Currently I am working a project that has have been using the pathlib library so I can work on my Windows desktop when I need too and on my MacBook Pro. Essentially be able to work between both operating systems. I have not have any issues at all until right now. Here is the set up:
I have a pipeline set up to automatically save a .joblib and a whole lot of .png files that will go to a directory called
output_dir = Path('../Trained_Models/Differential_gene_analysis/A Kidney Cancer Transcriptome Molecular Signature Identifies Tumors with Tumor Thrombus/Models train on TCGA data and test on Rodriguez data/Oct-XX-20XX')
For example, if I want to save a .joblib file under the name RandomForest_TumorThrombus_104.joblib,I would use the command
joblib.dump(model ,output_dir / 'RandomForest_TumorThrombus_104.joblib')
On my MacBook Pro, I have no issues when this is ran, but on Windows it gives me the following error
FileNotFoundError: [Errno 2] No such file or directory: '..\\Trained_Models\\Differential_gene_analysis\\A Kidney Cancer Transcriptome Molecular Signature Identifies Tumors with Tumor Thrombus\\Models train on TCGA data and test on Rodriguez data\\Oct-17-2022\\RandomForest_TumorThrombus_104.joblib'
I have tried to use the .resolve() method to get the absolute path but still gives me the same error. I have tried to experiment to try to see what is goin on such as using os.path.exists(). When using the os.path.exists() method I get True for the follwoing command:
os.path.exists(output_dir)
So it does indeed recognize that the directory exists. The next thing I tried was to rename the file to something like dddddd.joblib and that worked. But I find that only a few names for the file would allow me to save the files. During debug I found that the most recent Traceback occurs here:
with open(filename, 'wb') as f:```
I was wondering if anyone here had any idea what was going on here and how I can fix this issue? Please and Thank you.
The solution was to enable long paths on Windows.
I'm currently facing a problem with this team of 4.
Using binaries I downloaded on kiska's site. I'm able to compile cobol to C and run it with cobcrun or compile it to an executable. However I can 't get opencobol to find the postgres commands.
Here is the strat of my cobol script :
identification division.
program-id. pgcob.
data division.
working-storage section.
01 pgconn usage pointer.
01 pgres usage pointer.
01 resptr usage pointer.
01 resstr pic x(80) based.
01 result usage binary-long.
01 answer pic x(80).
procedure division.
display "Before connect:" pgconn end-display
call "PQconnectdb" using
by reference "dbname = postgres" & x"00"
by reference "host = 10.37.180.146" & "00"
returning pgconn
end-call
...
the call PQconnectdb fail with module ont found : PQconnectdb
I noticed that if i rename the libpq.dll the error message change to can't find entry point. So at least I'm sure it can get my dll.
After digging into the code of the call method of the libcob library. I found it it was possible to pre load some dll using an environment variable COB_PRE_LOAD but sitll no results.
Here is what look the script to compile the cobol :
call "C:\Program Files (x86)\Microsoft Visual Studio 9.0\VC\bin\amd64\vcvarsamd64.bat"
set COB_CONFIG_DIR=C:\OpenCobol\config
set COB_COPY_DIR=C:\OpenCobol\Copy
set COB_LIBS=%COB_LIBS% c:\OpenCobol\libpq.lib
set COB_LIBRARY_PATH=C:\OpenCobol\bin
set COB_PRE_LOAD=C:\OpenCobol\libpq.dll
#echo on
cobc -info
cobc -free -o pgcob -L:"C:\OpenCobol" -llibpq.lib test_cobol\postgres.cob
call cobcrun pgcob
I don't see anything missing, I'm using the 64-bit binaries from kiska's site and use the 64-bit cl.exe from Visual Studio, Postgres is a 64 bit version too (checked with dependencyChecker).
I even tryed to compile the generated C from Visual Studio, same result, but I may miss something, I'm pretty rotten in C and never really had to manage DLL or use Visual Studio.
What am I missing ?
COB_PRE_LOAD doesn't take any path or extension, see the short documentation for the available runtime configurations. I guess
set COB_LIBRARY_PATH=C:\OpenCobol\bin;C:\OpenCobol
set COB_PRE_LOAD=libpq
Will work. You can omit the C:\OpenCobol\bin if you did not placed any additional executables there.
If it doesn't work (even if it does) I'd try to get the C functions resolved at compile time. Either use
CALL STATIC "PQconnectdb" using ...
or an appropriate CALL-CONVENTION or leave the program as-is and use
cobc -free -o pgcob -L"C:\OpenCobol" -llibpq -K PQconnectdb test_cobol\postgres.cob
From cobc --help:
-K generate CALL to <entry> as static
In general: the binaries from kiska.net are quite outdated. I highly suggest getting newer ones from the official download site or ideally build them on your own from source, see the documentation for building GnuCOBOL with VisualStudio.
I am trying to run ReSharpers command line tool InspectCode.exe. It's running fine doing it's job with the expected output.
However after my earlier attempt to get plugins to work, this time with the new version it is supposed to be supported. There is a switch in the command line interface that allows to specify the extension you want to use.
/extensions (/x) – allows using ReSharper extensions that affect code analysis. To use an extension, specify its ID, which you can find by opening the extension package page in the ReSharper Gallery, and then the Package Statistics page. Multiple values are separated with the semicolon.
But I cannot get it to work properly. I cannot even provoke any reaction to the /x switch at all. No matter how or what I pass, I get no feedback from the executable and the output is identical. I don't even get an error message when passing obvious garbage.
I tried the following commandlines for the exact same result:
inspectcode.exe /o="rcli.xml" /swea /x="ReSharper.StyleCop" "my.sln"
inspectcode.exe /o="rcli.xml" /swea /x=ReSharper.StyleCop "my.sln"
inspectcode.exe /o="rcli.xml" /swea "my.sln"
inspectcode.exe /o="rcli.xml" /swea /x=ABCDEFG "my.sln"
Result
JetBrains Inspect Code 9.1.1
Running in 64-bit mode, .NET runtime 4.0.30319.18444 under Microsoft Windows NT
6.1.7601 Service Pack 1
Enabled solution-wide analysis according to Inspect Code command line Setting.
Analyzing files
[files]
Inspection report was written to rcli.xml
What am I doing wrong? How to get extensions to work?
I already tried the R# forums, but it took them more then 24h to approve my post and so far I'm not sure someone else even read it.
Unfortunately, the support for extensions was dropped in 9.0 due to the refactorings in the "ReSharper platform". I hope that JetBrains will bring it back soon.
See RSRP-436208.
This is a late answer that might help future readers (like myself). Currently inspectcode.exe will automatically look for and use any NuGet packages that are in the same folder as the executable (source).
Example for CleanCode extension:
if you have a R# instance on some machine and install the extension, it will be placed in C:\Users\{user}\AppData\Local\JetBrains\plugins\MO.CleanCode.5.6.15
copy MO.CleanCode.5.6.15.nupkg and paste it next to inspectcode.exe
when running inspectcode with verbosity = VERBOSE, the extension should appear in the Zones list:
$cmd = "..\JetBrains.ReSharper.CommandLineTools.2019.3.4\inspectcode.exe"
$outputFile = "..\Output\$($outputName).xml"
& $cmd -o="$outputFile" $sln --verbosity=VERBOSE
Zones: (52pcs)[CodeInspectionPageImplZone, DaemonEngineZone,
DaemonZone, IAmd64CpuArchitectureHostZone, IAspMvcZone,
IBatchToolEnvironmentZone, IClrImplementationHost Zone,
IClrPsiLanguageZone, ICodeEditingOptionsPageImplZone,
IConsoleEnvironmentZone, ICppProductZone, ICpuArchitectureHostZone,
IDocumentModelZone, IEnvironmentZone, IHostSolutionZone,
IInspectCodeConsoleEnvironmentZone, IInspectCodeEnvironmentZone,
IInspectCodeZone, ILanguageAspZone, ILanguageBuildScriptsZone,
ILanguageCppZone, I LanguageCSharpZone, ILanguageCssZone,
ILanguageHtmlZone, ILanguageIlZone, ILanguageJavaScriptZone,
ILanguageMsBuildZone, ILanguageNAntZone, ILanguageProtobufZone, ILa
nguageRazorZone, ILanguageRegExpZone, ILanguageResxZone,
ILanguageVBZone, ILanguageXamlZone, INetFrameworkHostZone, INuGetZone,
IOperatingSystemHostZone, IProjectMode lZone,
IPsiAssemblyFileLoaderImplZone, IPsiLanguageZone,
IPublicVisibilityZone, IRdFrameworkZone, IRiderModelZone,
ISinceClr2HostZone, ISinceClr4HostZone, ITextContro lsZone,
IToolsOptionsPageImplZone, IWebPsiLanguageZone, IWindowsNtHostZone,
PsiFeaturesImplZone, ReplaceableByIntelliJPlatformZone, SweaZone]
Packages: (23pcs)[JetBrains.ExternalAnnotations,
JetBrains.Platform.Core.Ide, JetBrains.Platform.Core.IisExpress,
JetBrains.Platform.Core.MsBuild, JetBrains.Platform. Core.Shell,
JetBrains.Platform.Core.Text, JetBrains.Platform.Interop.CommandLine,
JetBrains.Platform.Interop.dotMemoryUnit.Framework,
JetBrains.Platform.Interop.dotMe moryUnit.Interop.Console,
JetBrains.Platform.Interop.dotMemoryUnit.Interop.Ide,
JetBrains.Platform.RdProtocol, JetBrains.Psi.Features.Core,
JetBrains.Psi.Features.Cpp .Src.Core, JetBrains.Psi.Features.src,
JetBrains.Psi.Features.Tasks, JetBrains.Psi.Features.UnitTesting,
JetBrains.Psi.Features.Web.Core, JetBrains.ReSharperAutomatio
nTools.src.CleanupCode,
JetBrains.ReSharperAutomationTools.src.CommandLineCore,
JetBrains.ReSharperAutomationTools.src.CommandLineProducts,
JetBrains.ReSharperAutomat ionTools.src.DuplicatesFinder,
JetBrains.ReSharperAutomationTools.src.InspectCode, MO.CleanCode]
One certain problem is only reproducible on customer side.
We cannot reproduce it locally despite all our attempts.
But I know that TaskMgr in Windows 2008 R2 has a possibility to create dump file for a process. So, my question: is it possible to create dump on customer site for a certain process of our software and then investigate that dump file locally?
We already made a new build of our software (we saved a build sandbox and *.PDB files for all binaries). Then we installed that on site and now we are waiting when customer report that problem happens again so we will create a dump file for hanging process and then try to investigate it.
My question has 2 parts:
Would such method work at all?
If yes - how exactly to do that?
At the moment I have some doubt if that would work. Because I have tried to create a proof-test on my local Win 2008 R2 VM. I build all with .PDB files, then I run our software in a mode when it makes a long pause in the middle and I clicked "Create Dump File" in TaskMgr exactly when it does a pause (its simple call of Sleep(30000)). Then I tried to load that dump file in WinDbg and check what I could find there. First thing which makes me pessimistic about such way is a wrong stack trace. In particular - I cannot see a full stack trace in WinDbg. It shows me only stack trace for wow64.dll and ntdll.dll modules, I cannot see stack trace for our code.
In particular I see only this:
wow64cpu!TurboDispatchJumpAddressEnd+0x6c0
wow64cpu!TurboDispatchJumpAddressEnd+0x56b
wow64!Wow64SystemServiceEx+0x1ce
wow64!Wow64LdrpInitialize+0x42a
ntdll!RtlUniform+0x6e6
ntdll!RtlCreateTagHeap+0xa7
ntdll!LdrInitializeThunk+0xe
But when I try to attach process with debugger I see a full call-stack, like this:
ntdll.dll! 7754fd910
[Frames below may be incorrect and/or missing, no symbols loaded for ntdll.dll]
ntdll.dll!7754fd9l0
KernelBase.dll! 76ae3bd50
KernelBase.dll! 76ae44a 5Q
ScrVm.DLL!Profiler::DoSleep(intmilliseconds=30000) Line 205
ScrVm.DLL!Script::VmToolKit::iMethod_Sleep(unsigned char & han
ScrVm.DLL!CComponent::Invoke(const _SU::basic_string<char,std
ScrVm.DLL!Script::VirtualMachine::do_Invoke(Script::VmCommand
ScrVm.DLL!Script::VirtualMachine::InnerLoop( Line 4471
ScrVm.DLL!Script::VirtualMachine::Execute(unsigned long hFunc=
ScrVm.DLL!ScriptProcessor::Run(const _SU::basic_string<char,st
ScrVm.DLL!ScriptProcessor::ProcessDocumentO Line 285 + 0x40 by
ScrVm.DLL!DocumentProcessor::Process(BinaryDOM::Document * pDo
ScrVm.DLL!CFuncExecScript::ExecuteO Line 219
ScrVm.DLL!SrvManager::ExecuteO Line 586 +0xldbytes
ScrVm.DLL!SrvManager::Run(tag_TReqHdr "pRequestBuf=0x00187
ScrVm.DLL!SrvManager::HandleRequest(tag_TReqHdr " pRequest
ScrVm.DLL!SrvProcessRequest(tag_TReqHdr * pRequesffiuf=0x0
ScrVm.DLL!ProcessRequest(char "pRequesffiuf=0x001873b6, char "
ScrVm.DLL!ProcessRequest_DLL(char " achMsg=0x001873b6, char "a
siteExec212.exe!00409b2d0
siteExec212.exe!0040a4cfO
As you can see WinDbg seems only showing last 7 items in stack which are useless for me. Question - is it possible to discover the full stack trace from dump file created in TaskMgr in Windows 7/2008? Or at least - I need more items in stack trace, to see from what place in our code this call was made.
Note: compiler MS VisualStudio 2008, WinDbg 6.12 x64.
Since your process is 32 bit you must use the 32 bit version of Task Manager to create the dump. Default installs have it in C:\Windows\SysWow64\taskmgr.exe
Also, make sure to use the 32 bit version of windbg.
I installed moodle 1.9.12 and now I want to use Algebra notation in content. I enable "TeX Notation" and "Algebra Notation" in administrator panel and also install mimetext and dvips and Imagemagic on the server. fortunately Tex Notation works fine but I got the following error for Algebra:
sh: /var/www/html/moodle/filter/tex/mimetex.linux: not found
The shell command
"/var/www/html/moodle/filter/tex/mimetex.linux" -e "/var/www/moodledata/filter/algebra/de06d6c44d98ba4e42dffca988bf530b.gif" -- '\Large \frac{\sin\left(z\right)}{x^{2}+y^{2}}'
returned status = 127
File size of mimetex executable /var/www/html/moodle/filter/tex/mimetex.linux is 830675
The file permissions are: 100775
The md5 checksum of the file is 56bcc40de905ce92ebd7b083c76e019e
Image not found!
Note: /var/www/html/moodle/filter/tex/mimetex.linux exists on the server and is executable!!!
What is the problem?? Any idea?????
From what you have described, calling the general tex filter debug page works and does not show up the same error.
/filter/tex/texdebug.php works, but /filter/algebra/algebradebug.php does not.
If this is the case, perhaps you could check for an open_basedir, or safe_mode_exec_dir being set to include the current working directory, or otherwise restricting the execution of /var/www/html/moodle/filter/tex/mimetex.linux, while the current working directory is /var/www/html/moodle/filter/algebra.
You could look at this by visiting /admin/phpinfo.php at your site, and look carefully at the effective values of open_basedir, safe_mode and safe_mode_exec_dir.
You could also check the apache error log or add the following lines to the top of the algebra debug php file, and you might see some extra error messages:
$CFG->debug = 6143 ;
$CFG->debugdisplay= 1 ;
Hope that helps