* using log directory ‘/srv/hornik/tmp/CRAN/Rtwobitlib.Rcheck’ * using R Under development (unstable) (2024-04-16 r86435) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 17.0.6 (5) Debian flang-new version 17.0.6 (5) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘Rtwobitlib/DESCRIPTION’ ... OK * this is package ‘Rtwobitlib’ version ‘0.3.0’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [3s/4s] NOTE Maintainer: ‘Hervé Pagès ’ New submission * 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 serialization versions ... OK * checking whether package ‘Rtwobitlib’ can be installed ... [6s/6s] WARNING Found the following significant warnings: ./common.h:169:28: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] ./common.h:271:16: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] ./common.h:274:17: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] ./common.h:391:63: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] ./common.h:400:75: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] ./common.h:416:55: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] ./common.h:628:70: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] ./errAbort.h:28:29: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] ./errAbort.h:31:17: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] ./portable.h:28:20: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] common.c:342:55: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] common.c:352:13: warning: passing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] common.c:385:97: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] common.c:401:13: warning: passing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] common.c:415:75: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] common.c:1065:61: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] common.c:1073:17: warning: passing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] common.c:1085:70: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] ./localmem.h:37:31: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] localmem.c:104:31: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] localmem.c:173:23: warning: arithmetic on a pointer to void is a GNU extension [-Wgnu-pointer-arith] ./verbose.h:19:16: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] ./verbose.h:22:27: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] ./verbose.h:37:21: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] verbose.c:43:27: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] verbose.c:68:16: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] verbose.c:100:21: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] ./portimpl.h:19:20: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] osunix.c:27:20: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] ./dlist.h:43:25: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] dlist.c:17:25: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] ./memalloc.h:22:33: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] ./memalloc.h:25:26: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] ./memalloc.h:31:21: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] ./memalloc.h:35:19: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] memalloc.c:19:28: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] memalloc.c:68:33: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] memalloc.c:79:26: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] memalloc.c:314:21: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] memalloc.c:334:19: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] errAbort.c:34:17: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] ./hash.h:271:59: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] hash.c:555:15: warning: arithmetic on pointers to void is a GNU extension [-Wgnu-pointer-arith] hash.c:708:59: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] hash.c:719:17: warning: passing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] ./bits.h:104:20: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] bits.c:18:20: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] ./dnautil.h:21:17: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] dnautil.c:134:22: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] dnautil.c:356:24: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] dnautil.c:376:33: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] dnautil.c:404:28: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] dnautil.c:832:27: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] dnautil.c:1018:22: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] dnautil.c:1037:17: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] /srv/hornik/tmp/CRAN/Rtwobitlib.Rcheck/00LOCK-Rtwobitlib/00new/Rtwobitlib/include/kent/common.h:169:28: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] /srv/hornik/tmp/CRAN/Rtwobitlib.Rcheck/00LOCK-Rtwobitlib/00new/Rtwobitlib/include/kent/common.h:271:16: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] /srv/hornik/tmp/CRAN/Rtwobitlib.Rcheck/00LOCK-Rtwobitlib/00new/Rtwobitlib/include/kent/common.h:274:17: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] /srv/hornik/tmp/CRAN/Rtwobitlib.Rcheck/00LOCK-Rtwobitlib/00new/Rtwobitlib/include/kent/common.h:391:63: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] /srv/hornik/tmp/CRAN/Rtwobitlib.Rcheck/00LOCK-Rtwobitlib/00new/Rtwobitlib/include/kent/common.h:400:75: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] /srv/hornik/tmp/CRAN/Rtwobitlib.Rcheck/00LOCK-Rtwobitlib/00new/Rtwobitlib/include/kent/common.h:416:55: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] /srv/hornik/tmp/CRAN/Rtwobitlib.Rcheck/00LOCK-Rtwobitlib/00new/Rtwobitlib/include/kent/common.h:628:70: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] /srv/hornik/tmp/CRAN/Rtwobitlib.Rcheck/00LOCK-Rtwobitlib/00new/Rtwobitlib/include/kent/hash.h:271:59: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] /srv/hornik/tmp/CRAN/Rtwobitlib.Rcheck/00LOCK-Rtwobitlib/00new/Rtwobitlib/include/kent/dnautil.h:21:17: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] /srv/hornik/tmp/CRAN/Rtwobitlib.Rcheck/00LOCK-Rtwobitlib/00new/Rtwobitlib/include/kent/localmem.h:37:31: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] /srv/hornik/tmp/CRAN/Rtwobitlib.Rcheck/00LOCK-Rtwobitlib/00new/Rtwobitlib/include/kent/bits.h:104:20: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] See ‘/srv/hornik/tmp/CRAN/Rtwobitlib.Rcheck/00install.out’ for details. * used C compiler: ‘Debian clang version 17.0.6 (5)’ * checking package directory ... OK * checking for future file timestamps ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... NOTE Non-standard files/directories found at top level: ‘INSTALL.UNUSED’ ‘LICENSE.md’ ‘NOTES.txt’ ‘configure.ac.UNUSED’ * 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 ... [0s/0s] OK * checking whether the package can be loaded with stated dependencies ... [0s/0s] OK * checking whether the package can be unloaded cleanly ... [0s/0s] OK * checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK * checking whether the namespace can be unloaded cleanly ... [0s/0s] OK * checking loading without being on the library search path ... [0s/0s] OK * checking whether startup messages can be suppressed ... [0s/0s] 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 ... [2s/2s] OK * checking Rd files ... [0s/0s] 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 ... 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 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 ... [0s/0s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [1s/1s] OK Running ‘testthat.R’ [1s/1s] * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [1s/1s] OK * checking PDF version of manual ... [3s/3s] OK * checking HTML version of manual ... [0s/0s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 WARNING, 2 NOTEs