I want to install the lates version of MUSCLE downloaded from http://www.drive5.com/muscle/downloads.htm
named muscle3.8.31_i86win32.exe . As the guidelines
http://www.drive5.com/muscle/manual/install.html
says I have to write the below line in the command prompt:
C:\Program Files (x86)\muscle3.8.31_i86win32 -in seqs.fa -out seqs.afa
However, I faced this error:
MUSCLE v3.8.31 by Robert C. Edgar
http://www.drive5.com/muscle This software is donated to the public
domain. Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97.
* ERROR * Cannot open 'seqs.fa' errno=2
I am sure the file exists in the mentioned directory, but I don't why has this happened and how can I fix it. Any idea?
The program is reporting that the OS reported that the file doesn't exist. (That's what errno 2 is.)
Testing reveals that relatives paths are resolved relative to the current work directory as expected.
So, your operating system is saying there's no file named seqs.fa in the current work directory.
Double check the name of the file you have. Keep in mind that File Explorer hides known file extensions by default so using dir would be more reliable.
Related
I am using Conan package manager on Windows to create a package. The conan command to create the package copies files to a folder within %USERPROFILE%\.conan (or C:\Users\xxxxxxx\.conan). Then from this location it builds a Visual Studio project and ultimately calls doxygen.exe to create a .chm help file in a post-build command. The doxygen command fails with:
error : failed to run html help compiler on index.hhp
Further investigation reveals the hhc.exe command executed by doxygen is failing with:
C:\Users\xxxxxxx\.conan\data\Module\1.0.0\user\channel\build\524dc97e4a3dd1f774ea3897f9e4faf26c5457d2\Documentation>"C:/Program Files (x86)/HTML Help Workshop/hhc.exe" html\index.hhp
HHC5010: Error: Cannot open "C:\Users\xxxxxxx\data\Module\1.0.0\user\channel\build\524dc97e4a3dd1f774ea3897f9e4faf26c5457d2\Documentation\html\Module.chm". Compilation stopped.
Close inspection reveals that in the error message, the ".conan" folder is missing. Sure enough, I confirmed that hhc.exe fails when the index.hpp resides in a folder that has a parent folder that starts with a ".".
Attempts to resolve this:
changing the Doxyfile setting OUTPUT_DIRECTORY to "$(TMP)/DoxygenModule" resolves the error, but creates the .chm file in another location, which I do not prefer.
navigating to the 8DOT3 name of the ".conan" folder, which is "CONAN~1", to run the hhc.exe command, succeeds, but unfortunately I have no way of getting conan to use this 8DOT3 path for creating the package. E.g. C:\Users\xxxxxxx\CONAN~1\...
I can live with the using the %TMP% folder but would prefer generating the .chm in the current folder. Anyone have any ideas?
HTML Help Workshop v1.31 is installed on my machine at C:\Program Files (x86)\HTML Help Workshop, probably from a Visual Studio installation (not sure). I attempted using a version downloaded from Microsoft website (v1.30) as well, which made no difference.
Other info: Conan version 1.18.0, Doxygen version 1.8.14, Windows 10 Version 1809
Unfortunately not a solution, but this is a known limitation in the hhc.exe, see: https://social.msdn.microsoft.com/Forums/en-US/0681145c-223b-498c-b7bf-be83209cbf4e/issue-with-html-workshop-in-a-windows-container?forum=visualstudiogeneral
HTML Help 1.x command line compiler hhc.exe cannot compile CHM file to folder whose full path contains folder name starting with dot. If you have that problem, you probably specified output path with folder starting with dot, e.g. "d:\My files.NET\documentation". You can use dots in folder names but not at the beginning.
Edit 2019-11-15:
I've just pushed a proposed patch to github (pull request 7402, https://github.com/doxygen/doxygen/pull/7402).
This proposed patch changes inside doxygen from the current directory to the short named current directory, but just for the HTML Help compilation.
Edit 2019-11-16:
Code has been integrated in the master version on github.
This is not an answer either. Actually, you found the answer and workaround[s] yourself.
Use OUTPUT_DIRECTORY to specify a directory containing no folder names beginning with periods.
The error you described is a known issue of the MS HTML Help compiler. More general, the HTML Help compiler does not like some folder and file names. Try and stick with these characters _, a..z, A..Z, 0..9. Do not use these signs in particular ., -, # .
Please note that the proprietary CHM file format is about 20 years old (Windows 95, ...). HTML Help is in maintenance mode, which means no new features and bug fixes are expected for either the runtime or the compiler. All mainstream development on HH has stopped.
There is no way to avoid this error if a directory name above begins with a period. Not even if only the necessary files are written by Doxygen and compiling of the index.hhp is done by a third-party tool like FAR HTML using your path that contains .conan. This is because all applications are using the faulty HHA.dll.
The above applies of course to the entire workflow you have described. Maybe you can interrupt it.
Doxygen can be configured not to call the HTMLHelp compiler. Just uncheck the GENERATE_HTMLHELP option (DoxyWizard: Experts > Topics > HTML). You have all files generated by Doxygen in your preferred output directory - but of course without the CHM file. This can be imported later e.g. by HelpNDoc and compiled as a CHM file in another location.
If you can interrupt the workflow and can also make changes to Doxygen's settings, then a preference setting of OUTPUT_DIRECTORY to e.g. C:/CacheMenu/CONAN~1/DOXYGE~1 also works as expected (here used as test case).
No matter what you do, your workaround and copy and paste from another directory outside is a quick solution at this stage. Please note the EDIT in #albert's answer.
I have a problem using 'xcopy' command.
I'm building a C# project with msbuild. At the end of the build, a batch file is called to copy my assemblies from Debug/Release to some other folders.
Here is the problem, my build fail and the error log is 'xcopy is not recognized as an internal or external command, operable program or batch file'.
The path is correctly set, xcopy do works from a windows command line and from the visual studio command line (the one set with the project environment).
I tried to set the path in the batch file but it doesn't help.
Any suggestion?
I'm using windows 7
Cheers :)
I encountered the same problem.
It seems to be a problem with the path environment variable within Visual Studio.
When I added a "path" statement to the beginning of my build event, it produced the following output:
PATH=
This seems to indicate that the path is empty within the VS build environment.
When I specify the full path to xcopy like this, the problem went away:
%systemroot%\System32\xcopy ...
I'm not sure what caused Visual Studio to lose it's path.
Set Environment variable PATH = %SystemRoot%\system32;%SystemRoot%;%SystemRoot%\System32\Wbem;%SYSTEMROOT%\System32\WindowsPowerShell\v1.0\
This is not a problem with Windows 7 or 8. It's actually a problem with applications that update environment variables such as PATH.
The PATH is stored in the Registry as an "Expandable string value" (REG_EXPAND_SZ), but a lot of applications write it back to the Registry as a "String Value" (REG_SZ). If your path contains anything like %SYSTEMROOT%, this will not be expanded into C:\Windows (or whatever yours is) if the path is stored in a REG_SZ.
The fix is simply to edit your path manually from the control panel. You need to make a change (eg add a ; to the end of the path) and then apply it. This will fix up your path in the Registry to be a REG_EXPAND_SZ.
(Go to the System Control Panel and select Advanced System Settings. Edit the Path Environment variable in the lower box, and that should fix it.
You can tell whether your path is broken in this way by opening a command prompt and typing PATH. Your path will be listed. If you can see anything enclosed in % % then your path is not being expanded.
It happened to me after I updated one of my Visual Studio extensions, during which Visual Studio was closed and reopened by the updater. I could no longer properly build my project. I closed Visual Studio and reopened it and the problem went away.
I just experienced this for the first time with a batch file I use to copy an Access front-end app to the user's local machines. Their environment is a mix of Windows 7 & 8 and 32-64 bit machines. I noticed that the xcopy.exe was both in the System32 and the SysWOW64 folders and I wondered if there was some conflict. So -- I copied the xcopy.exe into the folder where the batch file resides and it now seems to be working. Just thought I'd share this.
Eileen
I also had a problem with xcopy (same error message) - with a very simple batch program that I use to backup files to a removable drive. Have been using that program for at least 5 years with never a problem. Then yesterday xcopy is unknown to Win7. The replacement of xcopy with %systemroot%\System32\xcopy at each instance solved the problem. Very strange.
Go to environment variable and correct PATh including ; in last.
It will work, this is not at all related to OS or Technology.
It's working for me, Not even need to restart OS, Just open new command prompt.
[Fixed for me]
After adding the correct paths to "Path" environmental variable it still doesn't work (for cmd and VisualStudio) (even after restarting the PC).
The problem was in broken register parameter:
[HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Control\Session Manager\Environment]
ParameterName=PATHEXT
I had the value .wlua;.|exe. Maybe was broken after installing something.
Everything works again after changing it to:
.COM;.EXE;.BAT;.CMD;.VBS;.VBE;.JS;.JSE;.WSF;.WSH;.MSC
Hope this helps if nothing other works.
I try to install/run emacs on a Win7 64-bit machine after using it for years on a WinXP 32-bit machine and run into a problem I do not find any help for in the documentation or on the web.
Symptom:
when starting runemacs.exe for the first time it creates the file
*C:\Users\USER\My Documents.emacs.d*
as one would expect (for my administrator as well as for my user account)
and comes up operational
from the second start of runemacs.exe it breaks in the startup phase,
displaying the scratch buffer, ringing the warning bell and displaying in
bottom line the error:
File exists: c:/Users/USER/My Documents/.emacs.d/
buffer messages specifies:
make-directory: File exists: c:/Users/USER/My Documents/.emacs.d/
if runemacs was called with a file to open, i.e. because the file type was
associated with it and the file was opened to edit, the file is not open
and ready to be edited, but a file can be opened via the menu File->Open File...
but my configurations in the file
C:\Users\USER\My Documents.emacs
are not loaded
My goal:
I want to regain the way I used emacs on the old WinXP 32-bit system:
click a file associated with emacs, get it opened and ready for editing, get my configurations in .emacs loaded automatically, i.e. work with emacs seamlessly.
Checks done and failed attempts to fix this:
I tried the following newly downloded versions of emacs
emacs-23.4-bin-i386.zip
emacs-23.2-bin-i386.zip (the one I used on the WinXP)
I had the emacs directory containing the directory stucture (bin, etc, ...)
located at:
C:\Program Files (x86)\emacs-23.4\ (my preferred location)
C:\Emacs\emacs-23.4\
in the download directory, where I originally extracted it
My HOME variable points to:
C:\Users\USER\My Documents (default)
C:\Users\USER\My Documents\ (tried)
My PATH variable contains:
C:\Program Files (x86)\emacs-23.4\bin (default)
or the corresponding other locations which I tried
The ownership and permissions of my C:\Users\USER\My Documents.emacs.d
look OK:
owner is the USER (administrator or standard_user)
permissions grant Full Control
Having originally installed emacs to *C:\Program Files (x86)\emacs-23.4*
using the administrator account, I also tried to use user account installation
instead (to check for some non- obvious parameter/access permission not set
right if the admin account is uses for setup)
For the runemacs.exe executable I manually set the compatibility settings to
Windows XP (Service Pack 3)
default setting after unpacking: no compatibility setting enabled
I removed the private configuration file C:\Users\USER\My Documents.emacs
(inherited from my XP installation) to check whether it produces a screw-up
All that did not change a bit of the described symptom, i.e. either I screwed up
in testing the above and missed a particular setting which should work, or I am looking into the wrong direction...
It is still unclear to me whether this has anything to do with:
W7 64-bit vs. XP 32-bit
environmental parameter screw-up
emacs configuration (.emacs, .emacs.d) screw-up
general stupidity (of me ;-)
... and why is it has emacs a problem with it in the first place, that the .emacs.d directory already exists... That should be the standard case...
Any help and wisdom much appreciated.
First of all, nice question. The details and listing of what you've already tried is helpful.
Some points:
Don't have spaces in key paths (Emacs, and %HOME%). Generally, things work
fine. But when things break it's often hard to debug and trace back to the
fact that some package author didn't take spaces properly into account.
Set a HOME environment variable to your %USER_PROFILE%. Make it
%USER_PROFILE%/home if you must, but I use the former.
Start by running emacs without any customization.
runemacs -Q
When that works, add your customizations one at a time.
n.b. This answer is not relevant to the original question (which was about Windows), but may be useful to Unix users searching for this error message
You will get this error also if emacs does not have the correct permissions on the .emacs.d directory.
Check it
ls -ld $HOME/.emacs.d
And make sure the user you are running under has rwx permissions!
I got similar problems when I installed the new version of emacs on a new installation of the ubuntu 12.10. I get the problem fixed by chmod 777 .emacs.d, that is, as the previous post pointed out, the emacs does not have the access right to .emacs.d directory. Hope this help.
When i am trying to open eclipse exe file , window is not opened , why this is happened , previously it is working fine but today it is not opened any changes i need to do?it will help full if any one gave quick fix .
thanks
Ramana
(The OP ramana solved it by uninstalling and re-installing Java, but below is another potential cause)
Check if your PATH hasn't changed somehow: see Java Tips: “Adventure” in resolving the Java error “Error occurred during initialization of VM”
Running Java.exe produce error in other directories (since the SDK’s bin is added to path.)
However running in it’s bin directory, it runs fine.
In the case of the ips mentioned before, the issue was:
The good news is that it is nothing supernatural or magical image but the bad news is that the Windows directory is the “protagonist” image.
From file search, it can be concluded that somehow certain mischievous program is copying some crucial java files into Windows directory which are stored in path, and so unless the java’s bin is the foremost in the path, one will bound to get the error.
The error occurs because java.exe or other Java executable expect some support files and directories to be found but obviously could not find it in Windows directory.
Running the java.exe in its bin directory will not produce error because Windows will use the current directory to which the file is run first before searching for it in the path.
That might not be the case for you, but that could still be related to a PATH issue.
I'm just trying to build a simple update (which I have done before) for an iphone app, but now for some reason I'm getting this error. Can anyone tell me what it means?
Command/Developer/Library/Xcode/Plug-ins/CoreBuildTasks.xcplugin/Contents/Resources/copyplist failed with exit code 127
sh: plutil: command not found
Here are the Build Results:
CopyPNGFile /Users/me/path/build/Dist-iphoneos/MyApp.app/img_000.png images/img_000.png
cd /Users/me/
setenv COPY_COMMAND /Developer/Library/PrivateFrameworks/DevToolsCore.framework/Resources/pbxcp
setenv PATH "/Developer/Platforms/iPhoneOS.platform/Developer/usr/bin:/Developer/usr/bin:/System/Library/Frameworks/JavaVM.frameworK/Versions/1.6/Home/"
"/Developer/Platforms/iPhoneOS.platform/Developer/Library/Xcode/Plug-ins/iPhoneOS Build System Support.xcplugin/Contents/Resources/copypng" -compress "" /Users/path/images/img_000.png /Users/me/path/build/Dist-iphoneos/MyApp.app/img_000.png
sh: dirname: command not found
CopyPlistFile /Users/me/path/build/Dist-iphoneos/MyApp.app/Entitlements.plist Entitlements.plist
cd /Users/me/
setenv PATH "/Developer/Platforms/iPhoneOS.platform/Developer/usr/bin:/Developer/usr/bin:/System/Library/Frameworks/JavaVM.frameworK/Versions/1.6/Home/"
/Developer/Library/Xcode/Plug-ins/CoreBuildTasks.xcplugin/Contents/Resources/copyplist --convert binary1 Entitlements.plist --outdir /Users/me/path/build/Dist-iphoneos/MyApp.app
sh: plutil: command not found
Your PATH variable is screwed up for some reason. You want to look into how exactly that happened. This is yours (colon-separated for emphasis):
setenv PATH "/Developer/Platforms/iPhoneOS.platform/Developer/usr/bin
:/Developer/usr/bin
:/System/Library/Frameworks/JavaVM.frameworK/Versions/1.6/Home/"
This is what a working PATH looks like:
setenv PATH "/Developer/Platforms/iPhoneOS.platform/Developer/usr/bin
:/Developer/usr/bin
:/usr/bin
:/bin
:/usr/sbin
:/sbin"
(line separation is to clarify how PATH variables are separating paths)
Notice how mine has /usr/bin:/bin:/usr/sbin:/sbin and yours does not? This is the problem right there. The shell script only finds executables in its path, and while the files are in /usr/bin/, it doesn't find them.
For an SO discussion on Xcode PATH's, see e.g. where is $PATH set in xcode?
Is it possible that your path environment variable is not set somehow?
You have:
setenv PATH "/Developer/Platforms/iPhoneOS.platform/Developer/usr/bin:/Developer/usr/bin:/System/Library/Frameworks/JavaVM.frameworK/Versions/1.6/Home/"
/Developer/Library/Xcode/Plug-ins/CoreBuildTasks.xcplugin/Contents/Resources/copyplist --convert binary1 Entitlements.plist --outdir /Users/me/path/build/Dist-iphoneos/MyApp.app
While I show:
setenv PATH "/Developer/Platforms/iPhoneSimulator.platform/Developer/usr/bin:/Developer/usr/bin:/opt/local/bin:/usr/local/bin:/bin:/sbin:/usr/bin:/usr/sbin"
builtin-infoPlistUtility test34-Info.plist -genpkginfo /Users/gnd/Desktop/test34/build/Debug-iphonesimulator/test34.app/PkgInfo -expandbuildsettings -format binary -platform iphonesimulator -o /Users/gnd/Desktop/test34/build/Debug-iphonesimulator/test34.app/Info.plist
I don't see /usr/bin in your path.
(in terminal:
echo ${PATH}
though most OS X GUI applications get their path from ~/.MacOSX/environment.plist not 100% sure about Xcode though.
Additional Info:
from the 'man bash' page:
When bash is invoked as an interactive login shell, or as a non-interactive shell with the --login option, it first reads and executes commands from the file /etc/profile, if that file exists. After reading that file, it looks for ~/.bash_profile, ~/.bash_login, and ~/.profile, in that order, and reads and executes commands from the first one that exists and is readable.
So if you have it in .bash_login but .bash_profile exists, then your change will not be seen.
Also note the comment about the GUI apps PATH definition alternate file above.
You may need to log out and then back in to get the change to "take".
I had same problem.... the problem is that plutil is not in any of the directories in PATH.
My solution was to make a copy from /usr/bin to /user/local/bin which is in the PATH.
No idea if the problem is Xcode, OS X or Apple.
plutil usually resides in /usr/bin. Make sure it's there. If it's not, you may have installed your Developer Tools without unchecking (or with unchecking) the System Tools checkbox, which puts the base Mac OS X programmer tools into /usr.
Tried reinstalling the SDK?
I have gone over the answers provided and none of them worked for me. The problem persisted.
I looked carefully at the error in xcode and notice that it was looking for the image in the wrong place. In my case I had copied and renamed the directory containing my project. None of the references to my images were updated.
I fixed my problem by right clicking the project file in finder and clicking Show Package Contents. I then opened the *.pbxproj in xcode. I did a find and replace on the file to replace the name of the old folder with the new folder.
After closing and opening xcode this solved my problem.
I hope this helps others...
I've seen this error before. The issue lies in a corrupted .png file. The error is pretty deceiving. Try deleting the affected .png and replace it back in your project from a backup or clean version of that file. That should clear up the build errors.
this error will also show if you deleted a file via finder (not in xcode) then try to archive. So make sure that none of your files are listed in red and if they are remove it from your project.