
To prevent NuGet from downloading packages during build, open the Visual Studio Options dialog, click on the Package Manager node and uncheck 'Allow NuGet to download missing packages'.
Installing 'xunit 1.9.2'.
Successfully installed 'xunit 1.9.2'.
Target PrepareForBuild:
Configuration: Debug Platform: AnyCPU
Created directory "bin/Debug/"
Created directory "obj/Debug/"
Target CopyFilesMarkedCopyLocal:
Copying file from '/tmp/RtmpnoZ4LD/devtools1d5e75fe3e9d/jmp75-rClr-a0cb9b6/src/packages/DynamicInterop.0.7.4/lib/net40/DynamicInterop.dll' to '/tmp/RtmpnoZ4LD/devtools1d5e75fe3e9d/jmp75-rClr-a0cb9b6/src/RclrTests/bin/Debug/DynamicInterop.dll'
Copying file from '/tmp/RtmpnoZ4LD/devtools1d5e75fe3e9d/jmp75-rClr-a0cb9b6/src/packages/R.NET.Community.1.6.5/lib/net40/RDotNet.dll' to '/tmp/RtmpnoZ4LD/devtools1d5e75fe3e9d/jmp75-rClr-a0cb9b6/src/RclrTests/bin/Debug/RDotNet.dll'
Copying file from '/tmp/RtmpnoZ4LD/devtools1d5e75fe3e9d/jmp75-rClr-a0cb9b6/src/packages/R.NET.Community.1.6.5/lib/net40/RDotNet.NativeLibrary.dll' to '/tmp/RtmpnoZ4LD/devtools1d5e75fe3e9d/jmp75-rClr-a0cb9b6/src/RclrTests/bin/Debug/RDotNet.NativeLibrary.dll'
Copying file from '/tmp/RtmpnoZ4LD/devtools1d5e75fe3e9d/jmp75-rClr-a0cb9b6/src/packages/xunit.1.9.2/lib/net20/xunit.dll' to '/tmp/RtmpnoZ4LD/devtools1d5e75fe3e9d/jmp75-rClr-a0cb9b6/src/RclrTests/bin/Debug/xunit.dll'
Copying file from '/tmp/RtmpnoZ4LD/devtools1d5e75fe3e9d/jmp75-rClr-a0cb9b6/src/Debug/ClrFacade.dll' to '/tmp/RtmpnoZ4LD/devtools1d5e75fe3e9d/jmp75-rClr-a0cb9b6/src/RclrTests/bin/Debug/ClrFacade.dll'
Copying file from '/tmp/RtmpnoZ4LD/devtools1d5e75fe3e9d/jmp75-rClr-a0cb9b6/src/Debug/ClrFacade.dll.mdb' to '/tmp/RtmpnoZ4LD/devtools1d5e75fe3e9d/jmp75-rClr-a0cb9b6/src/RclrTests/bin/Debug/ClrFacade.dll.mdb'
Target GenerateSatelliteAssemblies:
No input files were specified for target GenerateSatelliteAssemblies, skipping.
Target CoreCompile:
Tool /usr/lib/mono/4.5/mcs.exe execution started with arguments: /noconfig /debug:full /debug+ /optimize- /out:obj/Debug/RclrTests.dll ReflectionTests.cs Properties/AssemblyInfo.cs TestMethodBindings.cs RdotnetTests.cs obj/Debug/.NETFramework,Version=v4.0.AssemblyAttribute.cs /target:library /define:"DEBUG;TRACE" /nostdlib /reference:../packages/DynamicInterop.0.7.4/lib/net40/DynamicInterop.dll /reference:../packages/R.NET.Community.1.6.5/lib/net40/RDotNet.dll /reference:../packages/R.NET.Community.1.6.5/lib/net40/RDotNet.NativeLibrary.dll /reference:/usr/lib/mono/4.0/System.dll /reference:/usr/lib/mono/4.0/System.Numerics.dll /reference:/usr/lib/mono/4.0/System.Xml.Linq.dll /reference:/usr/lib/mono/4.0/System.Data.DataSetExtensions.dll /reference:/usr/lib/mono/4.0/Microsoft.CSharp.dll /reference:/usr/lib/mono/4.0/System.Data.dll /reference:/usr/lib/mono/4.0/System.Xml.dll /reference:../packages/xunit.1.9.2/lib/net20/xunit.dll /reference:/usr/lib/mono/4.0/System.Core.dll /reference:/tmp/RtmpnoZ4LD/devtools1d5e75fe3e9d/jmp75-rClr-a0cb9b6/src/Debug//ClrFacade.dll /reference:/usr/lib/mono/4.0/mscorlib.dll /warn:4
ReflectionTests.cs(83,17): warning CS0219: The variable `result' is assigned but its value is never used
RdotnetTests.cs(15,17): warning CS0219: The variable `sxpw' is assigned but its value is never used
Target DeployOutputFiles:
Copying file from '/tmp/RtmpnoZ4LD/devtools1d5e75fe3e9d/jmp75-rClr-a0cb9b6/src/RclrTests/obj/Debug/RclrTests.dll.mdb' to '/tmp/RtmpnoZ4LD/devtools1d5e75fe3e9d/jmp75-rClr-a0cb9b6/src/RclrTests/bin/Debug/RclrTests.dll.mdb'
Copying file from '/tmp/RtmpnoZ4LD/devtools1d5e75fe3e9d/jmp75-rClr-a0cb9b6/src/RclrTests/obj/Debug/RclrTests.dll' to '/tmp/RtmpnoZ4LD/devtools1d5e75fe3e9d/jmp75-rClr-a0cb9b6/src/RclrTests/bin/Debug/RclrTests.dll'
Done building project "/tmp/RtmpnoZ4LD/devtools1d5e75fe3e9d/jmp75-rClr-a0cb9b6/src/RclrTests/RclrTests.csproj".
Done building project "/tmp/RtmpnoZ4LD/devtools1d5e75fe3e9d/jmp75-rClr-a0cb9b6/src/rClr_monodev.sln".
Build succeeded.
Warnings:
/tmp/RtmpnoZ4LD/devtools1d5e75fe3e9d/jmp75-rClr-a0cb9b6/src/rClr_monodev.sln (Rebuild) ->
(Rebuild target) ->
/tmp/RtmpnoZ4LD/devtools1d5e75fe3e9d/jmp75-rClr-a0cb9b6/src/ClrFacade/ClrFacade.csproj (Rebuild) ->
/usr/lib/mono/4.5/Microsoft.Common.targets (ResolveAssemblyReferences target) ->
/usr/lib/mono/4.5/Microsoft.Common.targets: warning : Reference 'DynamicInterop' not resolved
/tmp/RtmpnoZ4LD/devtools1d5e75fe3e9d/jmp75-rClr-a0cb9b6/src/rClr_monodev.sln (Rebuild) ->
(Rebuild target) ->
/tmp/RtmpnoZ4LD/devtools1d5e75fe3e9d/jmp75-rClr-a0cb9b6/src/ClrFacade/ClrFacade.csproj (Rebuild) ->
/usr/lib/mono/4.5/Microsoft.CSharp.targets (CoreCompile target) ->
TestCases.cs(106,17): warning CS0219: The variable `breakpoint' is assigned but its value is never used
DataConversionHelper.cs(155,21): warning CS0162: Unreachable code detected
DataConversionHelper.cs(168,17): warning CS0162: Unreachable code detected
/tmp/RtmpnoZ4LD/devtools1d5e75fe3e9d/jmp75-rClr-a0cb9b6/src/rClr_monodev.sln (Rebuild) ->
(Rebuild target) ->
/tmp/RtmpnoZ4LD/devtools1d5e75fe3e9d/jmp75-rClr-a0cb9b6/src/RclrTests/TestApp/TestApp.csproj (Rebuild) ->
/usr/lib/mono/4.5/Microsoft.CSharp.targets (CoreCompile target) ->
Program.cs(16,17): warning CS0219: The variable `tz' is assigned but its value is never used
Program.cs(23,17): warning CS0219: The variable `yep' is assigned but its value is never used
/tmp/RtmpnoZ4LD/devtools1d5e75fe3e9d/jmp75-rClr-a0cb9b6/src/rClr_monodev.sln (Rebuild) ->
(Rebuild target) ->
/tmp/RtmpnoZ4LD/devtools1d5e75fe3e9d/jmp75-rClr-a0cb9b6/src/RclrTests/RclrTests.csproj (Rebuild) ->
/usr/lib/mono/4.5/Microsoft.CSharp.targets (CoreCompile target) ->
ReflectionTests.cs(83,17): warning CS0219: The variable `result' is assigned but its value is never used
RdotnetTests.cs(15,17): warning CS0219: The variable `sxpw' is assigned but its value is never used
8 Warning(s)
0 Error(s)
Time Elapsed 00:00:02.4553020
cp -u -p rClrMono.so ../inst/libs
if [ -e symbols.rds ] ; then cp -u -p symbols.rds ../inst/libs ; fi
# using rm -f to prevent the following, which seems to occur even when these should not be write-protected
# cp: cannot create regular file `../inst/libs/ClrFacade.dll': Permission denied
rm -f ../inst/libs/*.*
cp -u -p ./Debug/*.dll* ../inst/libs
g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o rClr.so rClrMono.o -L/usr/lib/pkgconfig/../../lib -lmonosgen-2.0 -lm -lrt -ldl -lpthread -lglib-2.0 -L/usr/lib/R/lib -lR
installing to /home/ubuntu/R/x86_64-pc-linux-gnu-library/3.2/rClr/libs
** R
** inst
** tests
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Assembly '/home/ubuntu/R/x86_64-pc-linux-gnu-library/3.2/rClr/libs/ClrFacade.dll' doesn't have an entry point.
* Assertion at sgen-alloc.c:774, condition `tlab_next_addr_offset != -1' not met
Stacktrace:
at <unknown> <0xffffffff>
at System.Reflection.Binder..cctor () <0x00014>
at (wrapper runtime-invoke) object.runtime_invoke_void (object,intptr,intptr,intptr) <0xffffffff>
at <unknown> <0xffffffff>
at Rclr.ClrFacade..cctor () <0x00010>
at (wrapper runtime-invoke) object.runtime_invoke_void (object,intptr,intptr,intptr) <0xffffffff>
Native stacktrace:
/usr/lib/libmonosgen-2.0.so.1(+0xd08cf) [0x7fa93d4228cf]
/lib/x86_64-linux-gnu/libpthread.so.0(+0x10340) [0x7fa942279340]
/lib/x86_64-linux-gnu/libc.so.6(gsignal+0x39) [0x7fa941edacc9]
/lib/x86_64-linux-gnu/libc.so.6(abort+0x148) [0x7fa941ede0d8]
/usr/lib/libmonosgen-2.0.so.1(+0x251199) [0x7fa93d5a3199]
/usr/lib/libmonosgen-2.0.so.1(+0x2513a7) [0x7fa93d5a33a7]
/usr/lib/libmonosgen-2.0.so.1(+0x2514f6) [0x7fa93d5a34f6]
/usr/lib/libmonosgen-2.0.so.1(+0x2130d4) [0x7fa93d5650d4]
/usr/lib/libmonosgen-2.0.so.1(+0xbe4bc) [0x7fa93d4104bc]
/usr/lib/libmonosgen-2.0.so.1(+0xc0164) [0x7fa93d412164]
/usr/lib/libmonosgen-2.0.so.1(+0xc5f50) [0x7fa93d417f50]
/usr/lib/libmonosgen-2.0.so.1(+0xd2a7d) [0x7fa93d424a7d]
[0x4077afb2]
Debug info from gdb:
=================================================================
Got a SIGABRT while executing native code. This usually indicates
a fatal error in the mono runtime or one of the native libraries
used by your application.
=================================================================
Aborted (core dumped)
ERROR: loading failed
* removing ‘/home/ubuntu/R/x86_64-pc-linux-gnu-library/3.2/rClr’
Error: Command failed (1)
I have noticed indeed that there were issues when running on the more recent Mono series 4.x. I had moved to use SGen with the latest releases of the 3.x series, because there were issues if using the 'default' Boehm GC libraries. It seems this is (or has been) vice and versa with the advent of Mono 4.x.
On the testing branch, there are provisions to switch between using SGen and Boehm:
# Makevars.in for rClr
# as of mono 4.0.3 on Debian, using monosgen fails. Need to offer the option to revert to boehm GC.
MONO_LIB ?= monosgen-2
# other acceptable option is MONO_LIB = mono-2
So if you want to try to compile against Boehm, if installing from R (with devtools) you may try:
Sys.setenv(MONO_LIB='mono-2')
of from a shell:
export MONO_LIB=mono-2
