############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:metaSeq.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings metaSeq_1.39.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/metaSeq.Rcheck’ * using R version 4.3.0 alpha (2023-04-03 r84154) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.2 LTS * using session charset: UTF-8 * checking for file ‘metaSeq/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘metaSeq’ version ‘1.39.0’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘metaSeq’ can be installed ... OK * checking installed package size ... NOTE installed size is 6.3Mb sub-directories of 1Mb or more: data 5.8Mb * 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 * 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: ‘NOISeq:::busca’ ‘NOISeq:::n.menor’ See the note in ?`:::` about the use of this operator. There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: ‘oneside.noiseq’ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE Found the following possibly unsafe calls: File ‘metaSeq/R/Accelerate.NOISeq.R’: assignInNamespace("busca", busca, ns = "NOISeq", envir = env) assignInNamespace("n.menor", nmenor, ns = "NOISeq", envir = env) assignInNamespace("busca", busca, ns = "NOISeq", envir = env) assignInNamespace("n.menor", nmenor, ns = "NOISeq", envir = env) File ‘metaSeq/R/Reset.Accelerate.NOISeq.R’: assignInNamespace("busca", original.busca, ns = "NOISeq", envir = env) assignInNamespace("n.menor", original.n.menor, ns = "NOISeq", envir = env) File ‘metaSeq/R/oneside.noiseq.R’: assignInNamespace("probdeg", custom.probdeg, ns = "NOISeq", envir = env) assignInNamespace("MD", custom.MD, ns = "NOISeq", envir = env) assignInNamespace("probdeg", original.probdeg, ns = "NOISeq", envir = env) assignInNamespace("MD", original.MD, ns = "NOISeq", envir = env) Accelerate.NOISeq: no visible global function definition for ‘data’ Accelerate.NOISeq: no visible binding for global variable ‘text.n.menor_unix’ Accelerate.NOISeq: no visible binding for global variable ‘text.busca_unix’ Accelerate.NOISeq: no visible global function definition for ‘assignInNamespace’ Accelerate.NOISeq: no visible binding for global variable ‘busca’ Accelerate.NOISeq: no visible binding for global variable ‘nmenor’ Accelerate.NOISeq: no visible binding for global variable ‘text.n.menor_win’ Accelerate.NOISeq: no visible binding for global variable ‘text.busca_win’ Reset.Accelerate.NOISeq: no visible global function definition for ‘assignInNamespace’ custom.MD: no visible global function definition for ‘combn’ custom.probdeg: no visible global function definition for ‘na.omit’ each.Fisher.ignore.test: no visible global function definition for ‘pchisq’ each.Fisher.test: no visible global function definition for ‘pchisq’ each.Stouffer.ignore.test: no visible global function definition for ‘qnorm’ each.Stouffer.ignore.test: no visible global function definition for ‘pnorm’ each.Stouffer.test: no visible global function definition for ‘qnorm’ each.Stouffer.test: no visible global function definition for ‘pnorm’ oneside.noiseq: no visible global function definition for ‘assignInNamespace’ original.MD: no visible global function definition for ‘combn’ original.probdeg: no visible global function definition for ‘na.omit’ original.probdeg: no visible binding for global variable ‘n.menor’ original.probdeg: no visible binding for global variable ‘busca’ Undefined global functions or variables: assignInNamespace busca combn data n.menor na.omit nmenor pchisq pnorm qnorm text.busca_unix text.busca_win text.n.menor_unix text.n.menor_win Consider adding importFrom("stats", "na.omit", "pchisq", "pnorm", "qnorm") importFrom("utils", "assignInNamespace", "combn", "data") to your NAMESPACE file. * checking Rd files ... OK * 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 installed files from ‘inst/doc’ ... NOTE The following files should probably not be installed: ‘Fig1.jpeg’, ‘Fig2.png’ Consider the use of a .Rinstignore file: see ‘Writing R Extensions’, or move the vignette sources from ‘inst/doc’ to ‘vignettes’. * 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 ... ‘metaSeq.Rnw’ using ‘UTF-8’... OK OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 5 NOTEs See ‘/home/biocbuild/bbs-3.17-bioc/meat/metaSeq.Rcheck/00check.log’ for details.