I didn't know where to post it.
I just have installed git-bash and arcanist project (http://www.phabricator.com/docs/phabricator/article/Arcanist_User_Guide.html).
Now when I type "arc help" on command prompt I get the following message :
bcohen#BCOHEN-L ~
$ arc help
←[1mNAME←[m
←[1marc←[m - arcanist, a code review and revision management utility
←[1mSYNOPSIS←[m
←[1marc←[m ←[4mcommand←[m [←[4moptions←[m] [←[4margs←[m]
This help file provides a detailed command reference.
←[1mCOMMAND REFERENCE←[m
←[1malias←[m
←[1malias←[m ←[4mcommand←[m
←[1malias←[m ←[4mcommand←[m ←[4mtarget←[m -- [←[4moptions←[m]
←[1mamend←[m [--revision ←[4mrevision_id←[m] [--show]
←[1manoid←[m
←[1mbackout←[m
←[1mbookmark←[m [←[4moptions←[m]
←[1mbookmark←[m ←[4mname←[m [←[4mstart←[m]
←[1mbranch←[m [←[4moptions←[m]
←[1mbranch←[m ←[4mname←[m [←[4mstart←[m]
←[1mbrowse←[m [←[4moptions←[m] ←[4mpath←[m ...
←[1mcall-conduit←[m ←[4mmethod←[m
←[1mclose←[m ←[4mtask_id←[m [←[4moptions←[m]
←[1mclose-revision←[m [←[4moptions←[m] ←[4mrevision←[m
←[1mcommit←[m [--revision ←[4mrevision_id←[m] [--show]
←[1mcover←[m [--rev ←[4mrevision←[m] [←[4mpath←[m ...]
←[1mdiff←[m [←[4mpaths←[m] (svn)
←[1mdiff←[m [←[4mcommit←[m] (git, hg)
For having colors, I must replace with sed the ← by \033 as following :
bcohen#BCOHEN-L ~
$ arc help |sed "s/?/\033/m"
NAME
arc - arcanist, a code review and revision management utility
SYNOPSIS
arc command [options] [args]
This help file provides a detailed command reference.
COMMAND REFERENCE
alias
alias command
alias command target -- [options]
amend [--revision revision_id] [--show]
anoid
backout
bookmark [options]
bookmark name [start]
branch [options]
branch name [start]
browse [options] path ...
call-conduit method
close task_id [options]
close-revision [options] revision
commit [--revision revision_id] [--show]
Do you have an idea ?
Maybe with an alias ?
Maybe by changing the encoding ?
Just a clue :
bcohen#BCOHEN-L ~
$ echo -e "\033[,4mtoto"
toto
This wode work whereas :
bcohen#BCOHEN-L ~
$ php -r 'echo "\033[1mtoto", PHP_EOL;'
←[1mtoto
doesn't work :(
Related
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!
Version
inkscape --version
Inkscape 0.48.4 r9939 (Jan 22 2014)
I'm running the following inkscape command:
inkscape -f test.svg \
--select=hanzi --verb=AlignHorizontalLeft --verb=EditDeselect \
--select=pinyin --verb=AlignHorizontalRight --verb=EditDeselect \
--select=hanzi --select=pinyin \
--verb=AlignVerticalCenter --verb=SelectionUnion \
--verb=FileSave --verb=FileQuit
And get the error:
Unable to find: AlignHorizontalLeft
Unable to find verb ID 'AlignHorizontalLeft' specified on the command line.
Unable to find: AlignHorizontalRight
Unable to find verb ID 'AlignHorizontalRight' specified on the command line.
Unable to find: AlignVerticalCenter
Unable to find verb ID 'AlignVerticalCenter' specified on the command line.
I can find related verbs when reading inkscape --verbs-list output.
What is the replacement for those verbs ? I need a solution as a cli command.
From IRC channel #inkscape:
ed8 | Any help for a replacement to the following verbs:
AlignHorizontalLeft, AlignHorizontalRight, AlignVerticalCenter in 0.48
?
su_v | ed8: those verbs only exist in trunk (i.e. they will be available in the next major release)
So you need to install using the PPA Inkscape trunk.
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
Problem
I am trying to do:
xdotool type 'date;'
but instead of the expected
date;
I get:
dateq
I have a greek keyboard, but when I issue the command the language is set to US. A note: when greek language is used, the key 'q' of the keyboard is used for the semicolon ';' (this is the default behavior/mapping)
Question
What can I do to get a semicolon with xdotool's type?
Some info
I am on Xfce 4.8 on XUbuntu
$ xfce4-terminal -V
xfce4-terminal 0.4.8 (Xfce 4.8)
$ setxkbmap -print -verbose 10
Setting verbose level to 10
locale is C
Applied rules from evdev:
rules: evdev
model: pc105
layout: us,gr
variant: ,
options: grp:caps_toggle
Trying to build keymap using the following components:
keycodes: evdev+aliases(qwerty)
types: complete
compat: complete
symbols: pc+us+gr:2+inet(evdev)+capslock(grouplock)
geometry: pc(pc105)
xkb_keymap {
xkb_keycodes { include "evdev+aliases(qwerty)" };
xkb_types { include "complete" };
xkb_compat { include "complete" };
xkb_symbols { include "pc+us+gr:2+inet(evdev)+capslock(grouplock)" };
xkb_geometry { include "pc(pc105)" };
};
$ sudo lsb_release -a
No LSB modules are available.
Distributor ID: Ubuntu
Description: Ubuntu 12.04.2 LTS
Release: 12.04
Codename: precise
try
setxkbmap <yourlocale>
before calling xdotool
This is a known bug. One thing you can try is upgrading to the newest version of xdotool. If that doesn't work, then check out this page, especially answer #29:
http://code.google.com/p/semicomplete/issues/detail?id=13
The issue was resolved by this pull request on 2014-04-07 (which is more than 3 years ago now). If anybody is still having this issue today, I think your best bet is upgrading xdotool.
These work for me:
echo "date;" | xvkbd -xsendevent -file -
xvkbd -xsendevent -text 'date;'
(remove the -xsendevent option and you get the same problem as with xdotool)
extending fazae's answer:
I have the latest version of xdotool, it seems. But the bug is still there:
$ xdotool --version
xdotool version 2.20110530.1
$ xdotool type ';'
$
'$' is typed instead of ';'.
$ xdotool type ':'
^
'^' is typed instead of ':'
FIX (example for the us and ru locales, alt+shift for toggling layouts): set locale to us, enable layout toggling with alt+shift:
$ setxkbmap us && xdotool type ':' && setxkbmap -option grp:alt_shift_toggle us,ru
:
update: the error only occurs when logged into R from within emacs
what works:
When I ssh into a remote server and run
$ ./foo.rb
from the bash shell, it works. Furthermore, if I launch R and execute
$ R
system('./foo.rb')
I am in a group with permission to read/write/execute the file. File permissions are -rwxrwx---
what doesn't work:
Launch emacs and start an R session:
M-x R
ssh-myserver:.
system('./foo.rb')
I get the following error:
ruby: Permission denied -- foo.rb (LoadError)
why is this? Is there a way to work around this?
I can not find any information from ?system or ?system2
Here is the output from sessionInfo()
> sessionInfo()
R version 2.12.2 (2011-02-25)
Platform: x86_64-redhat-linux-gnu (64-bit)
locale:
[1] C
attached base packages:
[1] grid stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] PECAn_0.1.1 xtable_1.5-6 gridExtra_0.7 RMySQL_0.7-5
[5] DBI_0.2-5 ggplot2_0.8.9 proto_0.3-8 reshape_0.8.3
[9] plyr_1.6 rjags_2.2.0-2 coda_0.13-5 lattice_0.19-17
[13] randtoolbox_1.09 rngWELL_0.9 MASS_7.3-11 XML_3.2-0
loaded via a namespace (and not attached):
[1] digest_0.4.2
Warning message:
'DESCRIPTION' file has 'Encoding' field and re-encoding is not possible
output of 'id' and 'env' from ssh and emacs, per comment by #sarnold (changed user names, group names, and ip addresses)
1. server
1.1 'id'
uid=1668(dleb) gid=1668(dleb) groups=117(ebusers),159(lab_admin),166(lab),1340(pal_web),1668(dleb)
1.2 'env'
LC_PAPER=en_US.UTF-8
LC_ADDRESS=en_US.UTF-8
LC_MONETARY=en_US.UTF-8
SHELL=/usr/local/bin/system-specific
KDE_NO_IPV6=1
SSH_CLIENT=888.888.888.88 51857 22
NCARG_FONTCAPS=/usr/lib64/ncarg/fontcaps
LC_NUMERIC=en_US.UTF-8
USER=dleb
LS_COLORS=
LC_TELEPHONE=en_US.UTF-8
KDEDIR=/usr
NCARG_GRAPHCAPS=/usr/lib64/ncarg/graphcaps
MAIL=/var/mail/dleb
PATH=/usr/kerberos/bin:/usr/local/bin:/bin:/usr/bin:/opt/dell/srvadmin/bin
LC_IDENTIFICATION=en_US.UTF-8
LC_COLLATE=en_US.UTF-8
R_LIBS=/home/a-m/dleb/lib/R
PWD=/home/dleb
NCARG_ROOT=/usr
KDE_IS_PRELINKED=1
LANG=en_US.UTF-8
NCARG_DATABASE=/usr/lib64/ncarg/database
MODULEPATH=/usr/share/Modules/modulefiles:/etc/modulefiles
LOADEDMODULES=
LC_MEASUREMENT=en_US.UTF-8
NCARG_LIB=/usr/lib64/ncarg
SSH_ASKPASS=/usr/libexec/openssh/gnome-ssh-askpass
NCARG_NCARG=/usr/share/ncarg
SHLVL=1
HOME=/home/a-m/dleb
LOGNAME=dleb
CVS_RSH=ssh
SSH_CONNECTION=888.888.888.88 51857 999.999.999.99 22
LC_CTYPE=en_US.UTF-8
MODULESHOME=/usr/share/Modules
LESSOPEN=|/usr/bin/lesspipe.sh %s
DISPLAY=localhost:15.0
LC_TIME=en_US.UTF-8
G_BROKEN_FILENAMES=1
LC_NAME=en_US.UTF-8
_=/bin/env
emacs/ess R session
2.1 system('id')
uid=1668(dleb) gid=1668(dleb) groups=117(ebusers),159(lab_admin),166(lab),1340(pal_web),1668(dleb)
2.2 system('env')
LN_S=ln -s
R_TEXI2DVICMD=/usr/bin/texi2dvi
LC_PAPER=en_US.UTF-8
SED=/bin/sed
LC_ADDRESS=en_US.UTF-8
R_PDFVIEWER=/usr/bin/xdg-open
LC_MONETARY=en_US.UTF-8
HOSTNAME=ebi-forecast
R_INCLUDE_DIR=/usr/include/R
R_PRINTCMD=lpr
SHELL=/usr/local/bin/system-specific
TERM=dumb
AWK=gawk
HISTSIZE=1
R_RD4DVI=ae
SSH_CLIENT=888.888.888.88 51159 22
KDE_NO_IPV6=1
R_RD4PDF=times,hyper
R_PAPERSIZE=a4
NCARG_FONTCAPS=/usr/lib64/ncarg/fontcaps
PERL=/usr/bin/perl
LC_NUMERIC=en_US.UTF-8
SSH_TTY=/dev/pts/14
LC_ALL=C
EMACS=t
USER=dleb
LC_TELEPHONE=en_US.UTF-8
LS_COLORS=
LD_LIBRARY_PATH=/usr/lib64/R/lib:/usr/local/lib64:/usr/lib/jvm/jre/lib/amd64/server:/usr/lib/jvm/jre/lib/amd64:/usr/lib/jvm/java/lib/amd64:/usr/java/packages/lib/amd64:/lib:/usr/lib
TAR=/bin/gtar
ENV=
R_ZIPCMD=/usr/bin/zip
KDEDIR=/usr
PAGER=/usr/bin/less
NCARG_GRAPHCAPS=/usr/lib64/ncarg/graphcaps
R_GZIPCMD=/usr/bin/gzip
PATH=/bin:/usr/bin:/usr/sbin:/usr/local/bin
LC_COLLATE=en_US.UTF-8
LC_IDENTIFICATION=en_US.UTF-8
EGREP=/bin/grep -E
PWD=/home/a-m/dleb/pecan
INPUTRC=/etc/inputrc
R_LIBS=/home/a-m/dleb/lib/R
NCARG_ROOT=/usr
R_SHARE_DIR=/usr/share/R
WHICH=/usr/bin/which
EDITOR=vi
LANG=en_US.UTF-8
KDE_IS_PRELINKED=1
R_LIBS_SITE=/usr/local/lib/R/site-library:/usr/local/lib/R/library:/usr/lib64/R/library:/usr/share/R/library
M ODULEPATH=/usr/share/Modules/modulefiles:/etc/modulefiles
NCARG_DATABASE=/usr/lib64/ncarg/database
LC_MEASUREMENT=en_US.UTF-8
LOADEDMODULES=
PS3=
R_BROWSER=/usr/bin/xdg-open
SSH_ASKPASS=/usr/libexec/openssh/gnome-ssh-askpass
NCARG_LIB=/usr/lib64/ncarg
HOME=/home/a-m/dleb
SHLVL=1
NCARG_NCARG=/usr/share/ncarg
R_ARCH=
TR=/usr/bin/tr
MAKE=make
R_UNZIPCMD=/usr/bin/unzip
LOGNAME=dleb
CVS_RSH=ssh
LC_CTYPE=en_US.UTF-8
SSH_CONNECTION=888.888.888.88 51159 999.999.999.99 22
R_BZIPCMD=/usr/bin/bzip2
MODULESHOME=/usr/share/Modules
LESSOPEN=|/usr/bin/lesspipe.sh %s
PROMPT_COMMAND=
R_HOME=/usr/lib64/R
DISPLAY=localhost:22.0
R_PLATFORM=x86_64-redhat-linux-gnu
INSIDE_EMACS=23.2.1,tramp:2.1.18-23.2
R_LIBS_USER=~/R/x86_64-redhat-linux-gnu-library/2.12
LC_TIME=en_US.UTF-8
R_DOC_DIR=/usr/share/doc/R-2.12.2
R_SESSION_TMPDIR=/tmp/RtmpqA6bpJ
HISTFILE=/home/a-m/dleb/.tramp_history
G_BROKEN_FILENAMES=1
LC_NAME=en_US.UTF-8
_=/bin/env
Assuming you started up R as the same user, you do. You error is not coming from a permissions problem for foo.rb, however, or else your shell would be giving the error. (i.e. sh: ./test.rb: Permission denied; see example below). Here, ruby itself is giving the error. Without knowing exactly what is in your foo.rb, I would suggest digging in there to see what it is trying to load/source, and checking the permissions on those.
#!/usr/bin/env ruby
puts 'Hello world'
Now in R....
> system('ls -l test.rb')
-rw-r--r-- 1 jcolby staff 40 Oct 21 08:23 test.rb
> system('./test.rb')
sh: ./test.rb: Permission denied
> system('chmod a+x test.rb')
> system('./test.rb')
Hello world
I presume the M ODULEPATH in the Emacs-derived output is simply a copy and paste typo.
The differences between the two env outputs is much greater than I expected; I've selected the ones that look slightly suspicious to me:
$ diff -u works fails
--- works 2011-10-24 15:04:02.000000000 -0700
+++ fails 2011-10-24 15:12:36.000000000 -0700
...
+LD_LIBRARY_PATH=/usr/lib64/R/lib:/usr/local/lib64:/usr/lib/jvm/jre/lib/amd64/server:/usr/lib/jvm/jre/lib/amd64:/usr/lib/jvm/java/lib/amd64:/usr/java/packages/lib/amd64:/lib:/usr/lib
...
-PATH=/usr/kerberos/bin:/usr/local/bin:/bin:/usr/bin:/opt/dell/srvadmin/bin
-PWD=/home/dleb
...
+PATH=/bin:/usr/bin:/usr/sbin:/usr/local/bin
...
+PWD=/home/a-m/dleb/pecan
...
In the emacs-derived session, your LD_LIBRARY_PATH environment variable may be changing specifics of which dynamically linked libraries are being used when executing ruby. If you ssh in to your server and execute your foo.rb with the changed LD_LIBRARY_PATH, does it work or fail?
LD_LIBRARY_PATH=/usr/lib64/R/lib:/usr/local/lib64:/usr/lib/jvm/jre/lib/amd64/server:/usr/lib/jvm/jre/lib/amd64:/usr/lib/jvm/java/lib/amd64:/usr/java/packages/lib/amd64:/lib:/usr/lib ./foo.rb
The PATH environment variable between the two sessions is different; perhaps you have permission to execute /usr/local/bin/ruby (or the libraries in /usr/local/lib/ruby/) but not /usr/bin/ruby (or the libraries in /usr/lib/ruby/). Does your script use #!env ruby or does it use #!/usr/bin/ruby (or some other fixed path)?
Your pwd in one instance is /home/dleb, the other /home/a-m/dleb/pecan -- but HOME is set to /home/a-m/dleb on both systems. Is /home/dleb a symbolic link or does it actually exist separate from /home/a-m/dleb? (This really is grasping at straws -- I don't think this is it, but this problem is baffling.)
One last thing to consider: is your server confined with a tool such as AppArmor, SELinux, TOMOYO, or SMACK? Any of these mandatory access control tools can prevent an application from writing in specific locations, perhaps they aren't yet configured for your site. Check dmesg(1) output to see if there are any rejection messages, most or all these tools log to dmesg(1) if auditd(8) isn't running.