* using log directory ‘/srv/hornik/tmp/CRAN_pretest/GRIN2.Rcheck’ * using R Under development (unstable) (2024-11-15 r87338) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 19.1.1 (1) Debian flang-new version 19.1.1 (1) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘GRIN2/DESCRIPTION’ ... OK * this is package ‘GRIN2’ version ‘1.0’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [3s/6s] NOTE Maintainer: ‘Abdelrahman Elsayed ’ New submission Possibly misspelled words in DESCRIPTION: al (10:332) et (10:329) * 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 ‘GRIN2’ can be installed ... [34s/34s] 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 ... [10s/10s] OK * checking whether the package can be loaded with stated dependencies ... [10s/10s] OK * checking whether the package can be unloaded cleanly ... [10s/10s] OK * checking whether the namespace can be loaded with stated dependencies ... [10s/10s] OK * checking whether the namespace can be unloaded cleanly ... [11s/11s] OK * checking loading without being on the library search path ... [11s/11s] 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 ... [49s/49s] 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 ... [0s/0s] 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 ... [53s/54s] OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [61s/62s] ERROR Error(s) in re-building vignettes: ... --- re-building ‘GRIN2.Rmd’ using rmarkdown ** Processing: /srv/hornik/tmp/CRAN_pretest/GRIN2.Rcheck/vign_test/GRIN2/vignettes/GRIN2_files/figure-html/genomewide.lesion.plot-1.png 1536x1344 pixels, 3x8 bits/pixel, RGB Input IDAT size = 310549 bytes Input file size = 311071 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 233612 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 = 233612 Output IDAT size = 233612 bytes (76937 bytes decrease) Output file size = 233690 bytes (77381 bytes = 24.88% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/GRIN2.Rcheck/vign_test/GRIN2/vignettes/GRIN2_files/figure-html/grin.stacked.barplot-1.png 1920x1920 pixels, 3x8 bits/pixel, RGB Input IDAT size = 117589 bytes Input file size = 117835 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 100371 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 = 100371 Output IDAT size = 100371 bytes (17218 bytes decrease) Output file size = 100449 bytes (17386 bytes = 14.75% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/GRIN2.Rcheck/vign_test/GRIN2/vignettes/GRIN2_files/figure-html/oncorprint.constellation.test.significant.genes-1.png 2496x1152 pixels, 3x8 bits/pixel, RGB Input IDAT size = 71052 bytes Input file size = 71226 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 = 67270 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 = 67270 Output IDAT size = 67270 bytes (3782 bytes decrease) Output file size = 67348 bytes (3878 bytes = 5.44% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/GRIN2.Rcheck/vign_test/GRIN2/vignettes/GRIN2_files/figure-html/oncorprint.pathways-1.png 2496x1728 pixels, 3x8 bits/pixel, RGB Input IDAT size = 134612 bytes Input file size = 134882 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 128377 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 = 127675 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 = 127675 Output IDAT size = 127675 bytes (6937 bytes decrease) Output file size = 127753 bytes (7129 bytes = 5.29% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/GRIN2.Rcheck/vign_test/GRIN2/vignettes/GRIN2_files/figure-html/gene.plot.wt1-1.png 1728x1536 pixels, 3x8 bits/pixel, RGB Input IDAT size = 94038 bytes Input file size = 94248 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 82448 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 = 82448 Output IDAT size = 82448 bytes (11590 bytes decrease) Output file size = 82526 bytes (11722 bytes = 12.44% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/GRIN2.Rcheck/vign_test/GRIN2/vignettes/GRIN2_files/figure-html/regional.lesion.plot-1.png 1536x1920 pixels, 3x8 bits/pixel, RGB Input IDAT size = 188117 bytes Input file size = 188459 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 142287 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 = 142287 Output IDAT size = 142287 bytes (45830 bytes decrease) Output file size = 142365 bytes (46094 bytes = 24.46% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/GRIN2.Rcheck/vign_test/GRIN2/vignettes/GRIN2_files/figure-html/locus.plot-1.png 1536x1344 pixels, 3x8 bits/pixel, RGB Input IDAT size = 61910 bytes Input file size = 62072 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 52782 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 = 52782 Output IDAT size = 52782 bytes (9128 bytes decrease) Output file size = 52860 bytes (9212 bytes = 14.84% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/GRIN2.Rcheck/vign_test/GRIN2/vignettes/GRIN2_files/figure-html/chromosome.plot-1.png 1536x1728 pixels, 3x8 bits/pixel, RGB Input IDAT size = 83496 bytes Input file size = 83694 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 70271 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 = 70271 Output IDAT size = 70271 bytes (13225 bytes decrease) Output file size = 70349 bytes (13345 bytes = 15.94% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/GRIN2.Rcheck/vign_test/GRIN2/vignettes/GRIN2_files/figure-html/reg.feature.plot-1.png 1536x1344 pixels, 3x8 bits/pixel, RGB Input IDAT size = 53641 bytes Input file size = 53791 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 48722 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 = 48722 Output IDAT size = 48722 bytes (4919 bytes decrease) Output file size = 48800 bytes (4991 bytes = 9.28% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/GRIN2.Rcheck/vign_test/GRIN2/vignettes/GRIN2_files/figure-html/JAK2.waterfall.plot-1.png 1152x1152 pixels, 3x8 bits/pixel, RGB Input IDAT size = 43738 bytes Input file size = 43876 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 33783 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 = 33783 Output IDAT size = 33783 bytes (9955 bytes decrease) Output file size = 33861 bytes (10015 bytes = 22.83% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/GRIN2.Rcheck/vign_test/GRIN2/vignettes/GRIN2_files/figure-html/lesion.expression.pathway-1.png 1152x1152 pixels, 3x8 bits/pixel, RGB Input IDAT size = 44712 bytes Input file size = 44850 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 38366 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 = 38366 Output IDAT size = 38366 bytes (6346 bytes decrease) Output file size = 38444 bytes (6406 bytes = 14.28% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/GRIN2.Rcheck/vign_test/GRIN2/vignettes/GRIN2_files/figure-html/loss.lesion.boundaries.significance.plot-1.png 1536x1536 pixels, 3x8 bits/pixel, RGB Input IDAT size = 55801 bytes Input file size = 55951 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 47062 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 = 47062 Output IDAT size = 47062 bytes (8739 bytes decrease) Output file size = 47140 bytes (8811 bytes = 15.75% decrease) Quitting from lines 695-704 [loss.annotated.genes.significance.plot] (GRIN2.Rmd) Error: processing vignette 'GRIN2.Rmd' failed with diagnostics: argument is of length zero --- failed re-building ‘GRIN2.Rmd’ SUMMARY: processing the following file failed: ‘GRIN2.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... [3s/3s] 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: 1 ERROR, 1 NOTE