############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:pgxRpi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings pgxRpi_1.2.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/pgxRpi.Rcheck’ * using R version 4.4.2 (2024-10-31) * 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 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘pgxRpi/DESCRIPTION’ ... OK * this is package ‘pgxRpi’ version ‘1.2.0’ * 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 ‘pgxRpi’ 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 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 pgxSegprocess: no visible binding for global variable ‘followup_state_id’ Undefined global functions or variables: followup_state_id * 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 ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed pgxLoader 84.941 0.776 152.631 pgxMetaplot 30.160 0.327 97.417 pgxFreqplot 12.104 0.278 16.414 segtoFreq 9.768 0.211 10.594 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: ── Failure ('test_frequency.R:10:5'): retrieve frequencies with pgxfreq by filter ── Expected `result <- read.table(url, header = T, sep = "\t")` to run without any errors. ℹ Actually got a with text: cannot open the connection to 'http://www.progenetix.org/services/intervalFrequencies/?filters=NCIT:C4323,pgx:icdom-85003&output=pgxfreq' ── Error ('test_frequency.R:11:5'): retrieve frequencies with pgxfreq by filter ── Error in `eval(code, test_env)`: object 'result' not found Backtrace: ▆ 1. └─testthat::expect_equal(dim(result), c(6212, 7)) at test_frequency.R:11:5 2. └─testthat::quasi_label(enquo(object), label, arg = "object") 3. └─rlang::eval_bare(expr, quo_get_env(quo)) [ FAIL 2 | WARN 1 | SKIP 0 | PASS 33 ] Error: Test failures Execution halted * 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 ERROR, 1 NOTE See ‘/Users/biocbuild/bbs-3.20-bioc/meat/pgxRpi.Rcheck/00check.log’ for details.