############################################################################## ############################################################################## ### ### Running command: ### ### /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD check --install=check:sesame.install-out.txt --library=/home/rapidbuild/bbs-3.21-bioc-rapid/R/site-library --timings sesame_1.25.3.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/sesame.Rcheck’ * using R Under development (unstable) (2025-01-20 r87609) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘sesame/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘sesame’ version ‘1.25.3’ * 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 ‘sesame’ 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 loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed imputeBetasByGenomicNeighbors 25.007 0.527 25.537 inferSex 17.521 0.175 17.700 inferSpecies 12.704 0.895 13.601 sesameQC_calcStats 13.285 0.017 13.305 imputeBetas 12.973 0.308 13.284 sesameQC_plotHeatSNPs 12.606 0.020 12.630 ELBAR 10.809 0.156 10.965 diffRefSet 10.642 0.180 10.824 sesameQC_plotBar 9.166 0.088 9.255 compareReference 7.900 0.167 8.068 getRefSet 7.647 0.056 7.704 compareMouseStrainReference 7.541 0.106 7.648 sesameQC_plotBetaByDesign 7.624 0.002 7.632 matchDesign 7.152 0.046 7.206 DMR 5.818 0.147 5.965 visualizeGene 5.777 0.103 5.884 estimateLeukocyte 5.381 0.117 5.498 dyeBiasCorrMostBalanced 5.224 0.100 5.326 inferStrain 4.708 0.520 5.230 DML 4.830 0.219 5.050 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... ERROR Error(s) in re-building vignettes: --- re-building ‘QC.Rmd’ using rmarkdown Failed to query server: Connection timed out Could not fetch https://www.googletagmanager.com/gtag/js?id=G-Z2XSZZYJHZ HttpExceptionRequest Request { host = "www.googletagmanager.com" port = 443 secure = True requestHeaders = [] path = "/gtag/js" queryString = "?id=G-Z2XSZZYJHZ" method = "GET" proxy = Nothing rawBody = False redirectCount = 10 responseTimeout = ResponseTimeoutDefault requestVersion = HTTP/1.1 } (InternalException (HostCannotConnect "www.googletagmanager.com" [Network.Socket.connect: : does not exist (Network unreachable)])) Error: processing vignette 'QC.Rmd' failed with diagnostics: pandoc document conversion failed with error 61 --- failed re-building ‘QC.Rmd’ --- re-building ‘inferences.Rmd’ using rmarkdown Failed to query server: Failed to activate service 'org.freedesktop.timedate1': timed out (service_start_timeout=25000ms) --- finished re-building ‘inferences.Rmd’ --- re-building ‘modeling.Rmd’ using rmarkdown Failed to query server: Failed to activate service 'org.freedesktop.timedate1': timed out (service_start_timeout=25000ms) --- finished re-building ‘modeling.Rmd’ --- re-building ‘nonhuman.Rmd’ using rmarkdown Failed to query server: Failed to activate service 'org.freedesktop.timedate1': timed out (service_start_timeout=25000ms) --- finished re-building ‘nonhuman.Rmd’ --- re-building ‘sesame.Rmd’ using rmarkdown Failed to query server: Failed to activate service 'org.freedesktop.timedate1': timed out (service_start_timeout=25000ms) --- finished re-building ‘sesame.Rmd’ SUMMARY: processing the following file failed: ‘QC.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 1 ERROR See ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/sesame.Rcheck/00check.log’ for details.