############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GeneTonic.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings GeneTonic_1.6.4.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/GeneTonic.Rcheck' * using R version 4.1.3 (2022-03-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'GeneTonic/DESCRIPTION' ... OK * this is package 'GeneTonic' version '1.6.4' * 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 'GeneTonic' 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 * loading checks for arch 'i386' ** 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 * loading checks for arch 'x64' ** 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 ... ** running examples for arch 'i386' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed ggs_backbone 8.05 0.23 8.50 gs_mds 7.94 0.16 8.10 ggs_graph 7.72 0.16 7.87 GeneTonic 7.48 0.29 8.00 summarize_ggs_hubgenes 7.63 0.09 7.72 gs_heatmap 7.28 0.28 7.57 gs_scores 6.71 0.11 6.81 gs_scoresheat 6.25 0.12 6.38 signature_volcano 6.26 0.08 6.34 gs_dendro 5.86 0.16 6.02 export_for_iSEE 5.75 0.11 5.86 checkup_gtl 5.48 0.24 5.72 checkup_GeneTonic 5.31 0.37 5.69 gs_horizon 5.52 0.09 5.60 distill_enrichment 5.46 0.12 5.58 gene_plot 5.38 0.11 5.49 gs_alluvial 5.12 0.28 6.08 gs_volcano 5.23 0.17 5.40 gs_radar 5.04 0.25 5.36 enhance_table 5.11 0.11 5.22 GeneTonic_list 4.74 0.35 5.08 gs_summary_overview_pair 4.95 0.11 5.06 happy_hour 4.97 0.08 5.05 ** running examples for arch 'x64' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed summarize_ggs_hubgenes 8.36 0.33 9.57 gs_mds 7.96 0.19 8.19 ggs_backbone 7.87 0.25 8.30 gs_heatmap 7.13 0.16 7.29 ggs_graph 7.00 0.22 7.21 gs_scores 6.88 0.28 7.15 GeneTonic 6.64 0.15 6.80 gs_scoresheat 6.07 0.17 6.25 gs_dendro 6.02 0.15 6.17 signature_volcano 5.62 0.09 5.72 export_for_iSEE 4.91 0.21 5.11 gs_summary_overview 4.84 0.17 5.02 * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'testthat.R' ERROR Running the tests in 'tests/testthat.R' failed. Last 13 lines of output: | |======================================================================| 99% | |======================================================================| 100% [ FAIL 1 | WARN 2 | SKIP 0 | PASS 242 ] == Failed tests ================================================================ -- Failure (test-ggs_graph.R:121:3): Backbone functionality up and running ----- vcount(bbg4) not equal to 0. 1/1 mismatches [1] 2 - 0 == 2 [ FAIL 1 | WARN 2 | SKIP 0 | PASS 242 ] Error: Test failures Execution halted ** running tests for arch 'x64' ... Running 'testthat.R' OK * 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 See 'C:/Users/biocbuild/bbs-3.14-bioc/meat/GeneTonic.Rcheck/00check.log' for details.