Re: Compilation help / error CS2001

Hi Chandler

The source is simply incomplete, you won't be able to build with the part
the was commited to GitHub, you can try to contact the maintainers, but you
can also simply create a dummy AssembyInfo.cs inside a Properties folder
and try to compile, although it may not be enough to make it work.

Anyway, the program is already compiled up there in GitHub, so you can
simply run it with:

mono ConPADE.exe -bamName TestData.bam


As it is a console program and uses mainly the .NET Bio libraries that are
compatible with Mono, so it should work.

Please note that Linux doesn't support Windows batch files (.bat) and that
you always need to call mono to run the program (unless you
configure binfmt to automate things, which I don't recommend), it is
preferable to write a shell script (normally a bash script) as a wrapper to
make it easier to call the program. Something like a file named conpade in
some folder in the PATH, marked with the executable bit (chmod +x) and with
content similar to:

#!/bin/sh
> /usr/bin/mono /opt/MicrosoftGenomics/ConPADE/ConPADE.exe "$@"


Then you would be able to simply use like in Windows:

conpade TestData.bam


Remember that Linux is case-sensitive, so 'conpade' is different from
'ConPADE'.

For more details, look at the old but still mostly valid documentation at
http://www.mono-project.com/archived/guiderunning_mono_applications/

Hope it helps,

Rafael Teixeira
O..:.)oooo

On Tue, May 30, 2017 at 9:36 PM, Chandler <[email protected]> wrote:

> I would like to install this program on our Linux machines for our users:
> https://github.com/MicrosoftGenomics/ConPADE
>
> but I am running into the error "CSC: error CS2001: Source file
> '/opt/MicrosoftGenomics/ConPADE/Properties/AssemblyInfo.cs' could not be
> found."
>
> The OS is RHEL 6.8 and i have installed mono-complete 5.0.1 using the
> "CentOS 6" repositories.  I copied the files from src/* to the root dir,
> since it was complaining about not finding those files, but maybe i'm just
> not doing it right with xbuild?  Or is it something the developer needs to
> address?  See below for full output.
>
> Thanks,
> Chandler / Systems Administrator
> Arizona Genomics Institute
> www.genome.arizona.edu
> --
>
> $ cd /opt/MicrosoftGenomics/ConPADE/
> /opt/MicrosoftGenomics/ConPADE$ cp src/* .
> /opt/MicrosoftGenomics/ConPADE$ xbuild ConPADE.csproj
>
> >>>> xbuild tool is deprecated and will be removed in future updates, use
> msbuild instead <<<<
>
> XBuild Engine Version 14.0
> Mono, Version 5.0.1.1
> Copyright (C) 2005-2013 Various Mono authors
>
> Build started 5/30/2017 5:18:13 PM.
> __________________________________________________
> Project "/opt/MicrosoftGenomics/ConPADE/ConPADE.csproj" (default
> target(s)):
>         Target PrepareForBuild:
>                 Configuration: Debug Platform: x86
>         Target GenerateSatelliteAssemblies:
>         No input files were specified for target
> GenerateSatelliteAssemblies, skipping.
>         Target _GenerateTargetFrameworkMonikerAttribute:
>         Skipping target "_GenerateTargetFrameworkMonikerAttribute"
> because its outputs are up-to-date.
>         Target CoreCompile:
>                 Tool /usr/lib/mono/4.5/csc.exe execution started with
> arguments: /noconfig /debug:full /debug:portable /optimize-
> /out:obj/x86/Debug/ConPADE.exe ConPADE.cs Properties/AssemblyInfo.cs
> Read.cs obj/x86/Debug/.NETFramework,Version=v4.5.AssemblyAttribute.cs
> /target:exe /define:"DEBUG;TRACE" /doc:bin/Debug/ConPADE.XML /nostdlib
> /platform:x86 /reference:./Bio.Core.dll /reference:./Bio.Desktop.dll
> /reference:./Bio.Platform.Helpers.dll /reference:/usr/lib/mono/4.5-api/System.dll
> /reference:/usr/lib/mono/4.5-api/System.Xml.Linq.dll
> /reference:/usr/lib/mono/4.5-api/System.Data.DataSetExtensions.dll
> /reference:/usr/lib/mono/4.5-api/Microsoft.CSharp.dll
> /reference:/usr/lib/mono/4.5-api/System.Data.dll
> /reference:/usr/lib/mono/4.5-api/System.Xml.dll
> /reference:/usr/lib/mono/4.5-api/System.Core.dll
> /reference:/usr/lib/mono/4.5-api//mscorlib.dll
> /reference:/usr/lib/mono/4.5-api/Facades/System.Collections.Concurrent.dll
> /reference:/usr/lib/mono/4.5-api/Facades/System.Collections.dll
> /reference:/usr/lib/mono/4.5-api/Facades/System.ComponentModel.Annotations.dll
> /reference:/usr/lib/mono/4.5-api/Facades/System.ComponentModel.EventBasedAsync.dll
> /reference:/usr/lib/mono/4.5-api/Facades/System.ComponentModel.dll
> /reference:/usr/lib/mono/4.5-api/Facades/System.Diagnostics.Contracts.dll
> /reference:/usr/lib/mono/4.5-api/Facades/System.Diagnostics.Debug.dll
> /reference:/usr/lib/mono/4.5-api/Facades/System.Diagnostics.Tools.dll
> /reference:/usr/lib/mono/4.5-api/Facades/System.Diagnostics.Tracing.dll
> /reference:/usr/lib/mono/4.5-api/Facades/System.Dynamic.Runtime.dll
> /reference:/usr/lib/mono/4.5-api/Facades/System.Globalization.dll
> /reference:/usr/lib/mono/4.5-api/Facades/System.IO.dll
> /reference:/usr/lib/mono/4.5-api/Facades/System.Linq.Expressions.dll
> /reference:/usr/lib/mono/4.5-api/Facades/System.Linq.Parallel.dll
> /reference:/usr/lib/mono/4.5-api/Facades/System.Linq.Queryable.dll
> /reference:/usr/lib/mono/4.5-api/Facades/System.Linq.dll
> /reference:/usr/lib/mono/4.5-api/Facades/System.Net.NetworkInformation.dll
> /reference:/usr/lib/mono/4.5-api/Facades/System.Net.Primitives.dll
> /reference:/usr/lib/mono/4.5-api/Facades/System.Net.Requests.dll
> /reference:/usr/lib/mono/4.5-api/Facades/System.ObjectModel.dll
> /reference:/usr/lib/mono/4.5-api/Facades/System.Reflection.Emit.ILGeneration.dll
> /reference:/usr/lib/mono/4.5-api/Facades/System.Reflection.Emit.Lightweight.dll
> /reference:/usr/lib/mono/4.5-api/Facades/System.Reflection.Emit.dll
> /reference:/usr/lib/mono/4.5-api/Facades/System.Reflection.Extensions.dll
> /reference:/usr/lib/mono/4.5-api/Facades/System.Reflection.Primitives.dll
> /reference:/usr/lib/mono/4.5-api/Facades/System.Reflection.dll
> /reference:/usr/lib/mono/4.5-api/Facades/System.Resources.ResourceManager.dll
> /reference:/usr/lib/mono/4.5-api/Facades/System.Runtime.Extensions.dll
> /reference:/usr/lib/mono/4.5-api/Facades/System.Runtime.InteropServices.WindowsRuntime.dll
> /reference:/usr/lib/mono/4.5-api/Facades/System.Runtime.InteropServices.dll
> /reference:/usr/lib/mono/4.5-api/Facades/System.Runtime.Numerics.dll
> /reference:/usr/lib/mono/4.5-api/Facades/System.Runtime.Serialization.Json.dll
> /reference:/usr/lib/mono/4.5-api/Facades/System.Runtime.Serialization.Primitives.dll
> /reference:/usr/lib/mono/4.5-api/Facades/System.Runtime.Serialization.Xml.dll
> /reference:/usr/lib/mono/4.5-api/Facades/System.Runtime.dll
> /reference:/usr/lib/mono/4.5-api/Facades/System.Security.Principal.dll
> /reference:/usr/lib/mono/4.5-api/Facades/System.ServiceModel.Duplex.dll
> /reference:/usr/lib/mono/4.5-api/Facades/System.ServiceModel.Http.dll
> /reference:/usr/lib/mono/4.5-api/Facades/System.ServiceModel.NetTcp.dll
> /reference:/usr/lib/mono/4.5-api/Facades/System.ServiceModel.Primitives.dll
> /reference:/usr/lib/mono/4.5-api/Facades/System.ServiceModel.Security.dll
> /reference:/usr/lib/mono/4.5-api/Facades/System.Text.Encoding.Extensions.dll
> /reference:/usr/lib/mono/4.5-api/Facades/System.Text.Encoding.dll
> /reference:/usr/lib/mono/4.5-api/Facades/System.Text.RegularExpressions.dll
> /reference:/usr/lib/mono/4.5-api/Facades/System.Threading.Tasks.Parallel.dll
> /reference:/usr/lib/mono/4.5-api/Facades/System.Threading.Tasks.dll
> /reference:/usr/lib/mono/4.5-api/Facades/System.Threading.dll
> /reference:/usr/lib/mono/4.5-api/Facades/System.Xml.ReaderWriter.dll
> /reference:/usr/lib/mono/4.5-api/Facades/System.Xml.XDocument.dll
> /reference:/usr/lib/mono/4.5-api/Facades/System.Xml.XmlSerializer.dll
> /warn:4
>                 Microsoft (R) Visual C# Compiler version 2.0.0.61404
>                 Copyright (C) Microsoft Corporation. All rights reserved.
> CSC: error CS2001: Source file '/opt/MicrosoftGenomics/ConPADE/Properties/AssemblyInfo.cs'
> could not be found.
>         Task "Csc" execution -- FAILED
>         Done building target "CoreCompile" in project
> "/opt/MicrosoftGenomics/ConPADE/ConPADE.csproj".-- FAILED
> Done building project "/opt/MicrosoftGenomics/ConPADE/ConPADE.csproj".--
> FAILED
>
> Build FAILED.
> Errors:
>
> /opt/MicrosoftGenomics/ConPADE/ConPADE.csproj (default targets) ->
> /usr/lib/mono/xbuild/14.0/bin/Microsoft.CSharp.targets (CoreCompile
> target) ->
>
>         CSC: error CS2001: Source file '/opt/MicrosoftGenomics/ConPADE/Properties/AssemblyInfo.cs'
> could not be found.
>
>          0 Warning(s)
>          1 Error(s)
>
> Time Elapsed 00:00:01.5263370
> /opt/MicrosoftGenomics/ConPADE$
>
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