Error in data.frame(..., check.names = FALSE) : arguments imply differing number of rows

[J. Legebeke]

Does anyone know the solution for the error message: 

Error in data.frame(..., check.names = FALSE) :

  arguments imply differing number of rows

I get this error when running the prepare_results.R script, as follows:

Rscript /tools/leafcutter/leafviz/prepare_results.R \

../intron_clustering/leafcutter_perind_numers.counts.gz \

"../outlier_intron_excision/A19_vs_controls_clusterPvals.txt" \

"../outlier_intron_excision/A19_vs_controls_effSize.txt" \

/home/jl2e19/tools/leafcutter/leafviz/annotation/hg38_v35_gencode \

-m ../A19_groups_file.txt \

-f 0.05 \

-o ./A19_vs_controls.rData

Thanks!

Full output:

Loading required package: leafcutter

Loading required package: Rcpp

Attaching package: 'dplyr'

The following objects are masked from 'package:data.table':

    between, first, last

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Preparing for visualisation

Results to be saved in: ./A19_vs_controls.rData

Using annotation at: /home/jl2e19/tools/leafcutter/leafviz/annotation/hg38_v35_gencode

Loading counts from ../intron_clustering/leafcutter_perind_numers.counts.gz

Loading metadata from ../A19_groups_file.txt

Loading exons from /home/jl2e19/tools/leafcutter/leafviz/annotation/hg38_v35_gencode_all_exons.txt.gz

Taking input= as a system command ('zless /home/jl2e19/tools/leafcutter/leafviz/annotation/hg38_v35_gencode_all_exons.txt.gz') and a variable has been used in the expression passed to `input=`. Please use fread(cmd=...). There is a security concern if you are creating an app, and the app could have a malicious user, and the app is not running in a secure environment; e.g. the app is running as root. Please read item 5 in the NEWS file for v1.11.6 for more information and for the option to suppress this message.

Warning message:

In fread(effect.sizes.file, data.table = F) :

  Detected 9 column names but the data has 10 columns (i.e. invalid file). Added 1 extra default column name for the first column which is guessed to be row names or an index. Use setnames() afterwards if this guess is not correct, or fix the file write command that created the file to create a valid file.

Error in data.frame(..., check.names = FALSE) :

  arguments imply differing number of rows: 369763, 0

Calls: cbind -> cbind -> data.frame

Execution halted