############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:NanoStringDiff.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings NanoStringDiff_1.37.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/NanoStringDiff.Rcheck’ * using R Under development (unstable) (2024-11-20 r87352) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘NanoStringDiff/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘NanoStringDiff’ version ‘1.37.0’ * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 ‘NanoStringDiff’ can be installed ... OK * used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ * used SDK: ‘MacOSX11.3.sdk’ * 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 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 ... NOTE PlotsPositiveHousekeeping: no visible global function definition for ‘read.table’ PlotsPositiveHousekeeping: no visible global function definition for ‘glm’ PlotsPositiveHousekeeping: no visible global function definition for ‘poisson’ PlotsPositiveHousekeeping: no visible global function definition for ‘rowVars’ PlotsPositiveHousekeeping: no visible global function definition for ‘par’ PlotsPositiveHousekeeping: no visible global function definition for ‘abline’ PlotsPositiveHousekeeping: no visible global function definition for ‘lm’ PlotsPositiveHousekeeping: no visible global function definition for ‘title’ PlotsPositiveHousekeeping: no visible global function definition for ‘textxy’ compute.baseSigma: no visible global function definition for ‘IQR’ createNanoStringSetFromCsv: no visible global function definition for ‘read.table’ est.dispersion : get.phihat: no visible global function definition for ‘optimize’ estNormalizationFactors: no visible global function definition for ‘glm’ estNormalizationFactors: no visible global function definition for ‘poisson’ estNormalizationFactors: no visible binding for global variable ‘median’ glm.LRT: no visible global function definition for ‘pchisq’ glm.LRT: no visible global function definition for ‘p.adjust’ glmfit.OneGroup : get.mu: no visible global function definition for ‘optimize’ glmfit.full: no visible global function definition for ‘lm’ glmfit.full: no visible global function definition for ‘median’ glmfit.full: no visible global function definition for ‘IQR’ glmfit.full : get.phi: no visible global function definition for ‘optimize’ glmfit.full : get.beta.full: no visible global function definition for ‘optim’ glmfit.reduce: no visible global function definition for ‘lm’ glmfit.reduce : get.beta.reduce: no visible global function definition for ‘optim’ rnegbinom: no visible global function definition for ‘rpois’ rnegbinom: no visible global function definition for ‘rgamma’ Undefined global functions or variables: IQR abline glm lm median optim optimize p.adjust par pchisq poisson read.table rgamma rowVars rpois textxy title Consider adding importFrom("graphics", "abline", "par", "title") importFrom("stats", "IQR", "glm", "lm", "median", "optim", "optimize", "p.adjust", "pchisq", "poisson", "rgamma", "rpois") importFrom("utils", "read.table") to your NAMESPACE file. * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Undocumented code objects: ‘compute.baseSigma’ ‘est.dispersion’ ‘fun5’ ‘glmfit.OneGroup’ ‘glmfit.full’ ‘glmfit.reduce’ ‘rnegbinom’ All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... NOTE Auto-generated content requiring editing in Rd file 'NanoStringDiff-package.Rd': \references: ‘This optional section can contain literature or other refere...’ \seealso: ‘Optional links to other man pages’ \examples: ‘\dontrun{ ## Optional simple examples of the most impor...’ * 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 is not available * checking sizes of PDF files under ‘inst/doc’ ... OK * checking installed files from ‘inst/doc’ ... NOTE The following files look like leftovers/mistakes: ‘NanoStringDiff.log’ Please remove them from your package. * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed glm.LRT 36.199 0.548 36.752 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... 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 ‘/Users/biocbuild/bbs-3.21-bioc/meat/NanoStringDiff.Rcheck/00check.log’ for details.