############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:chopsticks.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings chopsticks_1.58.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/chopsticks.Rcheck' * using R version 4.1.1 (2021-08-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'chopsticks/DESCRIPTION' ... OK * this is package 'chopsticks' version '1.58.0' * 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 'chopsticks' can be installed ... WARNING Found the following significant warnings: inputNew.c:687:5: warning: 'strncpy' output may be truncated copying 127 bytes from a string of length 127 [-Wstringop-truncation] inputNew.c:408:4: warning: 'strncpy' output may be truncated copying 127 bytes from a string of length 127 [-Wstringop-truncation] inputNew.c:404:4: warning: 'strncpy' output may be truncated copying 127 bytes from a string of length 127 [-Wstringop-truncation] inputNew.c:401:4: warning: 'strncpy' output may be truncated copying 127 bytes from a string of length 127 [-Wstringop-truncation] inputNew.c:398:4: warning: 'strncpy' output may be truncated copying 127 bytes from a string of length 127 [-Wstringop-truncation] inputNew.c:395:4: warning: 'strncpy' output may be truncated copying 127 bytes from a string of length 127 [-Wstringop-truncation] See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/chopsticks.Rcheck/00install.out' for details. * checking installed package size ... NOTE installed size is 5.7Mb sub-directories of 1Mb or more: data 4.1Mb * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences. * 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 * loading checks for arch 'i386' ** 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 * loading checks for arch 'x64' ** 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 ... OK * checking R code for possible problems ... OK * checking Rd files ... NOTE prepare_Rd: ibs.stats.Rd:28: Dropping empty section \references prepare_Rd: ibs.stats.Rd:49: Dropping empty section \seealso prepare_Rd: read.pedfile.info.Rd:31-32: Dropping empty section \examples prepare_Rd: read.pedfile.map.Rd:31-32: Dropping empty section \examples prepare_Rd: read.snps.chiamo.Rd:37-38: Dropping empty section \note prepare_Rd: read.wtccc.signals.Rd:58: Dropping empty section \seealso prepare_Rd: wtccc.sample.list.Rd:36-37: Dropping empty section \note prepare_Rd: wtccc.sample.list.Rd:39-40: Dropping empty section \examples * 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 ... WARNING Warning: package needs dependence on R (>= 2.10) * checking line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files for i386 is not available Note: information on .o files for x64 is not available File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/chopsticks/libs/i386/chopsticks.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/chopsticks/libs/x64/chopsticks.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) File 'chopsticks/libs/i386/chopsticks.dll': Found non-API call to R: 'R_data_class' File 'chopsticks/libs/x64/chopsticks.dll': Found non-API call to R: 'R_data_class' 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. The detected symbols are linked into the code but might come from libraries and not actually be called. Compiled code should not call non-API entry points in R. See 'Writing portable packages' in the 'Writing R Extensions' manual. * checking files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK ** running examples for arch 'x64' ... 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: 2 WARNINGs, 4 NOTEs See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/chopsticks.Rcheck/00check.log' for details.