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

Dirk Eddelbuettel edd at debian.org
Mon Jun 8 20:43:58 BST 2020


On 8 June 2020 at 21:25, Paul Gevers wrote:
| 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?

The "'origin' must be supplied" message makes it *extremely* likely that is
in fact a change made by R 4.0.0.  R is released once a year as a new minor
(plus patch releases) and *extremely* carefully vetted / prepared (and folks
who upload packages to CRAN always test against the coming version.

So the data.table team upstream surely had this fixed as well.  The
_released_ version of data.table still has the problem too as we can see at
CRAN:

https://cloud.r-project.org/web/checks/check_results_data.table.html

I would expect the next version to be fixed. In the mean time the bug could
be fixed in the test(s), or the tests could be (temporarily) suspended.

(I had a quick look at the code around tests 1390.* (in file
inst/tests/tests.Raw) but didn't immediately come up with a fix.

Dirk




| 
| 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: -----------------------]
| 
| x[DELETED ATTACHMENT signature.asc, application/pgp-signature]

-- 
http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org



More information about the R-pkg-team mailing list