* using log directory ‘/srv/hornik/tmp/CRAN_pretest/AnalyzAIRR.Rcheck’ * using R Under development (unstable) (2025-05-04 r88189) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 19.1.7 (3) Debian flang-new version 19.1.7 (3) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘AnalyzAIRR/DESCRIPTION’ ... OK * this is package ‘AnalyzAIRR’ version ‘1.2.2’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [4s/5s] NOTE Maintainer: ‘Vanessa Mhanna ’ New submission License components with restrictions and base license permitting such: GPL-3 + file LICENSE File 'LICENSE': GNU LESSER GENERAL PUBLIC LICENSE Version 3, 29 June 2007 Copyright (C) 2007 Free Software Foundation, Inc. Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. 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Possibly misspelled words in DESCRIPTION: AAI (4:14) AIRR (6:171) AnalyzAIRR (5:64, 8:2) Ig (2:44) bioinformatics (8:195) Size of tarball: 71295140 bytes * 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 executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘AnalyzAIRR’ can be installed ... [67s/68s] OK * checking package directory ... OK * checking for future file timestamps ... 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 ... [3s/3s] OK * checking whether the package can be loaded with stated dependencies ... [2s/2s] OK * checking whether the package can be unloaded cleanly ... [2s/2s] OK * checking whether the namespace can be loaded with stated dependencies ... [2s/2s] OK * checking whether the namespace can be unloaded cleanly ... [3s/3s] OK * checking loading without being on the library search path ... [3s/3s] OK * checking use of S3 registration ... 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 ... [15s/15s] OK * checking Rd files ... [0s/0s] OK * checking Rd metadata ... OK * checking Rd line widths ... 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 ... [8s/8s] OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [22s/22s] ERROR Running examples in ‘AnalyzAIRR-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: diffExpGroup > ### Title: Differential expression analysis > ### Aliases: diffExpGroup > > ### ** Examples > > > dds1 <- diffExpGroup(x = RepSeqData, + colGrp = "cell_subset" , + level = "V", + group = c("cell_subset", "amTreg", "nTreg")) Warning in DESeqDataSet(se, design = design, ignoreRank) : some variables in design formula are characters, converting to factors Error in validObject(.Object) : invalid class “DESeqDataSet” object: superclass "ExpData" not defined in the environment of the object's class Calls: diffExpGroup ... DESeqDataSet -> new -> initialize -> initialize -> validObject Execution halted Examples with CPU (user + system) or elapsed time > 5s user system elapsed CalcDissimilarity 6.016 0.352 6.37 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [29s/29s] OK Running ‘testthat.R’ [29s/29s] * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [106s/106s] ERROR Error(s) in re-building vignettes: ... --- re-building ‘dataloading.Rmd’ using rmarkdown --- finished re-building ‘dataloading.Rmd’ --- re-building ‘datamanipulation.Rmd’ using rmarkdown --- finished re-building ‘datamanipulation.Rmd’ --- re-building ‘datanormalization.Rmd’ using rmarkdown ** Processing: /srv/hornik/tmp/CRAN_pretest/AnalyzAIRR.Rcheck/vign_test/AnalyzAIRR/vignettes/datanormalization_files/figure-html/unnamed-chunk-2-1.png 960x576 pixels, 3x8 bits/pixel, RGB Input IDAT size = 63195 bytes Input file size = 63357 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 47735 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 47735 Output IDAT size = 47735 bytes (15460 bytes decrease) Output file size = 47813 bytes (15544 bytes = 24.53% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/AnalyzAIRR.Rcheck/vign_test/AnalyzAIRR/vignettes/datanormalization_files/figure-html/unnamed-chunk-3-1.png 960x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 22406 bytes Input file size = 22508 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 18663 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 18663 Output IDAT size = 18663 bytes (3743 bytes decrease) Output file size = 18741 bytes (3767 bytes = 16.74% decrease) --- finished re-building ‘datanormalization.Rmd’ --- re-building ‘exploratory.Rmd’ using rmarkdown ** Processing: /srv/hornik/tmp/CRAN_pretest/AnalyzAIRR.Rcheck/vign_test/AnalyzAIRR/vignettes/exploratory_files/figure-html/sd1-1.png 1344x960 pixels, 3x8 bits/pixel, RGB Input IDAT size = 43906 bytes Input file size = 44044 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 39361 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 39028 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 39028 Output IDAT size = 39028 bytes (4878 bytes decrease) Output file size = 39106 bytes (4938 bytes = 11.21% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/AnalyzAIRR.Rcheck/vign_test/AnalyzAIRR/vignettes/exploratory_files/figure-html/sd2-1.png 1344x960 pixels, 3x8 bits/pixel, RGB Input IDAT size = 45106 bytes Input file size = 45244 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 40755 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 40125 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 40125 Output IDAT size = 40125 bytes (4981 bytes decrease) Output file size = 40203 bytes (5041 bytes = 11.14% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/AnalyzAIRR.Rcheck/vign_test/AnalyzAIRR/vignettes/exploratory_files/figure-html/plot rarefaction-1.png 1536x768 pixels, 3x8 bits/pixel, RGB Input IDAT size = 100652 bytes Input file size = 100874 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 86516 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 86516 Output IDAT size = 86516 bytes (14136 bytes decrease) Output file size = 86594 bytes (14280 bytes = 14.16% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/AnalyzAIRR.Rcheck/vign_test/AnalyzAIRR/vignettes/exploratory_files/figure-html/plot plotStatScatter-1.png 1152x768 pixels, 3x8 bits/pixel, RGB Input IDAT size = 38764 bytes Input file size = 38890 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 31524 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 31524 Output IDAT size = 31524 bytes (7240 bytes decrease) Output file size = 31602 bytes (7288 bytes = 18.74% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/AnalyzAIRR.Rcheck/vign_test/AnalyzAIRR/vignettes/exploratory_files/figure-html/plot indices 2-1.png 1344x960 pixels, 3x8 bits/pixel, RGB Input IDAT size = 37715 bytes Input file size = 37841 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 36339 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 33247 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 33247 Output IDAT size = 33247 bytes (4468 bytes decrease) Output file size = 33325 bytes (4516 bytes = 11.93% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/AnalyzAIRR.Rcheck/vign_test/AnalyzAIRR/vignettes/exploratory_files/figure-html/plot renyi-1.png 1536x768 pixels, 3x8 bits/pixel, RGB Input IDAT size = 112886 bytes Input file size = 113120 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 84818 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 84818 Output IDAT size = 84818 bytes (28068 bytes decrease) Output file size = 84896 bytes (28224 bytes = 24.95% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/AnalyzAIRR.Rcheck/vign_test/AnalyzAIRR/vignettes/exploratory_files/figure-html/intervals-1.png 1536x1152 pixels, 3x8 bits/pixel, RGB Input IDAT size = 45263 bytes Input file size = 45401 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 41656 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 41656 Output IDAT size = 41656 bytes (3607 bytes decrease) Output file size = 41734 bytes (3667 bytes = 8.08% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/AnalyzAIRR.Rcheck/vign_test/AnalyzAIRR/vignettes/exploratory_files/figure-html/intervals 2-1.png 1536x1152 pixels, 3x8 bits/pixel, RGB Input IDAT size = 49056 bytes Input file size = 49194 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 44840 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 44840 Output IDAT size = 44840 bytes (4216 bytes decrease) Output file size = 44918 bytes (4276 bytes = 8.69% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/AnalyzAIRR.Rcheck/vign_test/AnalyzAIRR/vignettes/exploratory_files/figure-html/plot clone distri-1.png 1344x768 pixels, 3x8 bits/pixel, RGB Input IDAT size = 108653 bytes Input file size = 108887 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 84845 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 84845 Output IDAT size = 84845 bytes (23808 bytes decrease) Output file size = 84923 bytes (23964 bytes = 22.01% decrease) --- finished re-building ‘exploratory.Rmd’ --- re-building ‘gettingstarted.Rmd’ using rmarkdown --- finished re-building ‘gettingstarted.Rmd’ --- re-building ‘multisample.Rmd’ using rmarkdown ** Processing: /srv/hornik/tmp/CRAN_pretest/AnalyzAIRR.Rcheck/vign_test/AnalyzAIRR/vignettes/multisample_files/figure-html/comp sd1-1.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 12008 bytes Input file size = 12098 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 8723 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 8723 Output IDAT size = 8723 bytes (3285 bytes decrease) Output file size = 8801 bytes (3297 bytes = 27.25% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/AnalyzAIRR.Rcheck/vign_test/AnalyzAIRR/vignettes/multisample_files/figure-html/J usage -1.png 1152x480 pixels, 3x8 bits/pixel, RGB Input IDAT size = 37677 bytes Input file size = 37803 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 28900 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 28900 Output IDAT size = 28900 bytes (8777 bytes decrease) Output file size = 28978 bytes (8825 bytes = 23.34% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/AnalyzAIRR.Rcheck/vign_test/AnalyzAIRR/vignettes/multisample_files/figure-html/plot indices 3-1.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 7816 bytes Input file size = 7894 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 5983 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 5983 Output IDAT size = 5983 bytes (1833 bytes decrease) Output file size = 6061 bytes (1833 bytes = 23.22% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/AnalyzAIRR.Rcheck/vign_test/AnalyzAIRR/vignettes/multisample_files/figure-html/plot plotRenyiIndexG-1.png 672x480 pixels, 3x8 bits/pixel, RGB Input IDAT size = 24275 bytes Input file size = 24377 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 17715 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 17715 Output IDAT size = 17715 bytes (6560 bytes decrease) Output file size = 17793 bytes (6584 bytes = 27.01% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/AnalyzAIRR.Rcheck/vign_test/AnalyzAIRR/vignettes/multisample_files/figure-html/plotDistribVpJall-1.png 816x480 pixels, 3x8 bits/pixel, RGB Input IDAT size = 21211 bytes Input file size = 21313 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 18204 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 18204 Output IDAT size = 18204 bytes (3007 bytes decrease) Output file size = 18282 bytes (3031 bytes = 14.22% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/AnalyzAIRR.Rcheck/vign_test/AnalyzAIRR/vignettes/multisample_files/figure-html/plotDistribVpJall 2-1.png 816x480 pixels, 3x8 bits/pixel, RGB Input IDAT size = 23447 bytes Input file size = 23549 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 19663 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 19663 Output IDAT size = 19663 bytes (3784 bytes decrease) Output file size = 19741 bytes (3808 bytes = 16.17% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/AnalyzAIRR.Rcheck/vign_test/AnalyzAIRR/vignettes/multisample_files/figure-html/venn-1.png 768x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 62353 bytes Input file size = 62515 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 51319 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 51319 Output IDAT size = 51319 bytes (11034 bytes decrease) Output file size = 51397 bytes (11118 bytes = 17.78% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/AnalyzAIRR.Rcheck/vign_test/AnalyzAIRR/vignettes/multisample_files/figure-html/scatter-1.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 19514 bytes Input file size = 19616 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 14802 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 14802 Output IDAT size = 14802 bytes (4712 bytes decrease) Output file size = 14880 bytes (4736 bytes = 24.14% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/AnalyzAIRR.Rcheck/vign_test/AnalyzAIRR/vignettes/multisample_files/figure-html/scatter 2-1.png 768x288 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 20958 bytes Input file size = 21840 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 19785 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 19785 Output IDAT size = 19785 bytes (1173 bytes decrease) Output file size = 19863 bytes (1977 bytes = 9.05% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/AnalyzAIRR.Rcheck/vign_test/AnalyzAIRR/vignettes/multisample_files/figure-html/dissimilarity-1.png 288x480 pixels, 3x8 bits/pixel, RGB Input IDAT size = 14181 bytes Input file size = 14271 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 11986 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 11986 Output IDAT size = 11986 bytes (2195 bytes decrease) Output file size = 12064 bytes (2207 bytes = 15.46% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/AnalyzAIRR.Rcheck/vign_test/AnalyzAIRR/vignettes/multisample_files/figure-html/mds1-1.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 10145 bytes Input file size = 10235 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 8774 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 8774 Output IDAT size = 8774 bytes (1371 bytes decrease) Output file size = 8852 bytes (1383 bytes = 13.51% decrease) Quitting from multisample.Rmd:206-211 [diffexp] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `validObject()`: ! invalid class "DESeqDataSet" object: superclass "ExpData" not defined in the environment of the object's class --- Backtrace: ▆ 1. └─AnalyzAIRR::diffExpGroup(...) 2. └─AnalyzAIRR::.toDESeq2(x, colGrp = colGrp, level = level) 3. └─DESeq2::DESeqDataSetFromMatrix(...) 4. └─DESeq2::DESeqDataSet(se, design = design, ignoreRank) 5. └─methods::new("DESeqDataSet", se, design = design) 6. ├─methods::initialize(value, ...) 7. └─methods::initialize(value, ...) 8. └─methods::validObject(.Object) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'multisample.Rmd' failed with diagnostics: invalid class "DESeqDataSet" object: superclass "ExpData" not defined in the environment of the object's class --- failed re-building ‘multisample.Rmd’ --- re-building ‘onesample.Rmd’ using rmarkdown ** Processing: /srv/hornik/tmp/CRAN_pretest/AnalyzAIRR.Rcheck/vign_test/AnalyzAIRR/vignettes/onesample_files/figure-html/plotIndStatistics1-1.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 34264 bytes Input file size = 34390 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 23096 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 23096 Output IDAT size = 23096 bytes (11168 bytes decrease) Output file size = 23174 bytes (11216 bytes = 32.61% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/AnalyzAIRR.Rcheck/vign_test/AnalyzAIRR/vignettes/onesample_files/figure-html/J usage ind-1.png 864x576 pixels, 3x8 bits/pixel, RGB Input IDAT size = 140791 bytes Input file size = 141073 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 114257 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 114257 Output IDAT size = 114257 bytes (26534 bytes decrease) Output file size = 114335 bytes (26738 bytes = 18.95% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/AnalyzAIRR.Rcheck/vign_test/AnalyzAIRR/vignettes/onesample_files/figure-html/plotIndStatistics2-1.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 16754 bytes Input file size = 16856 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 12855 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 12855 Output IDAT size = 12855 bytes (3899 bytes decrease) Output file size = 12933 bytes (3923 bytes = 23.27% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/AnalyzAIRR.Rcheck/vign_test/AnalyzAIRR/vignettes/onesample_files/figure-html/plotIndMap-1.png 384x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 139458 bytes Input file size = 139740 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 102679 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 102679 Output IDAT size = 102679 bytes (36779 bytes decrease) Output file size = 102757 bytes (36983 bytes = 26.47% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/AnalyzAIRR.Rcheck/vign_test/AnalyzAIRR/vignettes/onesample_files/figure-html/plotIndIntervals-1.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 11420 bytes Input file size = 11510 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 9468 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 9468 Output IDAT size = 9468 bytes (1952 bytes decrease) Output file size = 9546 bytes (1964 bytes = 17.06% decrease) --- finished re-building ‘onesample.Rmd’ --- re-building ‘shiny.Rmd’ using rmarkdown --- finished re-building ‘shiny.Rmd’ SUMMARY: processing the following file failed: ‘multisample.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... [4s/4s] OK * checking HTML version of manual ... [1s/1s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 2 ERRORs, 1 NOTE