############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PanViz.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PanViz_1.7.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/PanViz.Rcheck’ * using R version 4.4.1 RC (2024-06-06 r86719) * 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 13.6.5 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘PanViz/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘PanViz’ version ‘1.7.0’ * 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 ‘PanViz’ 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 ... 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 R/sysdata.rda ... OK * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘PanViz-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: decompose_IMON > ### Title: decompose_IMON > ### Aliases: decompose_IMON > > ### ** Examples > > data("er_snp_vector") > G <- PanViz::get_IMON(snp_list = er_snp_vector, ego = 5, save_file = FALSE) | | | 0% | |=================================== | 50%Error in entrez_check(response) : HTTP failure: 429, too many requests. Functions that contact the NCBI should not be called in parallel. If you are using a shared IP, consider registerring for an API key as described in the rate-limiting section of rentrez tutorial. NCBI message: {"error":"API rate limit exceeded","api-key":"170.223.207.78","count":"4","limit":"3"} Calls: ... -> do.call -> -> entrez_check Execution halted * 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: 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. └─PanViz::get_grouped_IMON(...) 5. └─PanViz:::NCBI_dbSNP_query(snp_list, progress_bar) 6. ├─base::tryCatch(...) 7. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 8. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 9. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 10. └─rentrez::entrez_summary(db = "snp", id = split_data[[i]]) 11. ├─base::do.call(make_entrez_query, args) 12. └─rentrez (local) ``(...) 13. └─rentrez:::entrez_check(response) [ FAIL 1 | WARN 26 | SKIP 0 | PASS 15 ] 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: 2 ERRORs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/PanViz.Rcheck/00check.log’ for details.