cygwin bash script suddenly can't find ls, grep

cygwin bash script suddenly can't find ls, grep

[LMH]

Hello,

I have been working on a bash script and suddenly I started getting an
error that ls could not be found,

./remove_rows.sh: line 27: ls: command not found

I can run ls from the command line just fine. There is also an ls
command before line 27 that runs fine. This is the part of the script
that is causing problems (line numbers are included).

24 PATH=$(ls -d './'$SET'/'$FOLD'/'$FOLD'_anneal/'$PARAM_SET'/'$AN_SET)
25 echo $PATH
26
27 FILE_LIST=($(ls $PATH'/'*'out.txt'))
28 echo ${FILE_LIST[@]}

The echo $PATH command gives the correct output, but I get the error on
line 27. I have tried without the double parentheses, which wouldn't
give the result I want,

FILE_LIST=$(ls $PATH'/'*'out.txt')

but this gives the same error.

After this problem happened, I updated cygwin and restarted, but the
issue persists. Is there something wrong with my cygwin install? If
there happens to be some problem with my bash, please let me know, but
this is pretty simple stuff and I just can't see why ls would be found
at line 24 but not line 27.

The test script worked many times before this error and I didn't change
that part of the script that is causing the error.

LMH

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Re: cygwin bash script suddenly can't find ls, grep

[Ken Brown]

On 10/11/2014 8:04 PM, LMH wrote:
> Hello,
>
> I have been working on a bash script and suddenly I started getting an
> error that ls could not be found,
>
> ./remove_rows.sh: line 27: ls: command not found
>
> I can run ls from the command line just fine. There is also an ls
> command before line 27 that runs fine. This is the part of the script
> that is causing problems (line numbers are included).
>
> 24 PATH=$(ls -d './'$SET'/'$FOLD'/'$FOLD'_anneal/'$PARAM_SET'/'$AN_SET)
> 25 echo $PATH
> 26
> 27 FILE_LIST=($(ls $PATH'/'*'out.txt'))
> 28 echo ${FILE_LIST[@]}
>
> The echo $PATH command gives the correct output, but I get the error on
> line 27. I have tried without the double parentheses, which wouldn't
> give the result I want,
>
> FILE_LIST=$(ls $PATH'/'*'out.txt')
>
> but this gives the same error.
>
> After this problem happened, I updated cygwin and restarted, but the
> issue persists. Is there something wrong with my cygwin install? If
> there happens to be some problem with my bash, please let me know, but
> this is pretty simple stuff and I just can't see why ls would be found
> at line 24 but not line 27.

You've changed PATH in line 24.  Is 'ls' still in it?

Ken


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Re: cygwin bash script suddenly can't find ls, grep

[LMH]

Ken Brown wrote:
> On 10/11/2014 8:04 PM, LMH wrote:
>> Hello,
>>
>> I have been working on a bash script and suddenly I started getting an
>> error that ls could not be found,
>>
>> ./remove_rows.sh: line 27: ls: command not found
>>
>> I can run ls from the command line just fine. There is also an ls
>> command before line 27 that runs fine. This is the part of the script
>> that is causing problems (line numbers are included).
>>
>> 24 PATH=$(ls -d './'$SET'/'$FOLD'/'$FOLD'_anneal/'$PARAM_SET'/'$AN_SET)
>> 25 echo $PATH
>> 26
>> 27 FILE_LIST=($(ls $PATH'/'*'out.txt'))
>> 28 echo ${FILE_LIST[@]}
>>
>> The echo $PATH command gives the correct output, but I get the error on
>> line 27. I have tried without the double parentheses, which wouldn't
>> give the result I want,
>>
>> FILE_LIST=$(ls $PATH'/'*'out.txt')
>>
>> but this gives the same error.
>>
>> After this problem happened, I updated cygwin and restarted, but the
>> issue persists. Is there something wrong with my cygwin install? If
>> there happens to be some problem with my bash, please let me know, but
>> this is pretty simple stuff and I just can't see why ls would be found
>> at line 24 but not line 27.
> 
> You've changed PATH in line 24.  Is 'ls' still in it?
> 
> Ken

Good Lord, I guess I wasn't thinking very clearly trying to use PATH as
a variable for something else. I changed to,

FILE_DIR=$(ls -d './'$SET'/'$FOLD'/'$FOLD'_anneal/'$PARAM_SET'/'$AN_SET)
echo $FILE_DIR

FILE_LIST=($(ls $FILE_DIR'/'*'out.txt' ))
echo ${FILE_LIST[@]}

and everything is fine. I guess it was a bash issue after all. Thanks
for checking that out.

LMH




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Re: cygwin bash script suddenly can't find ls, grep

[Achim Gratz]

LMH writes:
> Good Lord, I guess I wasn't thinking very clearly trying to use PATH as
> a variable for something else. I changed to,
>
> FILE_DIR=$(ls -d './'$SET'/'$FOLD'/'$FOLD'_anneal/'$PARAM_SET'/'$AN_SET)
> echo $FILE_DIR
>
> FILE_LIST=($(ls $FILE_DIR'/'*'out.txt' ))
> echo ${FILE_LIST[@]}
>
> and everything is fine. I guess it was a bash issue after all. Thanks
> for checking that out.

Are you trying to re-write some Windows BAT/CMD script perhaps?  It
seems that you'd actually want to use find instead of ls and protect
yourself a bit against the possibility of one of these path or file
names containing whitespace.  The ls constructing FILE_LIST is probably
not needed because the shell already globs the file names before ls ever
gets to it.


Regards,
Achim.
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Re: cygwin bash script suddenly can't find ls, grep

[Thorsten Kampe]

* LMH (Sat, 11 Oct 2014 20:30:07 -0400)
> Good Lord, I guess I wasn't thinking very clearly trying to use
> PATH as
> a variable for something else. I changed to,
> 
> FILE_DIR=$(ls -d './'$SET'/'$FOLD'/'$FOLD'_anneal/'$PARAM_SET'/'$AN_SET)
> echo $FILE_DIR
> 
> FILE_LIST=($(ls $FILE_DIR'/'*'out.txt' ))
> echo ${FILE_LIST[@]}

That looks pretty ugly. You probably can replace all that with 

FILE_LIST=(./$SET/$FOLD/$FOLD_anneal/$PARAM_SET/$AN_SET/*out.txt)

Thorsten


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Re: cygwin bash script suddenly can't find ls, grep

[LMH]

Achim Gratz wrote:
> LMH writes:
>> Good Lord, I guess I wasn't thinking very clearly trying to use PATH as
>> a variable for something else. I changed to,
>>
>> FILE_DIR=$(ls -d './'$SET'/'$FOLD'/'$FOLD'_anneal/'$PARAM_SET'/'$AN_SET)
>> echo $FILE_DIR
>>
>> FILE_LIST=($(ls $FILE_DIR'/'*'out.txt' ))
>> echo ${FILE_LIST[@]}
>>
>> and everything is fine. I guess it was a bash issue after all. Thanks
>> for checking that out.
> 
> Are you trying to re-write some Windows BAT/CMD script perhaps?  It
> seems that you'd actually want to use find instead of ls and protect
> yourself a bit against the possibility of one of these path or file
> names containing whitespace.  The ls constructing FILE_LIST is probably
> not needed because the shell already globs the file names before ls ever
> gets to it.
> 
> 
> Regards,
> Achim.
> 

Thanks for the advice. I went to using something like,

FILE_LIST=($(ls
'./'$SET'/'$FOLD'/'$FOLD'_anneal/'$PARAM_SET'/'$AN_SET'/'*'out.txt' ))

instead of,

FILE_LIST='./'$SET'/'$FOLD'/'$FOLD'_anneal/'$PARAM_SET'/'$AN_SET'/'*'out.txt'

when I was creating a script because ls will throw an exception if there
is nothing found matching the glob. This is especially true when I am
using a long path with allot of variables. I often remove the ls once I
know the script is working. The the first syntax above also creates an
array.

FILE_DIR was assigned separately because it it used in some other places
in the script and convenient to have in scope.

I have also had problems evaluating strings that were created by
assigning with a glob.

If I had a file,
myfile_1.txt

and did,
file_name='myfile_'*'.txt'

and then,
if [ "$file_name" = "myfile_1.txt" ];

I have had issues getting the above conditional to evaluate as true.

If instead I do,
file_name=$(ls 'myfile_'*'.txt')

the conditional will evaluate properly.

Am I mistaken about this? I have not taken the time to run down all of
these issues when they occur, which I really should.

LMH

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Re: cygwin bash script suddenly can't find ls, grep

[LMH]

Thorsten Kampe wrote:
> * LMH (Sat, 11 Oct 2014 20:30:07 -0400)
>> Good Lord, I guess I wasn't thinking very clearly trying to use
>> PATH as
>> a variable for something else. I changed to,
>>
>> FILE_DIR=$(ls -d './'$SET'/'$FOLD'/'$FOLD'_anneal/'$PARAM_SET'/'$AN_SET)
>> echo $FILE_DIR
>>
>> FILE_LIST=($(ls $FILE_DIR'/'*'out.txt' ))
>> echo ${FILE_LIST[@]}
> 
> That looks pretty ugly. You probably can replace all that with 
> 
> FILE_LIST=(./$SET/$FOLD/$FOLD_anneal/$PARAM_SET/$AN_SET/*out.txt)
> 
> Thorsten
> 
> 
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> 
> 

Thank you for the suggestion. I have mad an additional post in response
to the previous message that addresses your suggestion as well.

LMH

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Re: cygwin bash script suddenly can't find ls, grep

[Robert Klemme]

On Tue, Oct 14, 2014 at 10:54 PM, LMH <lmh_users-groups@molconn.com> wrote:
> Thorsten Kampe wrote:
>> * LMH (Sat, 11 Oct 2014 20:30:07 -0400)
>>> Good Lord, I guess I wasn't thinking very clearly trying to use
>>> PATH as
>>> a variable for something else. I changed to,
>>>
>>> FILE_DIR=$(ls -d './'$SET'/'$FOLD'/'$FOLD'_anneal/'$PARAM_SET'/'$AN_SET)
>>> echo $FILE_DIR
>>>
>>> FILE_LIST=($(ls $FILE_DIR'/'*'out.txt' ))
>>> echo ${FILE_LIST[@]}
>>
>> That looks pretty ugly. You probably can replace all that with
>>
>> FILE_LIST=(./$SET/$FOLD/$FOLD_anneal/$PARAM_SET/$AN_SET/*out.txt)

More suggestions:

1. use lowercase variable names for variables used only inside your
script. Since variable names are case insensitive it will avoid
collisions like this and also improve readability of the code.
2. In bash you can set shell option "nullglob" to avoid a one element
array with the glob pattern if there is no matching file. In zsh it's
"setopt NULL_GLOB" I believe.
3. Since we do not know whether there are spaces in variables I would
replace the line above with (including suggestion 1):

file_list=("$set/$fold/$fold_anneal/$param_set/$an_set"/*out.txt)

Kind regards

robert


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