[R-pkg-team] Bug#962497: r-base breaks r-cran-data.table autopkgtest: 'origin' must be supplied

[Paul Gevers]

Source: r-base, r-cran-data.table
Control: found -1 r-base/4.0.1-1
Control: found -1 r-cran-data.table/1.12.8+dfsg-1
Severity: serious
Tags: sid bullseye
X-Debbugs-CC: debian-ci at lists.debian.org
User: debian-ci at lists.debian.org
Usertags: breaks needs-update

Dear maintainer(s),

With a recent upload of r-base the autopkgtest of r-cran-data.table
fails in testing when that autopkgtest is run with the binary packages
of r-base from unstable. It passes when run with only packages from
testing. In tabular form:

                       pass            fail
r-base                 from testing    4.0.1-1
r-cran-data.table      from testing    1.12.8+dfsg-1
versioned deps [0]     from testing    from unstable
all others             from testing    from testing

I copied some of the output at the bottom of this report.

Currently this regression is blocking the migration of r-base to testing
[1]. Due to the nature of this issue, I filed this bug report against
both packages. Can you please investigate the situation and reassign the
bug to the right package?

More information about this bug and the reason for filing it can be found on
https://wiki.debian.org/ContinuousIntegration/RegressionEmailInformation

Paul

[0] You can see what packages were added from the second line of the log
file quoted below. The migration software adds source package from
unstable to the list if they are needed to install packages from
r-base/4.0.1-1. I.e. due to versioned dependencies or breaks/conflicts.
[1] https://qa.debian.org/excuses.php?package=r-base

https://ci.debian.net/data/autopkgtest/testing/amd64/r/r-cran-data.table/5803495/log.gz

BEGIN TEST main.R

R version 4.0.1 (2020-06-06) -- "See Things Now"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> require(data.table)
Loading required package: data.table
>
> test.data.table()  # runs the main test suite of 5,000+ tests in
/inst/tests/tests.Rraw
getDTthreads(verbose=TRUE):
  omp_get_num_procs()            2
  R_DATATABLE_NUM_PROCS_PERCENT  unset (default 50)
  R_DATATABLE_NUM_THREADS        unset
  omp_get_thread_limit()         2147483647
  omp_get_max_threads()          2
  OMP_THREAD_LIMIT               unset
  OMP_NUM_THREADS                unset
  RestoreAfterFork               true
  data.table is using 1 threads. See ?setDTthreads.
test.data.table() running:
/usr/lib/R/site-library/data.table/tests/tests.Rraw.bz2

**** Suggested package bit64 is not installed. Tests using it will be
skipped.


**** Suggested package xts is not installed. Tests using it will be skipped.


**** Suggested package nanotime is not installed. Tests using it will be
skipped.


**** Suggested package R.utils is not installed. Tests using it will be
skipped.


**** Suggested package yaml is not installed. Tests using it will be
skipped.

Test 1390.3 produced 1 errors but expected 0
Expected:
Observed: 'origin' must be supplied
Test 1390.4 produced 1 errors but expected 0
Expected:
Observed: 'origin' must be supplied
Test 1390.5 produced 1 errors but expected 0
Expected:
Observed: 'origin' must be supplied
Test 1760 not run because this session either has no OpenMP or has been
limited to one thread (e.g. under UBSAN and ASAN)

10 longest running tests took 15s (38% of 40s)
      ID  time nTest
 1: 1888 2.860     9
 2: 1848 1.766     1
 3: 1874 1.753     5
 4: 1438 1.564   354
 5: 1912 1.530     2
 6: 1223 1.186   728
 7: 1648 1.171    45
 8: 1650 1.158    45
 9: 1652 1.143    45
10: 1437 1.116    36

Error in test.data.table() :
  3 errors out of 7311 in 40.4s elapsed (38.2s cpu) on Sun Jun  7
09:33:45 2020. [endian==little, sizeof(long double)==16,
sizeof(pointer)==8, TZ=Etc/UTC, locale='C', l10n_info()='MBCS=FALSE;
UTF-8=FALSE; Latin-1=FALSE', getDTthreads()='omp_get_num_procs()==2;
R_DATATABLE_NUM_PROCS_PERCENT==unset (default 50);
R_DATATABLE_NUM_THREADS==unset; omp_get_thread_limit()==2147483647;
omp_get_max_threads()==2; OMP_THREAD_LIMIT==unset;
OMP_NUM_THREADS==unset; RestoreAfterFork==true; data.table is using 1
threads. See ?setDTthreads.']. Search tests/tests.Rraw.bz2 for test
numbers: 1390.3, 1390.4, 1390.5.
In addition: Warning messages:
1: In parse(n = -1, file = file, srcfile = NULL, keep.source = FALSE) :
  invalid input found on input connection
'/usr/lib/R/site-library/data.table/tests/tests.Rraw.bz2'
2: In parse(n = -1, file = file, srcfile = NULL, keep.source = FALSE) :
  invalid input found on input connection
'/usr/lib/R/site-library/data.table/tests/tests.Rraw.bz2'
Execution halted
autopkgtest [09:33:45]: test run-unit-test: -----------------------]

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