* using log directory ‘/srv/hornik/tmp/CRAN_pretest/CAESAR.Suite.Rcheck’ * using R Under development (unstable) (2025-03-17 r87990) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 19.1.7 (1+b1) Debian flang-new version 19.1.7 (1+b1) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘CAESAR.Suite/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘CAESAR.Suite’ version ‘0.2.0’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [4s/4s] WARNING Maintainer: ‘Xiao Zhang ’ Insufficient package version (submitted: 0.2.0, existing: 0.2.0) * 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 ‘CAESAR.Suite’ can be installed ... [52s/52s] OK * used C++ compiler: ‘Debian clang version 19.1.7 (1+b1)’ * 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 ... [9s/9s] OK * checking whether the package can be unloaded cleanly ... [9s/9s] OK * checking whether the namespace can be loaded with stated dependencies ... [9s/9s] OK * checking whether the namespace can be unloaded cleanly ... [10s/10s] OK * checking loading without being on the library search path ... [10s/10s] 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 ... [43s/43s] 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 ... [2s/2s] OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK * checking pragmas in C/C++ headers and code ... OK * checking compilation flags used ... OK * checking compiled code ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [42s/41s] OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [156s/149s] ERROR Error(s) in re-building vignettes: ... --- re-building ‘STMOB.Rmd’ using rmarkdown trying URL 'https://github.com/XiaoZhangryy/CAESAR.Suite/blob/master/vignettes_data/MOB_ST.rda?raw=true' Content type 'application/octet-stream' length 5988380 bytes (5.7 MB) ================================================== downloaded 5.7 MB trying URL 'https://github.com/XiaoZhangryy/CAESAR.Suite/blob/master/vignettes_data/MOB_scRNA.rda?raw=true' Content type 'application/octet-stream' length 48066404 bytes (45.8 MB) ================================================== downloaded 45.8 MB Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Calculating gene variances 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Calculating feature variances of standardized and clipped values 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Calculating gene variances 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Calculating feature variances of standardized and clipped values 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Progress: ──────────────────────────────────────── 100% Progress: ───────────────────────────────────────────────────── 100% Progress: ─────────────────────────────────────────────────────────── 100% Progress: ────────────────────────────────────────────────────────────── 100% Progress: ─────────────────────────────────────────────────────────────── 100% Progress: ─────────────────────────────────────────────────────────────── 100% Progress: ──────────────────────────────────────────────────────────────── 100%** Processing: /srv/hornik/tmp/CRAN_pretest/CAESAR.Suite.Rcheck/vign_test/CAESAR.Suite/vignettes/STMOB_files/figure-html/unnamed-chunk-12-1.png 844x576 pixels, 3x8 bits/pixel, RGB Input IDAT size = 126860 bytes Input file size = 127118 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 96729 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 = 96729 Output IDAT size = 96729 bytes (30131 bytes decrease) Output file size = 96807 bytes (30311 bytes = 23.84% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/CAESAR.Suite.Rcheck/vign_test/CAESAR.Suite/vignettes/STMOB_files/figure-html/unnamed-chunk-13-1.png 844x576 pixels, 3x8 bits/pixel, RGB Input IDAT size = 128341 bytes Input file size = 128599 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 97991 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 = 97991 Output IDAT size = 97991 bytes (30350 bytes decrease) Output file size = 98069 bytes (30530 bytes = 23.74% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/CAESAR.Suite.Rcheck/vign_test/CAESAR.Suite/vignettes/STMOB_files/figure-html/unnamed-chunk-14-1.png 844x576 pixels, 3x8 bits/pixel, RGB Input IDAT size = 128341 bytes Input file size = 128599 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 97991 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 = 97991 Output IDAT size = 97991 bytes (30350 bytes decrease) Output file size = 98069 bytes (30530 bytes = 23.74% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/CAESAR.Suite.Rcheck/vign_test/CAESAR.Suite/vignettes/STMOB_files/figure-html/unnamed-chunk-15-1.png 844x576 pixels, 3x8 bits/pixel, RGB Input IDAT size = 92821 bytes Input file size = 93031 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 68226 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 = 68226 Output IDAT size = 68226 bytes (24595 bytes decrease) Output file size = 68304 bytes (24727 bytes = 26.58% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/CAESAR.Suite.Rcheck/vign_test/CAESAR.Suite/vignettes/STMOB_files/figure-html/unnamed-chunk-16-1.png 844x864 pixels, 3x8 bits/pixel, RGB Input IDAT size = 189490 bytes Input file size = 189844 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 170046 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 = 170046 Output IDAT size = 170046 bytes (19444 bytes decrease) Output file size = 170124 bytes (19720 bytes = 10.39% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/CAESAR.Suite.Rcheck/vign_test/CAESAR.Suite/vignettes/STMOB_files/figure-html/unnamed-chunk-19-1.png 844x480 pixels, 3x8 bits/pixel, RGB Input IDAT size = 49756 bytes Input file size = 49906 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 41497 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 = 41497 Output IDAT size = 41497 bytes (8259 bytes decrease) Output file size = 41575 bytes (8331 bytes = 16.69% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/CAESAR.Suite.Rcheck/vign_test/CAESAR.Suite/vignettes/STMOB_files/figure-html/unnamed-chunk-20-1.png 844x576 pixels, 3x8 bits/pixel, RGB Input IDAT size = 63220 bytes Input file size = 63382 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 49156 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 = 49156 Output IDAT size = 49156 bytes (14064 bytes decrease) Output file size = 49234 bytes (14148 bytes = 22.32% decrease) --- finished re-building ‘STMOB.Rmd’ --- re-building ‘XeniumBC.Rmd’ using rmarkdown trying URL 'https://github.com/XiaoZhangryy/CAESAR.Suite/blob/master/vignettes_data/BC_scRNAList.rda?raw=true' Content type 'application/octet-stream' length 2310272 bytes (2.2 MB) ================================================== downloaded 2.2 MB trying URL 'https://github.com/XiaoZhangryy/CAESAR.Suite/blob/master/vignettes_data/BC_XeniumList.rda?raw=true' Content type 'application/octet-stream' length 1256437 bytes (1.2 MB) ================================================== downloaded 1.2 MB trying URL 'https://github.com/XiaoZhangryy/CAESAR.Suite/blob/master/vignettes_data/BC_feature_imgList.rda?raw=true' Content type 'application/octet-stream' length 12559173 bytes (12.0 MB) ================================================== downloaded 12.0 MB Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Progress: ─────────── 100% Progress: ───────────────── 100% Progress: ─────────────────────── 100% Progress: ───────────────────────────────── 100% Progress: ────────────────────────────────────────── 100% Progress: ──────────────────────────────────────────────────── 100% Progress: ──────────────────────────────────────────────────────────── 100% Progress: ────────────────────────────────────────────────────────────── 100% Progress: ─────────────────────────────────────────────────────────────── 100% Progress: ──────────────────────────────────────────────────────────────── 100% Progress: ────────── 100% Progress: ───────────────── 100% Progress: ──────────────────────── 100% Progress: ──────────────────────────────── 100% Progress: ─────────────────────────────────────── 100% Progress: ──────────────────────────────────────────────── 100% Progress: ───────────────────────────────────────────────────────── 100% Progress: ───────────────────────────────────────────────────────────── 100% Progress: ─────────────────────────────────────────────────────────────── 100% Progress: ─────────────────────────────────────────────────────────────── 100% Progress: ──────────────────────────────────────────────────────────────── 100% Progress: ──────────────────────────────────────────────────────────────── 100%** Processing: /srv/hornik/tmp/CRAN_pretest/CAESAR.Suite.Rcheck/vign_test/CAESAR.Suite/vignettes/XeniumBC_files/figure-html/unnamed-chunk-12-1.png 1152x1512 pixels, 3x8 bits/pixel, RGB Input IDAT size = 529798 bytes Input file size = 530644 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 381671 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 = 381671 Output IDAT size = 381671 bytes (148127 bytes decrease) Output file size = 381749 bytes (148895 bytes = 28.06% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/CAESAR.Suite.Rcheck/vign_test/CAESAR.Suite/vignettes/XeniumBC_files/figure-html/unnamed-chunk-13-1.png 1152x1512 pixels, 3x8 bits/pixel, RGB Input IDAT size = 407870 bytes Input file size = 408536 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 290562 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 = 290562 Output IDAT size = 290562 bytes (117308 bytes decrease) Output file size = 290640 bytes (117896 bytes = 28.86% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/CAESAR.Suite.Rcheck/vign_test/CAESAR.Suite/vignettes/XeniumBC_files/figure-html/unnamed-chunk-16-1.png 1152x480 pixels, 3x8 bits/pixel, RGB Input IDAT size = 138203 bytes Input file size = 138473 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 113268 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 = 113268 Output IDAT size = 113268 bytes (24935 bytes decrease) Output file size = 113346 bytes (25127 bytes = 18.15% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/CAESAR.Suite.Rcheck/vign_test/CAESAR.Suite/vignettes/XeniumBC_files/figure-html/unnamed-chunk-17-1.png 1152x1512 pixels, 3x8 bits/pixel, RGB Input IDAT size = 303779 bytes Input file size = 304301 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 230022 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 = 230022 Output IDAT size = 230022 bytes (73757 bytes decrease) Output file size = 230100 bytes (74201 bytes = 24.38% decrease) Progress: 100% Progress: 100% Progress: 100% Progress: ──────────────────────────────────────────────────────────────── 100% Progress: 100% Progress: 100% Progress: ──────────────────────────────────────────────────────────────── 100% Progress: 100% Progress: 100% Progress: ──────────────────────────────────────────────────────────────── 100% Progress: 100% Progress: 100% Progress: 100% Progress: ──────────────────────────────────────────────────────────────── 100% Progress: 100% Progress: 100% Progress: 100% Progress: ──────────────────────────────────────────────────────────────── 100% Progress: 100% Progress: 100% Progress: ──────────────────────────────────────────────────────────────── 100% Progress: 100% Progress: 100% Progress: ──────────────────────────────────────────────────────────────── 100% Progress: 100% Progress: 100% Progress: 100% Progress: ──────────────────────────────────────────────────────────────── 100% Progress: 100% Progress: 100% Progress: ──────────────────────────────────────────────────────────────── 100% Quitting from XeniumBC.Rmd:343-358 [unnamed-chunk-21] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ NULL ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'XeniumBC.Rmd' failed with diagnostics: None of the requested features were found: GOBP_VASCULATURE_DEVELOPMENT in slot data --- failed re-building ‘XeniumBC.Rmd’ SUMMARY: processing the following file failed: ‘XeniumBC.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... [3s/3s] OK * checking HTML version of manual ... [0s/0s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR, 1 WARNING