############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:recount.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings recount_1.25.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/recount.Rcheck' * using R Under development (unstable) (2022-12-25 r83502 ucrt) * using platform: x86_64-w64-mingw32 (64-bit) * R was compiled by gcc.exe (GCC) 10.4.0 GNU Fortran (GCC) 10.4.0 * running under: Windows Server x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'recount/DESCRIPTION' ... OK * this is package 'recount' version '1.25.0' * 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 whether package 'recount' can be installed ... OK * checking installed package size ... NOTE installed size is 6.1Mb sub-directories of 1Mb or more: data 5.8Mb * 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 ... NOTE Note: found 347 marked UTF-8 strings * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in Makefiles ... OK * checking for GNU extensions in Makefiles ... OK * checking include directives in Makefiles ... OK * checking files in 'vignettes' ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed snaptron_query 0.41 0 12.83 geo_characteristics 0.37 0 5.38 * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'test-all.R' ERROR Running the tests in 'tests/test-all.R' failed. Last 13 lines of output: trying URL 'http://duffel.rail.bio/recount/v2/DRP000366/files_info.tsv_fake' [ FAIL 1 | WARN 0 | SKIP 0 | PASS 53 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-data.R:37'): Download URLs ─────────────────────────────────── download_study("DRP000366", type = "rse-fc", download = FALSE) not equal to "http://sciserver.org/public-data/recount2/data/fc_rc/rse_fc_DRP000366.Rdata". 1/1 mismatches x[1]: "http://idies.jhu.edu/recount/data/fc_rc/rse_fc_DRP000366.Rdata" y[1]: "http://sciserver.org/public-data/recount2/data/fc_rc/rse_fc_DRP000366.Rda y[1]: ta" [ FAIL 1 | WARN 0 | SKIP 0 | PASS 53 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... 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, 2 NOTEs See 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/recount.Rcheck/00check.log' for details.