Unable to download Genomic segmentation problems

[HussainAther]

When I run Rscript -e 'PeakSegPipeline::downloadProblems("hg38", "hg38_problems.bed")', I get the following error:

(peakerror) [athersh@biowulf PeakSegPipeline]$ Rscript -e 'PeakSegPipeline::downloadProblems("hg38", "hg38_problems.bed")'
trying URL 'http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/chromInfo.txt.gz'
Content type 'application/x-gzip' length 3804 bytes
==================================================
downloaded 3804 bytes

gunzip /tmp/RtmpFpRdQo/file60b26b2d758b.gz 
trying URL 'http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/gap.txt.gz'
Content type 'application/x-gzip' length 12165 bytes (11 KB)
==================================================
downloaded 11 KB

gunzip /tmp/RtmpFpRdQo/file60b26110032f.gz 
Error in fread(gap.bed) : 
  'input' must be a single character string containing a file name, a command, full path to a file, a URL starting 'http[s]://', 'ftp[s]://' or 'file://', or the input data itself
Calls: <Anonymous> -> gap2problems -> fread
Execution halted

[tdhock]

this commit fixes the issue https://github.com/tdhock/PeakSegPipeline/commit/fd313f05c3660840d012c46b086f9830c88cbb12

the output I get on my machine is

tdhock@recycled:~$ Rscript -e 'PeakSegPipeline::downloadProblems("hg38", "hg38_problems.bed")'
trying URL 'http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/chromInfo.txt.gz'
Content type 'application/x-gzip' length 3804 bytes
==================================================
downloaded 3804 bytes

gunzip /tmp/RtmpMQsQor/file7f192b96a785.gz 
trying URL 'http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/gap.txt.gz'
Content type 'application/x-gzip' length 12165 bytes (11 KB)
==================================================
downloaded 11 KB

gunzip /tmp/RtmpMQsQor/file7f19524fa649.gz 
tdhock@recycled:~$ head hg38_problems.bed 
chr1    10000   207666
chr1    257666  297968
chr1    347968  535988
chr1    585988  2702781
chr1    2746290 12954384
chr1    13004384    16799163
chr1    16849163    29552233
chr1    29553835    121976459
chr1    122026459   122224535
chr1    122224635   122503147
tdhock@recycled:~$ 

[HussainAther]

Working now thanks!