############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Harshlight.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings Harshlight_1.71.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/Harshlight.Rcheck' * using R Under development (unstable) (2022-12-25 r83502 ucrt) * using platform: x86_64-w64-mingw32 (64-bit) * R was compiled by gcc.exe (GCC) 10.4.0 GNU Fortran (GCC) 10.4.0 * running under: Windows Server x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'Harshlight/DESCRIPTION' ... OK * this is package 'Harshlight' version '1.71.0' * 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 hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'Harshlight' can be installed ... WARNING Found the following significant warnings: Harshlight.c:1471:26: warning: unknown conversion type character ')' in format [-Wformat=] Harshlight.c:1474:26: warning: unknown conversion type character ')' in format [-Wformat=] Harshlight.c:1532:107: warning: unknown conversion type character ')' in format [-Wformat=] Harshlight.c:1542:26: warning: unknown conversion type character ')' in format [-Wformat=] Harshlight.c:1543:26: warning: unknown conversion type character ')' in format [-Wformat=] Harshlight.c:1555:107: warning: unknown conversion type character ')' in format [-Wformat=] See 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/Harshlight.Rcheck/00install.out' for details. * used C compiler: 'gcc.exe (GCC) 12.2.0' * 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 dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... NOTE Calls with DUP: .C("cluster_defects", img <- as.integer(img), array.size <- as.integer(array.size), as.integer(size.limit), as.integer(connect), as.double(simul.pval), as.double(compact.pval), as.integer(type), status <- as.integer(0), DUP = FALSE, PACKAGE = "Harshlight") .C("diffuse_defects", img <- as.double(img), as.double(diffuse.bright), as.double(-diffuse.dark), as.integer(radius), diff.bright <- as.double(diff.bright), diff.dark <- as.double(diff.dark), as.double(quant), as.double(thres.dark), as.double(thres.bright), status <- as.integer(0), DUP = FALSE, NAOK = TRUE, PACKAGE = "Harshlight") .C("extended_defects", as.double(img), med.obs <- as.double(med.obs), as.integer(radius), status <- as.integer(0), NAOK = TRUE, DUP = FALSE, PACKAGE = "Harshlight") .C("image_dilation", as.double(img), result <- as.double(result), as.integer(radius), status <- as.integer(0), DUP = FALSE, PACKAGE = "Harshlight") .C("image_erosion", as.double(result), img <- as.double(img), as.integer(radius), status <- as.integer(0), DUP = FALSE, PACKAGE = "Harshlight") .C("simulations", simulation.bright <- as.integer(simulation.bright), as.double(compact.quant.bright), as.integer(compact.connect), status <- as.integer(0), DUP = FALSE, PACKAGE = "Harshlight") .C("simulations", simulation.dark <- as.integer(simulation.dark), as.double(compact.quant.dark), as.integer(compact.connect), status <- as.integer(0), DUP = FALSE, PACKAGE = "Harshlight") DUP is no longer supported and will be ignored. * checking R code for possible problems ... NOTE Harshlight: no visible binding for global variable 'sim' Harshlight: no visible binding for global variable 'sim.int' Undefined global functions or variables: sim sim.int * checking Rd files ... NOTE checkRd: (-1) sim.Rd:10: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_ \_ * checking Rd metadata ... 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 contents of 'data' directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files for x64 is not available File 'F:/biocbuild/bbs-3.17-bioc/R/library/Harshlight/libs/x64/Harshlight.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'rand', possibly from 'rand' (C) Found 'srand', possibly from 'srand' (C) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs nor [v]sprintf. The detected symbols are linked into the code but might come from libraries and not actually be called. See 'Writing portable packages' in the 'Writing R Extensions' manual. * checking sizes of PDF files under 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 4 NOTEs See 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/Harshlight.Rcheck/00check.log' for details.