I thought I found out how to create directories in this post
Creating directory with name containing real number in FORTRAN
But when I tried to create a directory in my Fortran 90 program
call system('mkdir -p out/test')
or
call system('mkdir out/test')
I don't get any compilation errors or warnings, but I get the following runtime error:
The syntax of the command is incorrect.
Any idea what is wrong? Any help is greatly appreciated!
From the error message I assume you are using Windows. Then, you have to use \ as a folder separator:
call system('mkdir out\test')
Also, -p (the Unix option to create parent folders) is invalid for Windows (and also not required).
Related
My Python 3.7.1 script generates a fasta file called
pRNA.sites.fasta
Within the same script, I call following system command:
cmd = "weblogo -A DNA < pRNA.sites.fasta > OUT.eps"
os.system(cmd)
print(cmd) #for debugging
I am getting the following error message and debugging message on the command line.
Error: Please provide a multiple sequence alignment
weblogo -A DNA < pRNA.sites.fasta > OUT.eps
"OUT.eps" file is generated but it's emtpy. On the other hand, if I run the following 'weblogo' command from the command line, It works just find. I get proper OUT.eps file.
$ weblogo -A DNA<pRNA.sites.fasta>OUT.eps
I am guessing my syntax for os.system call is wrong. Can you tell me what is wrong with it? Thanks.
Never mind. It turned out to be that I was not closing my file, "pRNA.sites.fasta" before I make system call that uses this file.
I use a program which create me postscript file before using ps2pdf to make it a readable pdf, i've made a program which add some string to overwrite the company new logo. (The first program can't import image file itself).
I add the string before the before-last line of the file (" showpage").
While running my program to add the logo there is no error.
With the option -dNOSAFER everything is fine, but by default it's set to -dSAFER, and an invalidfileaccess error pop, the files are 6 jpg images alone in their directory.
I don't want to make it run with the -dNOSAFER option on. As it will fully open the file system.
In the documentation I've seen that there is a "permitted path" setting, but i can't find nowhere to set this up. Is it just a command line option to set in the command launching the program ? Or is there a config file for GhostScript / ps2pdf where i can put the path to this directory as permitted path.
in this documentation :
http://www.ghostscript.com/doc/current/Use.htm
I only find
-dTTYPAUSE
Causes Ghostscript to read a character from /dev/tty, rather than
standard input, at the end of each page. This may be useful if input
is coming from a pipe. Note that -dTTYPAUSE overrides -dNOPAUSE. Also
note that -dTTYPAUSE requires opening the terminal device directly,
and may cause problems in combination with -dSAFER. Permission errors
can be avoided by adding the device to the permitted reading list
before invoking safer mode
gs -dTTYPAUSE -dDELAYSAFER -c '<< /PermitFileReading [ (/dev/tty)] >> setuserparams .locksafe' -dSAFER
The quote is just for the context but is this a way to put the permitted path ?
As gs automatically launch with the full system as readOnly there will be no difference ? There is no other find result for PermitFile in this page.
Try adding the required path to the search path with -I (Include) See Use.htm, section 8 How Ghostscript finds files. This should only be a problem if you are using 'run' or similar to read files from another location.
The section on TTYPAUSE is not relevant.
I am trying to zip a file using shell script command. I am using following command:
zip ./test/step1.zip $FILES
where $FILES contain all the input files. But I am getting a warning as follows
zip warning: name not matched: myfile.dat
and one more thing I observed that the file which is at last in the list of files in a folder has the above warning and that file is not getting zipped.
Can anyone explain me why this is happening? I am new to shell script world.
zip warning: name not matched: myfile.dat
This means the file myfile.dat does not exist.
You will get the same error if the file is a symlink pointing to a non-existent file.
As you say, whatever is the last file at the of $FILES, it will not be added to the zip along with the warning. So I think something's wrong with the way you create $FILES. Chances are there is a newline, carriage return, space, tab, or other invisible character at the end of the last filename, resulting in something that doesn't exist. Try this for example:
for f in $FILES; do echo :$f:; done
I bet the last line will be incorrect, for example:
:myfile.dat :
...or something like that instead of :myfile.dat: with no characters before the last :
UPDATE
If you say the script started working after running dos2unix on it, that confirms what everybody suspected already, that somehow there was a carriage-return at the end of your $FILES list.
od -c shows the \r carriage-return. Try echo $FILES | od -c
Another possible cause that can generate a zip warning: name not matched: error is having any of zip's environment variables set incorrectly.
From the man page:
ENVIRONMENT
The following environment variables are read and used by zip as described.
ZIPOPT
contains default options that will be used when running zip. The contents of this environment variable will get added to the command line just after the zip command.
ZIP
[Not on RISC OS and VMS] see ZIPOPT
Zip$Options
[RISC OS] see ZIPOPT
Zip$Exts
[RISC OS] contains extensions separated by a : that will cause native filenames with one of the specified extensions to be added to the zip file with basename and extension swapped.
ZIP_OPTS
[VMS] see ZIPOPT
In my case, I was using zip in a script and had the binary location in an environment variable ZIP so that we could change to a different zip binary easily without making tonnes of changes in the script.
Example:
ZIP=/usr/bin/zip
...
${ZIP} -r folder.zip folder
This is then processed as:
/usr/bin/zip /usr/bin/zip -r folder.zip folder
And generates the errors:
zip warning: name not matched: folder.zip
zip I/O error: Operation not permitted
zip error: Could not create output file (/usr/bin/zip.zip)
The first because it's now trying to add folder.zip to the archive instead of using it as the archive. The second and third because it's trying to use the file /usr/bin/zip.zip as the archive which is (fortunately) not writable by a normal user.
Note: This is a really old question, but I didn't find this answer anywhere, so I'm posting it to help future searchers (my future self included).
eebbesen hit the nail in his comment for my case (but i cannot vote for comment).
Another possible reason missed in the other comments is file exceeding the file size limit (4GB).
I converted my script for unix environment using dos2unix command and executed my script as ./myscript.sh instead bash myscript.sh.
I just discovered another potential cause for this. If the permissions of the directory/subdirectory don't allow the zip to find the file, it will report this error. Actually, if you run a chmod -R 444 on the directory, and then try to zip it, you will reproduce this error, and also have a "stored 0%" report, like this:
zip warning: name not matched: borrar/enviar
adding: borrar/ (stored 0%)
Hence, try changing the permissions of the file. If you are trying to send them through email, and those email filters (like Gmail's) invent silly filters of not sending executables, don't forget that making permissions very strict when making zip compression can be the cause of the error you are reporting, of "name not matched".
spaces are not allowed:
it would fail if there are more than one files(s) in $FILES unless you put them in loop
I also encountered this issue. In my case, the line separate is CRLF in my zip shell script which causes the problem. Using LF fixed it.
I'm trying to get PHP phar command line tool installed on my Debian VM, how here described:
(1) download the php-src, I assume it's in /tmp/php/src
(2) make the dir /tmp/phar
(3) Save this as /tmp/php-src/ext/phar/Makefile.
(4) cd /tmp/php-src/ext/phar
(5) run sudo make
Now after step 5 I get an error:
:/tmp/php-src/ext/phar# make
Makefile:11: *** missing separator (did you mean TAB instead of 8 spaces?). Stop.
As I know, there can be two possible causes for this error message:
Tabs in the make file. I've tested the file with od -t c Makefile. The file contains no tabs (\t).
It could be a bug of make v3.81 and need a patch or an upgrade to (yet instable: "Warning: This package is from the experimental distribution.") v3.82. I've downloaded and istalled (dpkg -i make_3.82-1_amd64.deb) it, but the error is still occuring.
What causes the error? How can it be avoided?
Thx
(Answered in a comment: See Question with no answers, but issue solved in the comments (or extended in chat))
#Beta wrote:
The line should begin with a tab, not a bunch of spaces.
The OP wrote:
I've replaced all 8-spaces sequences with tabs and can execute the make script now.
I used:
cat Makefile|sed "s/ /\t/" > Makefile
I'm trying out CCNetConfig (warning, website a little slow). Great app, one annoyance.
I can see in the documentation and even in the source code (Look at the end of the Initialize method) that I should be able to pass in a command line parameter to automatically load the configuration file.
I have tried:
-f E:\CruiseControl.Net\server\ccnet.config
-file E:\CruiseControl.Net\server\ccnet.config
-f=E:\CruiseControl.Net\server\ccnet.config
-file=E:\CruiseControl.Net\server\ccnet.config
And the same 4 switches with quotes around the file name just in case.
They all produce errors or just don't work. Has anyone had success doing this?
Thanks in advance.
Try moving it to a different path. Try the simplest thing: c:\ccnet.config.
I'm guessing it's the source of the problem because I recall CCNetConfig gave me sh!t early on when I tried to open files in paths that had spaces in them (e..g in Program Files).
According to my version of CCNet the command line flag for using a different config file is -c or --config, so the following should do it...
-c "E:\CruiseControl.Net\server\ccnet.config"
...which works for me.
I don't know why it uses a non-standard flag, but there you go.