featureCounts was called under minconda in Linux subsystem on a Windows 10 computer.
featureCounts -a /mnt/d/.../__.txt -F SAF -readExtensions3 200 -o ___.tsv -O file1.bam file2.bam file3p.bam file4.bam file5.bam file6.bam file7.bam file8.bam
This always results in an error message
featureCounts: invalid option -- 'r'
Version 2.0.1
Usage: featureCounts [options] -a <annotation_file> -o <output_file> input_file1 [input_file2] ...
## Mandatory arguments:
-a <string> Name of an annotation file. GTF/GFF format by default. See...
And then reprinting the required and optional arguments for featureCounts function.
Does anyone know what does the error message "invalid option --'r'" mean? And how can I fix it?
Is there any difference between calling featureCounts in command prompt (or Terminal on Mac) and calling it in Linux/miniconda3?
It seems that you mistyped option name, it should be --readExtension3 with two dashes in front of it and without 's' in the end. I had a similar problem with --fraction which led me here!
i'm trying to install Oracle11g, and this happened, is there a way to fix this?
i had tried to reboot and run the script runfixup.sh still can't resolve the problem.
I'm trying to install Oracle 11gR2 on Oracle Linux 7.4.
While the installer is performing prerequisite checks, we are getting error:
This is a prerequisite condition to test whether the OS kernel parameter semmni is properly set.
More details :
Expected Value : 128
Actual Value : 0
Now if I execute as root:
/sbin/sysctl -a | grep sem
kernel.sem = 32000 1024000000 500 128
Which means that semmni=128.
Can somebody tell me what I'm I doing wrong?
You need to issue the following command
[root#localhost ~]# /sbin/sysctl -p
the changes to take effect.
And then the value(the rightmost one returning below) might be checked by issuing
[root#localhost ~]# more /proc/sys/kernel/sem
32000 1024000000 500 128
I am installing cl-jupyter, there is a problem in quicklisp like this:
$ sbcl --load ./cl-jupyter.lispThis is SBCL 1.3.1.debian, an implementation of ANSI Common Lisp.
More information about SBCL is available at <http://www.sbcl.org/>.
SBCL is free software, provided as is, with absolutely no warranty.
It is mostly in the public domain; some portions are provided under
BSD-style licenses. See the CREDITS and COPYING files in the
distribution for more information.
... initialization mode... please wait...
To load "cl-jupyter":
Load 1 ASDF system:
cl-jupyter
; Loading "cl-jupyter"
.........; cc -o /home/keys/.cache/common-lisp/sbcl-1.3.1.debian-linux-x64/home/keys/quicklisp/dists/quicklisp/software/pzmq-20170403-git/grovel__grovel-tmpGHU3ALSV.o -c -m64 -fPIC -I/home/keys/quicklisp/dists/quicklisp/software/cffi_0.19.0/ /home/keys/.cache/common-lisp/sbcl-1.3.1.debian-linux-x64/home/keys/quicklisp/dists/quicklisp/software/pzmq-20170403-git/grovel__grovel.c
/home/keys/.cache/common-lisp/sbcl-1.3.1.debian-linux-x64/home/keys/quicklisp/dists/quicklisp/software/pzmq-20170403-git/grovel__grovel.c:6:17: fatal error: zmq.h: file not found
compilation terminated.
While evaluating the form starting at line 5, column 0
of #P"/home/keys/cl-jupyter/./cl-jupyter.lisp":
debugger invoked on a CFFI-GROVEL:GROVEL-ERROR in thread #<THREAD "main thread" RUNNING {100399C6A3}>: Subprocess (:PROCESS #<SB-IMPL::PROCESS :EXITED 1>)
with command ("cc" "-o" "/home/keys/.cache/common-lisp/sbcl-1.3.1.debian-linux-x64/home/keys/quicklisp/dists/quicklisp/software/pzmq-20170403-git/grovel__grovel-tmpGHU3ALSV.o" "-c" "-m64" "-fPIC" "-I/home/keys/quicklisp/dists/quicklisp/software/cffi_0.19.0/" "/home/keys/.cache/common-lisp/sbcl-1.3.1.debian-linux-x64/home/keys/quicklisp/dists/quicklisp/software/pzmq-20170403-git/grovel__grovel.c")
exited with error code 1
Type HELP for debugger help, or (SB-EXT:EXIT) to exit from SBCL.
restarts (invokable by number or by possibly-abbreviated name):
0: [RETRY ] Retry PROCESS-OP on #<GROVEL-FILE "pzmq" "grovel">.
1: [ACCEPT ] Continue, treating PROCESS-OP on #<GROVEL-FILE "pzmq" "grovel"> as having been successful.
2: Retry ASDF operation.
3: [CLEAR-CONFIGURATION-AND-RETRY] Retry ASDF operation after resetting the configuration.
4: [ABORT ] Give up on "cl-jupyter"
5: [RETRY ] Retry EVAL of current toplevel form.
6: [CONTINUE ] Ignore error and continue loading file "/home/keys/cl-jupyter/./cl-jupyter.lisp".
7: Abort loading file "/home/keys/cl-jupyter/./cl-jupyter.lisp".
8: Ignore runtime option --load "./cl-jupyter.lisp".
9: Skip rest of --eval and --load options.
10: Skip to toplevel READ/EVAL/PRINT loop.
11: [EXIT ] Exit SBCL (calling #'EXIT, killing the process).
(CFFI-GROVEL:GROVEL-ERROR "~a" #<UIOP/RUN-PROGRAM:SUBPROCESS-ERROR {100691C9F3}>)
As you can see,it says "quicklisp/dists/quicklisp/software/pzmq-20170403-git/grovel__grovel.c" can not be found.
so I am trying to find if there is a .c file in the original quicklisp package,but actually not.Why this problem happened,and hoe do I fix it?
zmq.h is the file that can't be found. You have to install a library that provides that header file for the Lisp side to compile properly.
I'm trying to install Orbfit4.2 on a using linux mint maya edition. I'm trying to follow the on line help. I have unzipped the tared file, configured with $ ./config -0 gfortran and then $ make. Both appears to be successful. I am now trying to create the DE405 data files in the /orbfit/src/jpleph directory. I have downloaded the header.405 and the ascp*date* ascii files into the directory from JPL. I have run $ make ephemerides and get the following;
cat header.405 ascp1960.405 ascp1980.405 ascp2000.405 ascp2020.405> input.430
asc2eph.x < input.430
/bin/sh: 1: asc2eph.x: not found
make: *** [ephemerides] Error 127
(I have also used input value of 405 instead of 430)
I have also tried just running from with in
the directory
$ ./asc2eph.x which was the previous method before the Makefile was included. All I get with this is 'authors' introductory message and the flashing working box-still running 6 hrs later.
If anybody has any experience or advice with installing Orbfit 4.2 from the start or can help me move on from the above blockage I would appreciate.
Note I am a real novice and would appreciate idiot step by step guide- I'm the idiot.
Eric
The Makefile assumes that the current directory "." is in your path. This is a security risk. You can either edit the Makefile to rename these binaries:
$ diff -u Makefile.orig Makefile
--- Makefile.orig 2014-01-09 07:14:10.000000000 -0800
+++ Makefile 2014-10-21 11:40:00.850236839 -0700
## -10,7 +10,7 ##
make clean
ephemerides: input asc2eph.x
- asc2eph.x < input.430
+ ./asc2eph.x < input.430
mv JPLEPH jpleph
make clean
Or you can add . to your path (but this is insecure!) by doing
$ PATH=.:$PATH
An XCode project on OSX 10.6 fails building due to exit code 3 when trying to run Rez. What does this mean? I'm sure the files exist and all paths are set correctly, and have valid content. Google and AltaVista turn up nothing but others with the same question.
More generally, since I have a talent for creating errors on OSX, is there a list of all possible exit codes for Rez and what they mean? Are these standard among all of Apples command line programs?
UPDATE:
Here's the first .r file that Rez tries to compile, but stops with exit code 3:
// The About box and resources are created in PIUtilities.r.
// You can easily override them, if you like.
#define plugInName "HackFormat"
#define plugInCopyrightYear "1957"
#define plugInDescription \
"Hackup of sample plugin SimpleFormat to test plugin making procedures (DSW)"
// Dictionary (aete) resources:
#define vendorName "DarenTheMonkey"
#define plugInAETEComment "simpleformat example file format module"
#define plugInSuiteID 'sdK4'
#define plugInClassID 'simP'
#define plugInEventID typeNull // must be this
#include "PIDefines.h"
#include "Types.r"
#include "SysTypes.r"
#include "PIGeneral.r"
#include "PIUtilities.r"
#include "PITerminology.h"
#include "PIActions.h"
#include "HackFormatTerminology.h" // Terminology for plug-in.
//-------------------------------------------------------------------------------
// PiPL resource
//-------------------------------------------------------------------------------
resource 'PiPL' (ResourceID, plugInName " PiPL", purgeable)
{
{
Kind { ImageFormat },
Name { plugInName },
Version { (latestFormatVersion ", /* must be exactly this */
keyInherits, /* must be keyInherits */
classFormat, /* parent: Format, Import, Export */
"parent class format", /* optional description */
flagsSingleProperty, /* if properties, list below */
"foo",
keyMyFoo,
typeBoolean,
"foobar",
flagsSingleProperty,
"bar",
keyMyBar,
typeBoolean,
"foobar",
flagsSingleProperty
/* no properties */
},
{}, /* elements (not supported) */
/* class descriptions */
},
{}, /* comparison ops (not supported) */
{} /* any enumerations */
}
};
resource StringResource (kHistoryEntry, "History", purgeable)
{
plugInName ": ref num=^0."
};
// end file
and, from the xcode Build Results window, (just for this first .r file; rest are same)
Build HackFormat of project hackformat with configuration Debug
Check dependencies
[WARN]Warning: The Copy Bundle Resources build phase contains this target's Info.plist file 'Info.plist'.
Rez tmp/hackformat.build/Debug/HackFormat.build/ResourceManagerResources/Objects/HackFormat-A69F02213383561.rsrc HackFormat.r
cd /home/dwilson/proj/PSPlug/hackformat
/Developer/Tools/Rez -o /home/dwilson/proj/PSPlug/hackformat/tmp/hackformat.build/Debug/HackFormat.build/ResourceManagerResources/Objects/HackFormat-A69F02213383561.rsrc -d SystemSevenOrLater=1 -useDF -script Roman -arch x86_64 -i /home/dwilson/proj/PSPlug/hackformat/Debug -i /home/dwilson/proj/PSPlug/hackformat/sampcomm -i sampcomm -i /home/dwilson/proj/PSPlug/hackformat -i /home/dwilson/proj/PSPlug/hackformat/sampcomm -i /home/dwilson/SW/SDK/AdobePS/adobe_photoshop_cs5_sdk_mac/photoshopapi/photoshop -i /home/dwilson/SW/SDK/AdobePS/adobe_photoshop_cs5_sdk_mac/photoshopapi/pica_sp -i /Developer/Headers/FlatCarbon -i /home/dwilson/SW/SDK/AdobePS/adobe_photoshop_cs5_sdk_mac/photoshopapi/resources -i /home/dwilson/proj/PSPlug/hackformat/Debug -i /home/dwilson/proj/PSPlug/hackformat/Debug/include -i sampcomm /home/dwilson/proj/PSPlug/hackformat/../../../common/includes/MachOMacrezXcode.h -isysroot /Developer/SDKs/MacOSX10.5.sdk /home/dwilson/proj/PSPlug/hackformat/HackFormat.r
### /Developer/Tools/Rez - SysError 0 during open of "/home/dwilson/proj/PSPlug/hackformat/../../../common/includes/MachOMacrezXcode.h".
Fatal Error!
### /Developer/Tools/Rez - Fatal Error, can't recover.
/home/dwilson/proj/PSPlug/hackformat/../../../common/includes/MachOMacrezXcode.h: ### /Developer/Tools/Rez - Since errors occurred, /home/dwilson/proj/PSPlug/hackformat/tmp/hackformat.build/Debug/HackFormat.build/ResourceManagerResources/Objects/HackFormat-A69F02213383561.rsrc's resource fork was not written.
Command /Developer/Tools/Rez failed with exit code 3
From the Rez man page:
Rez can return the following status codes:
0 no errors
1 error in parameters
2 syntax error in resource description file
3 I/O or program error
man I'm just tagging along on this. I get Command /Developer/usr/bin/Rez failed with exit code 3
I've been looking everywhere for a comprehensive list of exit codes without any luck. Or at least any information on exit code 3.
Update: I just found this in here http://developer.apple.com/library/mac/#documentation/Darwin/Reference/ManPages/man1/codesign.1.html (I'm not sure if this applies in any way to xcode as it seems to be part of the darwin documentation and I know very little about it):
codesign exits 0 if all operations succeed. This indicates that all codes were signed, or all codes
verified properly as requested. If a signing or verification operation fails, the exit code is 1. Exit
code 2 indicates invalid arguments or parameters.
Exit code 3 indicates that during verification, all
path(s) were properly signed but at least one of them failed to satisfy the requirement specified with
the -R option.
For verification, all path arguments are always investigated before the program exits. For all other
operations, the program exits upon the first error encountered, and any further path arguments are
ignored, unless the --continue option was specified, in which case codesign will defer the failure exit
until after it has attempted to process all path arguments in turn.
Again I'm not sure but seems to be a permissions problem. Will investigate further!
I have found the problem! In Project Setting, there was a bad path in Rez Prefix File. It's supposed to be a path to a file MachOMacrezXcode.h. Now it is obvious that this file wasn't being found when I look at the Build Results. I have copied this file into my project source (since I want no dependencies on the original sample code I'm taking source from) and fixed the path.