Illegal left brace in line 2680

[weedcentipede]

Hi, I'm getting the following error with my anaconda installation (with my data and with the run_tuto.sh) This issue is similar than #13, and there's report of this issue in other repositories

started: 16:16:56
make_html.pl -f mirdeep_runs/run_26_05_2019_t_16_16_10/output.mrd -p mirdeep_runs/run_26_05_2019_t_16_16_10/tmp/precursors.coords -v 0 -s mirdeep_runs/run_26_05_2019_t_16_16_10/survey.csv -c -e -r /home/bio/anaconda3/bin//../Rfam_for_miRDeep.fa -y 26_05_2019_t_16_16_10 -o  -V 2.0.0.8 

Unescaped left brace in regex is illegal here in regex; marked by <-- HERE in m/option{ <-- HERE t}\s*=\s*(\S+)/ at /home/bio/anaconda3/bin/make_html.pl line 2680.

ended: 16:16:56
total:0h:0m:0s

Find attached the log file error-conda.log

Also I got a similar error with the installation via install.pl, find attached error-installpl.log I installed the module via conda and cpan

There's any solution for the issue? Cheers, Luis Alfonso.

[Drmirdeep]

Hi Luis, the issue is explained already in the reference #13 and since we are not maintaining the conda version I cannot really help. The github version is already more advanced, maybe an update conda version has it solved already. However, the leftbraces 'warning' message and the missing csv file may be actually two different issues. If you can provide a little working example with files that would be helpful to test. Otherwise have a look if the file mirdeep_runs/run_26_05_2019_t_16_16_10/survey.csv is present and not empty to.

Cheers, Sebastian

[weedcentipede]

miRDeep2 score  estimated signal-to-noise   excision gearing
10  0   1
9   0   1
8   0   1
7   0   1
6   0   1
5   0   1
4   0   1
3   0   1
2   0   1
1   0   1
0   0   1
-1  0   1
-2  0   1
-3  0   1
-4  0   1
-5  0   1
-6  0   1
-7  0   1
-8  0   1
-9  0   1
-10 0   1

That's the content of the survey.csv file where do I send the files?

[Drmirdeep]

Your file looks empty (estimated signal to noise is 0) so I suspect the issues arise somewhere before. You are also missing the PDF::API2 package. Anyhow, I can only suggest to download the latest miRDeep2 release from git hub and run the install.pl. If running the tutorial then still gives warnings let us know. We cannot give support for the conda package since we did not provide it, plus it seems to use not the recent miRDeep2 release.

[weedcentipede]

The PDF:API2 error was apparently raised for the conda and the install.pl version installed simultaneously. I'll write other issue about the empty file,

Cheers.