############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:rcellminer.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings rcellminer_2.27.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/rcellminer.Rcheck’ * using R version 4.4.0 Patched (2024-04-24 r86482) * using platform: x86_64-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 Monterey 12.7.4 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘rcellminer/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘rcellminer’ version ‘2.27.0’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘rcellminer’ can be installed ... OK * 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 whether startup messages can be suppressed ... OK * checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘shiny’ All declared Imports should be used. * 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 ... WARNING checkRd: (7) cmVersion.Rd:17: Invalid email address: vinodh.rajapakse AT nih.gov checkRd: (-1) drugDB.Rd:13-14: Lost braces in \itemize; meant \describe ? checkRd: (-1) drugDB.Rd:15-38: Lost braces in \itemize; meant \describe ? checkRd: (-1) drugDB.Rd:17-18: Lost braces in \itemize; meant \describe ? checkRd: (-1) drugDB.Rd:19: Lost braces in \itemize; meant \describe ? checkRd: (-1) drugDB.Rd:20: Lost braces in \itemize; meant \describe ? checkRd: (-1) drugDB.Rd:21: Lost braces in \itemize; meant \describe ? checkRd: (-1) drugDB.Rd:22: Lost braces in \itemize; meant \describe ? checkRd: (-1) drugDB.Rd:23-24: Lost braces in \itemize; meant \describe ? checkRd: (-1) drugDB.Rd:25: Lost braces in \itemize; meant \describe ? checkRd: (-1) drugDB.Rd:26: Lost braces in \itemize; meant \describe ? checkRd: (-1) drugDB.Rd:27: Lost braces in \itemize; meant \describe ? checkRd: (-1) drugDB.Rd:28: Lost braces in \itemize; meant \describe ? checkRd: (-1) drugDB.Rd:29: Lost braces in \itemize; meant \describe ? checkRd: (-1) drugDB.Rd:30: Lost braces in \itemize; meant \describe ? checkRd: (-1) drugDB.Rd:31: Lost braces in \itemize; meant \describe ? checkRd: (-1) drugDB.Rd:32: Lost braces in \itemize; meant \describe ? checkRd: (-1) drugDB.Rd:33: Lost braces in \itemize; meant \describe ? checkRd: (-1) drugDB.Rd:34-35: Lost braces in \itemize; meant \describe ? checkRd: (-1) drugDB.Rd:36: Lost braces in \itemize; meant \describe ? checkRd: (7) drugDB.Rd:45: Invalid email address: vinodh.rajapakse AT nih.gov checkRd: (-1) elNetMolDataNCI60.Rd:14: Lost braces in \itemize; meant \describe ? checkRd: (-1) elNetMolDataNCI60.Rd:15-17: Lost braces in \itemize; meant \describe ? checkRd: (-1) elNetMolDataNCI60.Rd:18: Lost braces in \itemize; meant \describe ? checkRd: (-1) elNetMolDataNCI60.Rd:19-20: Lost braces in \itemize; meant \describe ? checkRd: (-1) elNetMolDataNCI60.Rd:21-22: Lost braces in \itemize; meant \describe ? checkRd: (-1) elNetMolDataNCI60.Rd:23-40: Lost braces in \itemize; meant \describe ? checkRd: (-1) elNetMolDataNCI60.Rd:25: Lost braces in \itemize; meant \describe ? checkRd: (-1) elNetMolDataNCI60.Rd:26: Lost braces in \itemize; meant \describe ? checkRd: (-1) elNetMolDataNCI60.Rd:27: Lost braces in \itemize; meant \describe ? checkRd: (-1) elNetMolDataNCI60.Rd:28: Lost braces in \itemize; meant \describe ? checkRd: (-1) elNetMolDataNCI60.Rd:29: Lost braces in \itemize; meant \describe ? checkRd: (-1) elNetMolDataNCI60.Rd:30: Lost braces in \itemize; meant \describe ? checkRd: (-1) elNetMolDataNCI60.Rd:31: Lost braces in \itemize; meant \describe ? checkRd: (-1) elNetMolDataNCI60.Rd:32: Lost braces in \itemize; meant \describe ? checkRd: (-1) elNetMolDataNCI60.Rd:33: Lost braces in \itemize; meant \describe ? checkRd: (-1) elNetMolDataNCI60.Rd:34: Lost braces in \itemize; meant \describe ? checkRd: (-1) elNetMolDataNCI60.Rd:35: Lost braces in \itemize; meant \describe ? checkRd: (-1) elNetMolDataNCI60.Rd:36: Lost braces in \itemize; meant \describe ? checkRd: (-1) elNetMolDataNCI60.Rd:37-38: Lost braces in \itemize; meant \describe ? checkRd: (7) elNetMolDataNCI60.Rd:47: Invalid email address: vinodh.rajapakse AT nih.gov checkRd: (7) fingerprintList.Rd:14: Invalid email address: augustin AT mail.nih.gov * 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 LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed getFeatureDataFromMatList 4.095 0.461 5.359 * 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, 1 NOTE See ‘/Users/biocbuild/bbs-3.20-bioc/meat/rcellminer.Rcheck/00check.log’ for details.