We are analyzing sequencing data while filtering and trimming fastq files encountered following error. Is the following error due to unavailability of core for processing commands?
Error in colnames<-(*tmp*, value = c("cs103_R1_dada.fastq", "cs110_R1_dada.fastq", : attempt to set 'colnames' on an object with less than two dimensions In addition: Warning message: In mclapply(seq_len(n), do_one, mc.preschedule = mc.preschedule, : all scheduled cores encountered errors in user code >
As pengchy suggested there may be something wrong with function.
try the same call by using lapply and error message will be more informative.
To clarify on what #f2003596 and #HelloWorld said: This just means that a crash occurred within the function you called, i.e. while it was executing that function. But this does not necessarily mean that your function is incorrect. For example, you get the same error when a variable has not been found.
That would mean your R function has a crash.
Note: If you include an unexpected argument in mclapply you also can get this error message. I put mC.cores instead of mc.cores by mistake and I got it.
Related
I working on a version bump on the cc65 and encountered a problem with the linuxdoc-tools. Since I can't fix the linuxdoc-tools and there is a simple workaround possible I decided to add an if statement to inform the user together with the workaround:
if {! [file exists ${prefix}/bin/perl] } {
ui_error "
«${prefix}/bin/perl» is missing but the linuxdoc-tools depends on it.
Please create an appropriate symbolic link for linuxdoc-tools to work.
"
exit 1
}
Crude but the best I can do since I'm neither the perl5 nor the linuxdoc-tools maintainer and I don't want to spend to much time on a version bump.
However, the MacPorts doesn't understand exit 1 and ui_error won't stop execution on its own.
How do I stop the execution so not to waste the users time on a build which will otherwise fail right at the end.
Use return -code error "error message", or the shorthand for the same thing, error "error message".
Note that you should use ui_error before that to print a human-readable message for the user – while the error message is also being printed, it can sometimes get lost in the output.
Additionally, note that $prefix/bin/perl is a build dependency of linuxdoc-tools. If it is also needed at runtime, you should submit a pull request that adds depends_run path:bin/perl:perl5 to the port rather than attempting to fix this bug in your port.
A practical example of the bug "in action" is the following:
Attacker sends: /hello-%08x.%08x.%08x.%08x
Server logs:
[17:17:28] Consoled: 'hello-082aeefc.00000131.0061b64c.00000011' run
from 192.168.0.3:32768
Update:
The bug is caused by the logging function NetManager_LogMessage which
takes the text to dump, adds a timestamp (using snprintf) and then
passes the whole string to the function File_printf without the needed
format argument (%s) and how to fix it?
What i have done wrong and why its happening?
I debug in IDA and when i test to Crash the Server. It returns the Memory Invalid access error.
My main question: Please may you list a few examples of what SDL_GetError would print?
I want to use SDL_GetError to help me debug, however I don't know what to expect or how to create my own intentional errors.
The libsdl wiki says:
The message is only applicable when an SDL function has signaled an
error. You must check the return values of SDL function calls to determine
when to appropriately call SDL_GetError().
however http://sdl.beuc.net/sdl.wiki/SDL_GetError says:
Although this example uses SDL_Init, SDL_GetError provides an error
message for any failed SDL operation.
so which is it? Only some or all? None of the SDL wikis/documentations I have seen give a list of example error messages, so I don't know how to initiate an error, or what to expect in terms of content and format. Is
Error in `./foo': double free or corruption (top):
an SDL_GetError message or is that caused by something else?
The wiki entry for SDL_Error lists the error strings:
SDL_errorcode | The corresponding error string
SDL_ENOMEM | Out of memory
SDL_EFREAD | Error reading from datastream
SDL_EFWRITE | Error writing to datastream
SDL_EFSEEK | Error seeking in datastream
SDL_UNSUPPORTED | Unknown SDL error
SDL_LASTERROR | Unknown SDL error
any other value | Unknown SDL error
See also SDL_error.c. One of the wiki entries seems to be incorrect. The correct error code - error string pair would be:
SDL_UNSUPPORTED | That operation is not supported
You can set custom errors messages with SDL_SetError - see the .c above. Finally, "double free or corruption" is not an error caused by SDL, but most likely by a double free. I suggest gdb/valgrind to debug it.
I am working on a remote red-hat server and there I'm developing a c application to insert data in to a remote oracle database. So first i installed the OCI instant client rpm on the server and tried to compile a sample program. after certain linkages I could compile it. But then when I am going to run it. It exits giving an error saying
ORA-12162: TNS:net service name is incorrectly specified
The sample code I used is from the blog (refer to this code in case you need to clarify the things.where I’m quoting only few pieces to this post) René Nyffenegger's collection of things on the web
René Nyffenegger on Oracle
(refer to this code in case you need to clarify the things.where I’m quoting only few pieces to this post)
In the code I added some prints to check for the error And it seems like It gets stuck in the OCIServerAttach() function r gives a printed walue of -1
r=OCIServerAttach(srv, err, dbname, strlen(dbname), (ub4) OCI_DEFAULT);
printf("r value %d",r);
if (r != OCI_SUCCESS) {
checkerr(err, r);
goto clean_up;
}
Another point is that in the compilation process it gives a warning saying that a certain libry is not include. but the exicutable file is created. Here is the massage I get in the compilation process.
[laksithe#loancust ~]$ gcc -L$ORACLE_HOME/lib/ -L$ORACLE_HOME/rdbms/lib/ -o oci_test oci_test.o -L/usr/lib/oracle/12.1/client64/lib -lclntsh `cat $ORACLE_HOME/lib/sysliblist`
cat: /lib/sysliblist: No such file or directory
Going through the web I found that by creating a tnsnames.ora file with the connection details I could solve the problem. But even It didn't work for me. Here is the link for that blog blog
It has been a week since this error and I cold'nt solve it. could someone please help me.
connection string format I used is abc.ghi.com:1521/JKLMN
My recommendation is to bypass tnsnames completely. Oracle has always allowed you to put in the direct connection details, but EZConnect makes that even easier.
When you format your connection string, instead of listing the TNS name, use the actual connection properties in the following format:
servername:port/service name
For Example
MyOracle.MyCompany.Com:1521/SalesReporting
Your connection string might also require direct=true, but I'm honestly not sure.
I like the idea of tnsnames, but it's a double edged sword. When it works, it's great. When it doesn't, you want to throw something. With EZConnect, it always works.
By the way, if you don't know the properties of the three items above, find a machine that connect via tnsnames and:
tnsping <your TNS-named database>
I use file:consult function to read data from config file of my application. But some times i got error: {badmatch,{error,system_limit}} How can i avoid this?
I read about ERL_MAX_PORTS, but i haven't this variable:
echo $ERL_MAX_PORTS
i got empty string. How i can correctly set ERL_MAX_PORTS or can i find other methods to avoid this error?
Thank you