Add error handling for gzipped file decompression and external command failures in fread()

[Mukulyadav2004]

fixes #5415

This PR enhances fread()'s error handling to provide actionable error messages when system commands fail or file decompression encounters issues (like disk full scenarios). Previously, these failures could result in warnings or silent truncation.

The current implementation of fread() has two silent failure modes that can lead to data corruption and hard-to-debug issues:

• Gzipped file decompression failures: When R.utils::decompressFile() fails due to insufficient disk space or other issues, the function silently continues with a truncated file, leading to partial data reads and warnings that are easily missed in non-interactive sessions.

• External command failures: When using the cmd parameter, failed external commands (non-zero exit codes) are not detected, potentially leading to processing of empty or incomplete files.

Solution-

• As R.utils::decompressFile() is called without error handling, allowing silent failures so I wrapped R.utils::decompressFile() in tryCatch() to catch decompression failures and added comprehensive error message that explains the likely cause (disk full) and mention disc space and tmpdir argument.

• And System command exit codes are not checked thus missing command failures, so to fix - Captured the return status from system() command and added exit code validation with error message.

• Also in both modifications - moved on.exit(unlink(tmpFile), add=TRUE) before command execution to prevent storage leaks.

@tdhock @jangorecki @Anirban166 @joshhwuu can you please review.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 98.69%. Comparing base (5bb6450) to head (4e0e2ba).
Report is 5 commits behind head on master.

Additional details and impacted files

@@           Coverage Diff           @@
##           master    #7097   +/-   ##
=======================================
  Coverage   98.69%   98.69%           
=======================================
  Files          79       79           
  Lines       14680    14687    +7     
=======================================
+ Hits        14489    14496    +7     
  Misses        191      191           

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

🚀 New features to boost your workflow:

• ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

[MichaelChirico]

I still see the tests failing, PTAL & ping if you're stuck

[Mukulyadav2004]

Thanks! I tried making the file in 2nd test more corrupted cuz might be the corrupted gzip file not corrupted enough. But its still failing, can you please review the second test.

[MichaelChirico]

Oh, I managed to do it:

tmp <- tempfile()
file.create(tmp)
conn <- file(tmp, 'wb')
# this is data.table:::known_signatures$gzip
writeBin(as.raw(c(31, 139)), conn)
close(conn)

fread(tmp)
# Error in readBin(inn, what = raw(0L), size = 1L, n = BFR.SIZE) : 
#   error reading from the connection
# In addition: Warning message:
# In readBin(inn, what = raw(0L), size = 1L, n = BFR.SIZE) :
#   invalid or incomplete compressed data

[Mukulyadav2004]

Thank you for the working example. I've updated the test to use your approach

[MichaelChirico]

thanks!

[MichaelChirico]

Slightly worried the warnings/errors we observe could be more platform-dependent than we've detected here. Let's see if anything comes out of the more thorough GLCI suite.