* using log directory ‘/data/gannet/ripley/R/packages/tests-Intel/CaseBasedReasoning.Rcheck’ * using R Under development (unstable) (2024-06-24 r86824) * using platform: x86_64-pc-linux-gnu * R was compiled by Intel(R) oneAPI DPC++/C++ Compiler 2024.2.0 (2024.2.0.20240602) ifx (IFX) 2024.2.0 20240602 * running under: Fedora Linux 36 (Workstation Edition) * using session charset: UTF-8 * using option ‘--no-stop-on-test-error’ * checking for file ‘CaseBasedReasoning/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘CaseBasedReasoning’ version ‘0.3’ * package encoding: UTF-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 ‘CaseBasedReasoning’ can be installed ... [2m/13m] WARNING Found the following significant warnings: /usr/lib/gcc/x86_64-redhat-linux/12/../../../../include/c++/12/bits/stl_tempbuf.h:263:8: warning: 'get_temporary_buffer>' is deprecated [-Wdeprecated-declarations] See ‘/data/gannet/ripley/R/packages/tests-Intel/CaseBasedReasoning.Rcheck/00install.out’ for details. * used C++ compiler: ‘Intel(R) oneAPI DPC++/C++ Compiler 2024.2.0 (2024.2.0.20240602)’ * 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 code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... [7s/42s] OK * checking whether the package can be loaded with stated dependencies ... [6s/38s] OK * checking whether the package can be unloaded cleanly ... [7s/43s] OK * checking whether the namespace can be loaded with stated dependencies ... [6s/35s] OK * checking whether the namespace can be unloaded cleanly ... [7s/25s] OK * checking loading without being on the library search path ... [7s/30s] 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 ... [29s/141s] 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 C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... NOTE GNU make is a SystemRequirements. * 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 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 ... [9s/55s] OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [39s/300s] ERROR Error(s) in re-building vignettes: --- re-building ‘distance_measures.rmd’ using rmarkdown --- finished re-building ‘distance_measures.rmd’ --- re-building ‘get_started.rmd’ using rmarkdown ** Processing: /data/gannet/ripley/R/packages/tests-Intel/CaseBasedReasoning.Rcheck/vign_test/CaseBasedReasoning/vignettes/get_started_files/figure-html/proportional hazard-1.png 768x768 pixels, 3x8 bits/pixel, RGB Input IDAT size = 60960 bytes Input file size = 61122 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 52056 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 52056 Output IDAT size = 52056 bytes (8904 bytes decrease) Output file size = 52134 bytes (8988 bytes = 14.71% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-Intel/CaseBasedReasoning.Rcheck/vign_test/CaseBasedReasoning/vignettes/get_started_files/figure-html/distance_matrix-1.png 768x768 pixels, 3x8 bits/pixel, RGB Input IDAT size = 18631 bytes Input file size = 18733 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 16600 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 16600 Output IDAT size = 16600 bytes (2031 bytes decrease) Output file size = 16678 bytes (2055 bytes = 10.97% decrease) --- finished re-building ‘get_started.rmd’ +-+get_started.html *** caught segfault *** address (nil), cause 'unknown' An irrecoverable exception occurred. R is aborting now ... SUMMARY: processing the following file failed: ‘get_started.rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... [10s/42s] OK * checking HTML version of manual ... 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 See ‘/data/gannet/ripley/R/packages/tests-Intel/CaseBasedReasoning.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 33:51.51, 305.61 + 33.95