############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:SAIGEgds.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings SAIGEgds_2.7.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/SAIGEgds.Rcheck’ * using R Under development (unstable) (2024-10-21 r87258) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘SAIGEgds/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘SAIGEgds’ version ‘2.7.1’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘SAIGEgds’ can be installed ... OK * used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ * checking C++ specification ... NOTE Specified C++11: please drop specification unless essential * checking installed package size ... INFO installed size is 6.2Mb sub-directories of 1Mb or more: libs 4.4Mb * 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 ... 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 loading without being on the library search path ... OK * checking dependencies in R code ... NOTE Unexported objects imported by ':::' calls: ‘SeqArray:::.IsForking’ ‘SeqArray:::.McoreParallel’ ‘SeqArray:::.NumParallel’ ‘SeqArray:::.seqProgForward’ ‘SeqArray:::.seqProgress’ ‘SeqArray:::process_index’ ‘survey:::saddle’ See the note in ?`:::` about the use of this operator. * 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: seqAssocGLMM_ACAT_O.Rd: seqParallel, seqUnitFilterCond seqAssocGLMM_ACAT_V.Rd: seqParallel, seqUnitFilterCond seqAssocGLMM_Burden.Rd: seqParallel, seqUnitFilterCond seqAssocGLMM_SKAT.Rd: seqParallel, seqUnitFilterCond seqAssocGLMM_SPA.Rd: compression.gdsn, seqParallel seqseqFitLDpruning.Rd: seqParallel 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 ... 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 ... INFO 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 compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed seqAssocGLMM_ACAT_O 6.366 0.044 6.410 seqAssocGLMM_ACAT_V 6.086 0.025 6.113 seqAssocGLMM_Burden 5.854 0.016 5.871 SAIGEgds-package 5.580 0.024 5.607 seqAssocGLMM_SKAT 5.510 0.019 5.529 seqAssocGLMM_SPA 5.501 0.012 5.512 seqFitNullGLMM_SPA 5.127 0.006 5.134 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 4 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/SAIGEgds.Rcheck/00check.log’ for details.