############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:ExpressionAtlas.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings ExpressionAtlas_1.24.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/ExpressionAtlas.Rcheck’ * using R version 4.2.1 (2022-06-23) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ExpressionAtlas/DESCRIPTION’ ... OK * this is package ‘ExpressionAtlas’ version ‘1.24.0’ * 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 ‘ExpressionAtlas’ 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 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 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 ... OK * 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 files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘ExpressionAtlas-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: searchAtlasExperiments > ### Title: Search for Expression Atlas experiments > ### Aliases: ' searchAtlasExperiments ' > > ### ** Examples > > > # Search for experiments on salt in rice. > atlasRes <- searchAtlasExperiments( properties = "salt", species = "rice" ) Searching for Expression Atlas experiments matching your query ... Query successful. Specification mandates value for attribute async attributes construct error Couldn't find end of Start Tag script line 18 Opening and ending tag mismatch: meta line 16 and script Opening and ending tag mismatch: meta line 16 and head Specification mandates value for attribute data-sticky-container Opening and ending tag mismatch: img line 16 and a Opening and ending tag mismatch: a line 16 and h1 Opening and ending tag mismatch: h1 line 16 and div Opening and ending tag mismatch: input line 16 and div Opening and ending tag mismatch: input line 16 and fieldset Opening and ending tag mismatch: div line 16 and form Opening and ending tag mismatch: fieldset line 16 and div Opening and ending tag mismatch: form line 16 and div Opening and ending tag mismatch: div line 16 and header Opening and ending tag mismatch: img line 16 and a Opening and ending tag mismatch: a line 16 and span Opening and ending tag mismatch: span line 16 and div Opening and ending tag mismatch: div line 16 and script Opening and ending tag mismatch: input line 16 and fieldset Opening and ending tag mismatch: input line 16 and fieldset Opening and ending tag mismatch: input line 16 and form Opening and ending tag mismatch: input line 16 and form Opening and ending tag mismatch: form line 16 and div Opening and ending tag mismatch: fieldset line 16 and div Opening and ending tag mismatch: input line 16 and section Opening and ending tag mismatch: fieldset line 16 and div Specification mandates value for attribute defer attributes construct error Couldn't find end of Start Tag script line 154 Opening and ending tag mismatch: footer line 15 and script Opening and ending tag mismatch: input line 15 and footer Specification mandates value for attribute defer attributes construct error Couldn't find end of Start Tag script line 174 Opening and ending tag mismatch: form line 14 and script EntityRef: expecting ';' Opening and ending tag mismatch: div line 14 and body Opening and ending tag mismatch: div line 14 and html EndTag: '