Bug#1070009: r-cran-data.table: Update to current upstream
The file 'issue_563_fread.txt' appears to be an input to data.table::fread() for a test on encodings, glancing at the context. I can run 'R CMD check --as-cran data.table_1.15.4.tar.gz' just fine [1] here without any failing tests (and I have no locale or anything set). It's not my package but if I were you the natural step would be a combination of pausing the offending tests and filing an upstream issue notifying upstream that you had to do so. It is now a pretty active team so you may get some help from them. Dirk [1] I also have a local R env.vars set to report timing issues at lower thresholds than CRAN itself (to be aware for the packages I (co-)author so I get a bit more line noise: ## ... earlier lines omitted, this is on x86_64 with Ubuntu 23.10 ## * checking tests ... Running ‘autoprint.R’ Running R code in ‘autoprint.R’ had CPU time 4.2 times elapsed time Comparing ‘autoprint.Rout’ to ‘autoprint.Rout.save’ ... OK Running ‘froll.R’ [9s/9s] Running ‘knitr.R’ Running R code in ‘knitr.R’ had CPU time 3.7 times elapsed time Comparing ‘knitr.Rout’ to ‘knitr.Rout.save’ ... OK Running ‘main.R’ [30s/25s] Running ‘nafill.R’ Running R code in ‘nafill.R’ had CPU time 3.2 times elapsed time Running ‘other.R’ Running ‘programming.R’ Running R code in ‘programming.R’ had CPU time 2.5 times elapsed time Running ‘types.R’ Running R code in ‘types.R’ had CPU time 4.4 times elapsed time [47s/35s] NOTE * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [76s/20s] OK * checking PDF version of manual ... [5s/4s] OK * checking HTML version of manual ... [2s/2s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 NOTE See ‘/tmp/r/data.table.Rcheck/00check.log’ for details. edd@rob:/tmp/r$ -- dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
Bug#1070009: r-cran-data.table: Update to current upstream
The package is pristine at CRAN https://cran.r-project.org/web/checks/check_results_data.table.html (apart from some new warnings several packages now get about interal R API headers, nothing to do with tests) Maybe you can sort this with upstream -- data.table is effectively holding up r-base (and has been for months since the R 4.3.3 release) which is not exactly ideal. Dirk -- dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
Bug#1070009: r-cran-data.table: Update to current upstream
Hi Dirk,
thanks for the bug report. I even tried to upgrade to 1.15.0 in Februar
but stumbled about a test suite error[1] of the Debian package which
prevented me from uploading.
Am Sun, Apr 28, 2024 at 09:03:08AM -0500 schrieb Dirk Eddelbuettel:
>
> This should likely reduce some autopkgtest noise too in both data.table
> itself and some of the packages depending on it.
The autopkgtest of current version 1.15.4 has[2]:
> test.data.table() # runs the main test suite of 5,000+ tests in
> /inst/tests/tests.Rraw
getDTthreads(verbose=TRUE):
OpenMP version (_OPENMP) 201511
omp_get_num_procs()2
R_DATATABLE_NUM_PROCS_PERCENT unset (default 50)
R_DATATABLE_NUM_THREADSunset
R_DATATABLE_THROTTLE unset (default 1024)
omp_get_thread_limit() 2147483647
omp_get_max_threads() 2
OMP_THREAD_LIMIT unset
OMP_NUM_THREADSunset
RestoreAfterFork true
data.table is using 1 threads with throttle==1024. See ?setDTthreads.
test.data.table() running:
/usr/lib/R/site-library/data.table/tests/tests.Rraw.bz2
Test 2194.7 produced 0 errors but expected 1
Expected: Internal error.*types or lengths incorrect
Observed:
Tue Apr 30 05:47:51 2024 endian==little, sizeof(long double)==16,
longdouble.digits==64, sizeof(pointer)==8, TZ==unset,
Sys.timezone()=='Etc/UTC', Sys.getlocale()=='C', l10n_info()=='MBCS=FALSE;
UTF-8=FALSE; Latin-1=FALSE; codeset=ANSI_X3.4-1968', getDTthreads()=='OpenMP
version (_OPENMP)==201511; omp_get_num_procs()==2;
R_DATATABLE_NUM_PROCS_PERCENT==unset (default 50);
R_DATATABLE_NUM_THREADS==unset; R_DATATABLE_THROTTLE==unset (default 1024);
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 with throttle==1024. See ?setDTthreads.',
zlibVersion()==1.3 ZLIB_VERSION==1.3
Error: 1 error(s) out of 11067. Search tests/tests.Rraw.bz2 for test number(s)
2194.7. Duration: 42.5s elapsed (41.9s cpu).
In addition: Warning message:
In readLines(testDir("issue_563_fread.txt")) :
invalid input found on input connection
'/usr/lib/R/site-library/data.table/tests/issue_563_fread.txt'
Execution halted
I've checked the two files
/usr/lib/R/site-library/data.table/tests/tests.Rraw.bz2
/usr/lib/R/site-library/data.table/tests/issue_563_fread.txt
which do not look suspicious in any way.
Any hint how to fix this test would be welcome.
Kind regards
Andreas.
[1] https://salsa.debian.org/r-pkg-team/r-cran-data.table/-/jobs/5291564
[2] https://salsa.debian.org/r-pkg-team/r-cran-data.table/-/jobs/5660288
--
https://fam-tille.de
Bug#1070009: r-cran-data.table: Update to current upstream
Package: r-cran-data.table Version: 1.14.10+dfsg-1 Severity: normal data.table had a release 1.15.0 in January -- the first new one in three years! -- and two follow-ups since bringing it 1.15.4 at CRAN. Please update the Debian package to the current upstream version. This should likely reduce some autopkgtest noise too in both data.table itself and some of the packages depending on it. Dirk -- dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
