############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:netZooR.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings netZooR_1.13.8.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/netZooR.Rcheck’ * using R version 4.5.1 (2025-06-13) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.2 LTS * using session charset: UTF-8 * checking for file ‘netZooR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘netZooR’ version ‘1.13.8’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 38 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally. * 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 ‘netZooR’ can be installed ... OK * checking installed package size ... INFO installed size is 5.6Mb sub-directories of 1Mb or more: data 1.7Mb extdata 2.9Mb * 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 whether startup messages can be suppressed ... OK * checking dependencies in R code ... WARNING '::' or ':::' import not declared from: ‘cmdstanr’ * 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 ... WARNING Missing link(s) in Rd file 'normalizeTissueAware.Rd': ‘limma::qsmooth’ ‘limma::normalizeQuantiles’ See section 'Cross-references' in the 'Writing R Extensions' manual. Found the following Rd file(s) with Rd \link{} targets missing package anchors: bladder.Rd: ExpressionSet-class normalizeTissueAware.Rd: limma::qsmooth, limma::normalizeQuantiles skin.Rd: ExpressionSet-class 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 ... WARNING Data with usage in Rd file 'bladder.Rd' but not in code: ‘bladder’ Data with usage in Rd file 'skin.Rd' but not in code: ‘skin’ * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... WARNING Output for data("bladder", package = "netZooR"): No dataset created in 'envir' Warning message: In utils::data(list = fileName, package = pkgname, envir = dataEnv) : data set ‘bladder’ not found Output for data("skin", package = "netZooR"): No dataset created in 'envir' Warning message: In utils::data(list = fileName, package = pkgname, envir = dataEnv) : data set ‘skin’ not found * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘netZooR-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: annotateFromBiomart > ### Title: Annotate your Expression Set with biomaRt > ### Aliases: annotateFromBiomart > > ### ** Examples > > u <- 'https://netzoo.s3.us-east-2.amazonaws.com/netZooR/unittest_datasets/' > bladder <- paste0(u, 'yarn/bladder.rdata') > skin <- paste0(u, 'yarn/skin.rdata') > download.file(bladder, destfile='data/bladder.rdata') Warning in download.file(bladder, destfile = "data/bladder.rdata") : URL https://netzoo.s3.us-east-2.amazonaws.com/netZooR/unittest_datasets/yarn/bladder.rdata: cannot open destfile 'data/bladder.rdata', reason 'No such file or directory' Warning in download.file(bladder, destfile = "data/bladder.rdata") : download had nonzero exit status > download.file(skin, destfile='data/skin.rdata') Warning in download.file(skin, destfile = "data/skin.rdata") : URL https://netzoo.s3.us-east-2.amazonaws.com/netZooR/unittest_datasets/yarn/skin.rdata: cannot open destfile 'data/skin.rdata', reason 'No such file or directory' Warning in download.file(skin, destfile = "data/skin.rdata") : download had nonzero exit status > data(skin) Warning in data(skin) : data set ‘skin’ not found > # subsetting and changing column name just for a silly example > skin <- skin[1:10,] Error in skin[1:10, ] : incorrect number of dimensions Execution halted * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 4 WARNINGs See ‘/home/biocbuild/bbs-3.22-bioc/meat/netZooR.Rcheck/00check.log’ for details.