• using R Under development (unstable) (2023-11-28 r85644)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     clang version 17.0.5     flang-new version 17.0.5
• running under: Fedora Linux 36 (Workstation Edition)
• using session charset: UTF-8
• using option ‘--no-stop-on-test-error’
• checking for file ‘data.table/DESCRIPTION’ ... OK
• this is package ‘data.table’ version ‘1.14.8’
• checking package namespace information ... OK
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking if there is a namespace ... OK
• checking for executable files ... OK
• checking for hidden files and directories ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking whether package ‘data.table’ can be installed ... [57s/130s] WARNING Found the following significant warnings:   assign.c:470:83: warning: format specifies type 'int' but the argument has type 'R_xlen_t' (aka 'long') [-Wformat]   assign.c:518:22: warning: format string is not a string literal (potentially insecure) [-Wformat-security]   assign.c:650:35: warning: more '%' conversions than data arguments [-Wformat-insufficient-args]   assign.c:794:96: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]   forder.c:107:30: warning: format string is not a string literal (potentially insecure) [-Wformat-security]   forder.c:121:19: warning: format string is not a string literal (potentially insecure) [-Wformat-security]   forder.c:255:27: warning: format string is not a string literal (potentially insecure) [-Wformat-security]   forder.c:270:23: warning: format string is not a string literal (potentially insecure) [-Wformat-security]   forder.c:272:21: warning: format string is not a string literal (potentially insecure) [-Wformat-security]   forder.c:283:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]   forder.c:284:23: warning: format string is not a string literal (potentially insecure) [-Wformat-security]   forder.c:304:25: warning: format string is not a string literal (potentially insecure) [-Wformat-security]   forder.c:322:17: warning: format string is not a string literal (potentially insecure) [-Wformat-security]   forder.c:340:14: warning: format string is not a string literal (potentially insecure) [-Wformat-security]   forder.c:404:3: warning: format string is not a string literal (potentially insecure) [-Wformat-security]   forder.c:426:7: warning: format string is not a string literal (potentially insecure) [-Wformat-security]   forder.c:428:7: warning: format string is not a string literal (potentially insecure) [-Wformat-security]   forder.c:430:7: warning: format string is not a string literal (potentially insecure) [-Wformat-security]   forder.c:443:5: warning: format string is not a string literal (potentially insecure) [-Wformat-security]   forder.c:445:5: warning: format string is not a string literal (potentially insecure) [-Wformat-security]   forder.c:447:5: warning: format string is not a string literal (potentially insecure) [-Wformat-security]   forder.c:453:7: warning: format string is not a string literal (potentially insecure) [-Wformat-security]   forder.c:455:7: warning: format string is not a string literal (potentially insecure) [-Wformat-security]   forder.c:459:5: warning: format string is not a string literal (potentially insecure) [-Wformat-security]   forder.c:462:5: warning: format string is not a string literal (potentially insecure) [-Wformat-security]   forder.c:465:5: warning: format string is not a string literal (potentially insecure) [-Wformat-security]   forder.c:467:5: warning: format string is not a string literal (potentially insecure) [-Wformat-security]   forder.c:495:5: warning: format string is not a string literal (potentially insecure) [-Wformat-security]   forder.c:511:9: warning: format string is not a string literal (potentially insecure) [-Wformat-security]   forder.c:553:7: warning: format string is not a string literal (potentially insecure) [-Wformat-security]   forder.c:599:11: warning: format string is not a string literal (potentially insecure) [-Wformat-security]   forder.c:706:8: warning: format string is not a string literal (potentially insecure) [-Wformat-security]   forder.c:720:47: warning: format string is not a string literal (potentially insecure) [-Wformat-security]   forder.c:725:57: warning: format string is not a string literal (potentially insecure) [-Wformat-security]   forder.c:1045:36: warning: format string is not a string literal (potentially insecure) [-Wformat-security]   forder.c:1154:15: warning: format string is not a string literal (potentially insecure) [-Wformat-security]   forder.c:1261:38: warning: format string is not a string literal (potentially insecure) [-Wformat-security]   forder.c:1265:57: warning: format string is not a string literal (potentially insecure) [-Wformat-security]   forder.c:1270:29: warning: format string is not a string literal (potentially insecure) [-Wformat-security]   forder.c:1302:7: warning: format string is not a string literal (potentially insecure) [-Wformat-security]   forder.c:1315:29: warning: format string is not a string literal (potentially insecure) [-Wformat-security]   forder.c:1332:7: warning: format string is not a string literal (potentially insecure) [-Wformat-security]   forder.c:1366:9: warning: format string is not a string literal (potentially insecure) [-Wformat-security]   fread.c:1888:54: warning: format specifies type 'int' but the argument has type 'int64_t' (aka 'long') [-Wformat]   fsort.c:168:102: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]   fsort.c:245:49: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]   fsort.c:249:54: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]   fwrite.c:626:28: warning: format specifies type 'int' but the argument has type 'const void *' [-Wformat]   fwrite.c:711:68: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]   fwrite.c:731:15: warning: format string is not a string literal (potentially insecure) [-Wformat-security]   fwrite.c:746:64: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]   fwrite.c:814:10: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]   fwrite.c:825:10: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]   fwrite.c:915:21: warning: format string is not a string literal (potentially insecure) [-Wformat-security]   gsumm.c:90:38: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]   gsumm.c:90:48: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]   gsumm.c:90:56: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]   gsumm.c:90:67: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]   gsumm.c:609:90: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]   gsumm.c:612:93: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]   gsumm.c:638:92: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]   gsumm.c:1411:72: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]   ijoin.c:323:89: warning: data argument not used by format string [-Wformat-extra-args]   init.c:153:139: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]   init.c:168:71: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]   init.c:169:77: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]   init.c:171:83: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]   init.c:172:106: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]   init.c:173:105: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]   init.c:173:119: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]   init.c:174:81: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]   init.c:175:79: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]   init.c:176:87: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]   init.c:177:77: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]   init.c:178:79: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]   init.c:179:79: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]   init.c:180:81: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]   init.c:184:95: warning: format specifies type 'int' but the argument has type 'R_xlen_t' (aka 'long') [-Wformat]   rbindlist.c:212:37: warning: format string is not a string literal (potentially insecure) [-Wformat-security]   rbindlist.c:233:50: warning: format string is not a string literal (potentially insecure) [-Wformat-security]   rbindlist.c:234:48: warning: format string is not a string literal (potentially insecure) [-Wformat-security]   rbindlist.c:494:31: warning: format string is not a string literal (potentially insecure) [-Wformat-security]   reorder.c:17:115: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]   reorder.c:27:136: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]   snprintf.c:217:136: warning: format specifies type 'char *' but the argument has type 'int' [-Wformat]   subset.c:270:26: warning: format string is not a string literal (potentially insecure) [-Wformat-security] See the install log for details.
• used C compiler: ‘clang version 17.0.5’
• checking installed package size ... OK
• checking package directory ... OK
• checking ‘build’ directory ... OK
• checking DESCRIPTION meta-information ... OK
• checking top-level files ... OK
• checking for left-over files ... OK
• checking index information ... OK
• checking package subdirectories ... OK
• checking R files for non-ASCII characters ... OK
• checking R files for syntax errors ... OK
• checking whether the package can be loaded ... OK
• checking whether the package can be loaded with stated dependencies ... OK
• checking whether the package can be unloaded cleanly ... OK
• checking whether the namespace can be loaded with stated dependencies ... OK
• checking whether the namespace can be unloaded cleanly ... OK
• checking loading without being on the library search path ... OK
• checking whether startup messages can be suppressed ... OK
• checking use of S3 registration ... OK
• checking dependencies in R code ... OK
• checking S3 generic/method consistency ... OK
• checking replacement functions ... OK
• checking foreign function calls ... OK
• checking R code for possible problems ... [50s/138s] OK
• checking Rd files ... OK
• checking Rd metadata ... OK
• checking Rd line widths ... OK
• checking Rd cross-references ... OK
• checking for missing documentation entries ... OK
• checking for code/documentation mismatches ... OK
• checking Rd \usage sections ... OK
• checking Rd contents ... OK
• checking for unstated dependencies in examples ... OK
• checking line endings in shell scripts ... OK
• checking line endings in C/C++/Fortran sources/headers ... OK
• checking line endings in Makefiles ... OK
• checking compilation flags in Makevars ... NOTE Package has both ‘src/Makevars.in’ and ‘src/Makevars’. Installation with --no-configure' is unlikely to work. If you intended ‘src/Makevars’ to be used on Windows, rename it to ‘src/Makevars.win’ otherwise remove it. If ‘configure’ created ‘src/Makevars’, you need a ‘cleanup’ script.
• checking for GNU extensions in Makefiles ... OK
• checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
• checking use of PKG_*FLAGS in Makefiles ... OK
• checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
• checking include directives in Makefiles ... OK
• checking pragmas in C/C++ headers and code ... OK
• checking compilation flags used ... OK
• checking compiled code ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [7s/21s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [166s/388s] ERROR   Running ‘autoprint.R’   Comparing ‘autoprint.Rout’ to ‘autoprint.Rout.save’ ... OK   Running ‘froll.R’ [48s/111s]   Running ‘knitr.R’   Comparing ‘knitr.Rout’ to ‘knitr.Rout.save’ ... OK   Running ‘main.R’ [111s/257s]   Running ‘nafill.R’   Running ‘other.R’   Running ‘types.R’ Running the tests in ‘tests/main.R’ failed. Complete output:   > require(data.table)   Loading required package: data.table   >   > test.data.table() # runs the main test suite of 5,000+ tests in /inst/tests/tests.Rraw   getDTthreads(verbose=TRUE):     OpenMP version (_OPENMP) 202011     omp_get_num_procs() 24     R_DATATABLE_NUM_PROCS_PERCENT unset (default 50)     R_DATATABLE_NUM_THREADS unset     R_DATATABLE_THROTTLE unset (default 1024)     omp_get_thread_limit() 2     omp_get_max_threads() 24     OMP_THREAD_LIMIT 2     OMP_NUM_THREADS unset     RestoreAfterFork true     data.table is using 2 threads with throttle==1024. See ?setDTthreads.   test.data.table() running: /data/gannet/ripley/R/packages/tests-clang/data.table.Rcheck/data.table/tests/tests.Rraw   Test 1658.58 did not produce correct output:   Expected: <<a,b\n1,0\+1i\n2,-1-1i\n3,$>>   Observed: <<a,b\n1,0+1i\n2,-1-1i\n3,+0i>>   Test 1743.231 produced 0 warnings but expected 1   Expected: NAs introduced by coercion.*left as type 'character'   Observed:   Test 1962.0473 produced 0 errors but expected 1   Expected: DT is an empty list() of 0 columns   Observed:   Test 2040.1 produced 1 errors but expected 0   Expected:   Observed: 'by' or 'keyby' must evaluate to a vector or a list of vectors (where 'list' includes data.table and data.frame which are lists, too)   Test 2040.2 produced 1 errors but expected 0   Expected:   Observed: 'by' or 'keyby' must evaluate to a vector or a list of vectors (where 'list' includes data.table and data.frame which are lists, too)   Test 2060.6 ran without errors but failed check that x equals y:   > x = fcoalesce(z1, 0 + (0+0i))   First 6 of 6 (type 'complex'):   [1] 0+1i NA 1-1i NA 0+3i NA   > y = `[<-`(z1, na_idx, 0 + (0+0i))   First 6 of 6 (type 'complex'):   [1] 0+1i 0+0i 1-1i 0+0i 0+3i 0+0i   'is.NA' value mismatch: 0 in current 3 in target   Test 2060.601 ran without errors but failed check that x equals y:   > x = fcoalesce(z1, z2)   First 6 of 6 (type 'complex'):   [1] 0+1i NA 1-1i NA 0+3i NA   > y = `[<-`(z1, na_idx, c(4 - (0+2i), NA, NA))   First 6 of 6 (type 'complex'):   [1] 0+1i 4-2i 1-1i NA 0+3i NA   'is.NA' value mismatch: 2 in current 3 in target   Test 2060.602 ran without errors but failed check that x equals y:   > x = fcoalesce(z1, z2, z3)   First 6 of 6 (type 'complex'):   [1] 0+1i NA 1-1i NA 0+3i NA   > y = `[<-`(z1, na_idx, c(4 - (0+2i), 5 - (0+1i), NA))   First 6 of 6 (type 'complex'):   [1] 0+1i 4-2i 1-1i 5-1i 0+3i NA   'is.NA' value mismatch: 1 in current 3 in target   Test 2060.604 ran without errors but failed check that x equals y:   > x = z1   First 6 of 6 (type 'complex'):   [1] 0+1i NA 1-1i NA 0+3i NA   > y = `[<-`(z1, na_idx, c(4 - (0+2i), 5 - (0+1i), NA))   First 6 of 6 (type 'complex'):   [1] 0+1i 4-2i 1-1i 5-1i 0+3i NA   'is.NA' value mismatch: 1 in current 3 in target      Tue Nov 28 12:27:33 2023 endian==little, sizeof(long double)==16, longdouble.digits==64, sizeof(pointer)==8, TZ==unset, Sys.timezone()=='Europe/London', Sys.getlocale()=='LC_CTYPE=en_GB.utf8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=C;LC_MONETARY=en_GB.UTF-8;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_IDENTIFICATION=C', l10n_info()=='MBCS=TRUE; UTF-8=TRUE; Latin-1=FALSE; codeset=UTF-8', getDTthreads()=='OpenMP version (_OPENMP)==202011; omp_get_num_procs()==24; R_DATATABLE_NUM_PROCS_PERCENT==unset (default 50); R_DATATABLE_NUM_THREADS==unset; R_DATATABLE_THROTTLE==unset (default 1024); omp_get_thread_limit()==2; omp_get_max_threads()==24; OMP_THREAD_LIMIT==2; OMP_NUM_THREADS==unset; RestoreAfterFork==true; data.table is using 2 threads with throttle==1024. See ?setDTthreads.', zlibVersion()==1.2.11 ZLIB_VERSION==1.2.11   Error in test.data.table() :     9 errors out of 9917. Search tests/tests.Rraw for test numbers: 1658.58, 1743.231, 1962.0473, 2040.1, 2040.2, 2060.6, 2060.601, 2060.602, 2060.604.   Execution halted
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes in ‘inst/doc’ ... OK
• checking re-building of vignette outputs ... [78s/203s] OK
• checking PDF version of manual ... [16s/42s] OK
• checking HTML version of manual ... [9s/27s] OK
• checking for non-standard things in the check directory ... OK
• checking for detritus in the temp directory ... OK
• DONE

Status: 1 ERROR, 1 WARNING, 1 NOTE