I use the Linux kernel style in my C code, even though it's not related to the kernel. Running checkpatch.pl produces ERROR: Missing Signed-off-by: line(s). How to ignore it?
To intentionally silence the ERROR: Missing Signed-off-by: line(s) one can pass the --no-signoff parameter, e.g.:
git show | checkpatch.pl --no-tree --no-signoff
This can also be added on a new line to the .checkpatch.conf file to avoid having to type it.
Related
I have used Trimmomatic-0.39 few times already for trimming some sequencing data. This time I tried the option -baseout as stated in the manual but it does not recognise it as a valid option and the command does not run. If I run the command, as I usually I do with all the output files listed, it works though.
I type in the command line:
java -jar trimmomatic-0.39.jar PE -phred33 -trimlog trimmed_file18_log.log -baseout file18.fastq.gz file18-R1.fastq.gz file18-R2.fastq.gz ILLUMINACLIP:NexteraPE-PE.fa:2:30:10 MAXINFO:25:0.2 MINLEN:20
What I get back is:
Unknown option -baseout file18.fastq.gz
Usage:
PE [-version] [-threads <threads>] [-phred33|-phred64] [-trimlog <trimLogFile>] [-summary <statsSummaryFile>] [-quiet] [-validatePairs] [-basein <inputBase> | <inputFile1> <inputFile2>] [-baseout <outputBase> | <outputFile1P> <outputFile1U> <outputFile2P> <outputFile2U>] <trimmer1>...
or: .....
I get back the same error message even if I move the '-baseout file18.fastq.gz' option after '...jar PE' and before the list of all the other options.
I have checked about the function of "-n" --
"Displays active TCP connections, however, addresses and port numbers are expressed numerically and no attempt is made to determine names."
But I can't see why "-n" can make netstat exit immediately?
From a quick check, I don't see the same description for the "-n" option as you do, and it doesn't make netstat run continuously.
As you didn't specify the version and exact command you are using, I tried both the version that comes with RH7.6 (net-tools 2.10-alpha) and the latest from source code (net-tools 3.14-alpha). The net-tools source code can be found in github [1].
As I couldn't find the exact option you describe, I tried all flags (without combinations) that don't require an argument. As far as I can tell the only options that cause netstat to not exit immediately are '-g' and '-c'. '-c' makes sense as it is the flag for running netstat continuously. For '-g' it isn't as obvious as the continuous behavior is coming from reading the /proc/net/igmp and /proc/net/igmp6 files line-by-line. The first file is read quickly but the igmp6 file takes much longer (1 line per ~1 sec). The '-g' option isn't really continuous, but just takes a lot of time to finish.
From the code, the only reason for continuous execution is (appears 4 times in the code):
if (i || !flag_cnt)
break;
wait_continous();
'i' is a return code from a function and the 'break' command is to break from an infinite for loop, so basically the code will run continuously only if flag_cnt is set (only happens when '-c' is provided) and there were no errors with previous commands.
For the specific issue above there could be a few reasons:
The option involves reading from a file and it takes very long time to finish, but it is not really continuous.
There's a correlation between the given option and flag_cnt, which cause flag_cnt to be set.
There's a call to wait_continous() which doesn't follow the condition above.
As I said, I couldn't reproduce the issue in the original question, nor could I find any flag with the description above. Also, non of the flags besides '-c' caused netstat to run continuously.
If you still want to figure this out I suggest you take a look at your code, or at least specify the net-tools version you use. The kernel version is also important as some code would be compiled-out due to missing kernel support.
[1] https://github.com/ecki/net-tools
I am running developmental scientific code. I am stuck on a cryptic error message, and am curious what the OpenMDAO team thinks. When I run the code in serial, it works with no issues. When I run it under mpirun, OpenMDAO throws a cryptic error message:
Traceback (most recent call last):
File "test/exampleOptimizationAEP.py", line 129, in <module>
prob['ratedPower'] = ratedPower
.....
File "/scratch/jquick/test/lib/python2.7/site-packages/openmdao-1.7.3-py2.7.egg/openmdao/core/vec_wrapper.py", line 1316, in __setitem__
(self.name, name))
AttributeError: 'params' has not been initialized, setup() must be called before 'ratedPower' can be accessed
I am not sure how to approach this. There is nothing obviously different about the ratedPower variable in the code. What information does this error give me about what is going wrong?
This is a bug in OpenMDAO <= v1.7.2. Look at the output of check_setup and see the list of parameters without associated unknowns. You will find that variable in there. When running in parallel (because of the bug), you can not set any hanging params (ones without associated unknowns) in your setup script.
The way to fix it is to add an IndepVarComp to any variable you need to initialize the value of.
Here is a basic script with getopt command and assigned variables.
If someone were to type in
MyScript -a
with no words or numbers added after the -a, then an error message would pop up! The same happens if you replace -a with any other assigned variables. If I wanted no error message to appear, how would I go about doing this?
Hints/advice is preferred over a simply strict answer!
From the bash manual:
getopts can report errors in two ways. If the first character of optstring is a colon, silent error reporting is used. In normal operation diagnostic messages are printed when invalid options or missing option arguments are encountered. If the variable OPTERR is set to 0, no error messages will be displayed, even if the first character of optstring is not a colon.
Since you tag the question with Unix and don't mention bash, you may or may not be so lucky, but the answer is to read the manual page carefully.
It's a bit annoying that when I hit a break point in XCode 4, values of Watch Expressions are always grayed out. I have to create dummy variables pointing to the thing I want to watch in order to get around it.
The log says the following errors when I run the app:
warning: Unable to read symbols for /Developer/Platforms/iPhoneOS.platform/DeviceSupport/4.3.3 (8J2)/Symbols/System/Library/Frameworks/IOKit.framework/IOKit (file not found).
warning: Tried to remove a non-existent library: /Developer/Platforms/iPhoneOS.platform/DeviceSupport/4.3.3 (8J2)/Symbols/System/Library/Frameworks/IOKit.framework/IOKit
Current language: auto; currently objective-c++
warning: Unable to read symbols for /Developer/Platforms/iPhoneOS.platform/DeviceSupport/4.3.3 (8J2)/Symbols/Developer/usr/lib/libXcodeDebuggerSupport.dylib (file not found).
How can I fix this?
As for myself, I debug variables using two handy GDB console commands. You can enter them when in debug mode in debug console after GDB mark. I use "p" command for printing basic C type variables:
p [[[self pointerToMyClass] anotherPointerToOtherClass] someIntValue]
And I use "po" command for printing content of arrays, for checking objects:
po [[[self pointerToMyClass] anotherPointerToOtherClass] someNSArray]
po [[[self pointerToMyClass] anotherPointerToOtherClass] myUIImageView]