############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNcbi_1.11.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'E:/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNcbi.Rcheck' * using R Under development (unstable) (2024-10-26 r87273 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using options '--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error' * checking for file 'biodbNcbi/DESCRIPTION' ... OK * this is package 'biodbNcbi' version '1.11.0' * 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 hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'biodbNcbi' can be installed ... OK * checking installed package size ... INFO installed size is 8.1Mb sub-directories of 1Mb or more: testref 7.6Mb * checking package directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Title field: should not end in a period. * 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 ... 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 ... OK * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: NcbiCcdsConn.Rd: BiodbFactory, BiodbConn NcbiCcdsEntry.Rd: BiodbHtmlEntry NcbiEntrezConn.Rd: BiodbConn Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... SKIPPED * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking files in 'vignettes' ... SKIPPED * checking examples ... SKIPPED * checking for unstated dependencies in 'longtests' ... WARNING 'library' or 'require' call not declared from: 'biodbNci' * checking tests in 'longtests' ... Running 'testthat.R' OK * DONE Status: 1 WARNING, 2 NOTEs See 'E:/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNcbi.Rcheck/00check.log' for details.