* using log directory ‘/srv/hornik/tmp/CRAN_pretest/CAESAR.Rcheck’ * using R Under development (unstable) (2024-09-01 r87083) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 18.1.8 (9) Debian flang-new version 18.1.8 (9) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘CAESAR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘CAESAR’ version ‘0.1.0’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [3s/3s] ERROR Maintainer: ‘Xiao Zhang ’ New submission Conflicting package names (submitted: CAESAR, existing: caesar [file:///data/Repositories/CRAN]) Conflicting package names (submitted: CAESAR, existing: caesar [CRAN archive]) Possibly misspelled words in DESCRIPTION: omics (4:17, 14:30, 14:174, 14:644) scRNA (14:324, 14:588) The Title field starts with the package name. The Title field should be in title case. Current version is: ‘CAESAR: a cross-technology and cross-resolution framework for spatial omics annotation’ In title case that is: ‘CAESAR: a Cross-Technology and Cross-Resolution Framework for Spatial Omics Annotation’ Size of tarball: 7447462 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 ‘CAESAR’ can be installed ... [59s/59s] OK * used C++ compiler: ‘Debian clang version 18.1.8 (9)’ * checking package directory ... OK * checking for future file timestamps ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Author field differs from that derived from Authors@R Author: ‘Xiao Zhang [aut,cre], Wei Liu [aut], Jin Liu [aut]’ Authors@R: ‘Xiao Zhang [aut, cre], Wei Liu [aut], Jin Liu [aut]’ * 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 ... [42s/42s] OK * checking Rd files ... [0s/0s] NOTE checkRd: (-1) toydata.Rd:17: Lost braces in \itemize; meant \describe ? checkRd: (-1) toydata.Rd:18: Lost braces in \itemize; meant \describe ? checkRd: (-1) toydata.Rd:19: Lost braces in \itemize; meant \describe ? checkRd: (-1) toydata.Rd:20: Lost braces in \itemize; meant \describe ? checkRd: (-1) toydata.Rd:21: Lost braces in \itemize; meant \describe ? * 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 ... [81s/80s] NOTE Examples with CPU (user + system) or elapsed time > 5s user system elapsed CAESAR.coembedding.image 11.403 0.067 11.476 CAESAR.CTDEP 5.897 1.528 6.667 CoUMAP.plot 7.018 0.145 7.133 CoUMAP 6.678 0.003 6.648 CAESAR.coembedding 5.309 0.076 5.390 CAESAR.enrich.score 4.698 0.380 5.082 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [139s/125s] ERROR Error(s) in re-building vignettes: ... --- re-building ‘STMOB.Rmd’ using rmarkdown trying URL 'https://github.com/XiaoZhangryy/CAESAR/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/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%** Processing: /srv/hornik/tmp/CRAN_pretest/CAESAR.Rcheck/vign_test/CAESAR/vignettes/STMOB_files/figure-html/unnamed-chunk-12-1.png 844x576 pixels, 3x8 bits/pixel, RGB Input IDAT size = 123304 bytes Input file size = 123562 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 91873 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 = 91873 Output IDAT size = 91873 bytes (31431 bytes decrease) Output file size = 91951 bytes (31611 bytes = 25.58% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/CAESAR.Rcheck/vign_test/CAESAR/vignettes/STMOB_files/figure-html/unnamed-chunk-13-1.png 844x576 pixels, 3x8 bits/pixel, RGB Input IDAT size = 124639 bytes Input file size = 124897 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 92944 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 = 92944 Output IDAT size = 92944 bytes (31695 bytes decrease) Output file size = 93022 bytes (31875 bytes = 25.52% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/CAESAR.Rcheck/vign_test/CAESAR/vignettes/STMOB_files/figure-html/unnamed-chunk-14-1.png 844x576 pixels, 3x8 bits/pixel, RGB Input IDAT size = 124639 bytes Input file size = 124897 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 92944 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 = 92944 Output IDAT size = 92944 bytes (31695 bytes decrease) Output file size = 93022 bytes (31875 bytes = 25.52% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/CAESAR.Rcheck/vign_test/CAESAR/vignettes/STMOB_files/figure-html/unnamed-chunk-15-1.png 844x576 pixels, 3x8 bits/pixel, RGB Input IDAT size = 90408 bytes Input file size = 90618 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 66024 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 = 66024 Output IDAT size = 66024 bytes (24384 bytes decrease) Output file size = 66102 bytes (24516 bytes = 27.05% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/CAESAR.Rcheck/vign_test/CAESAR/vignettes/STMOB_files/figure-html/unnamed-chunk-16-1.png 844x864 pixels, 3x8 bits/pixel, RGB Input IDAT size = 191126 bytes Input file size = 191480 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 167122 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 = 167122 Output IDAT size = 167122 bytes (24004 bytes decrease) Output file size = 167200 bytes (24280 bytes = 12.68% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/CAESAR.Rcheck/vign_test/CAESAR/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.Rcheck/vign_test/CAESAR/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/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/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/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.Rcheck/vign_test/CAESAR/vignettes/XeniumBC_files/figure-html/unnamed-chunk-12-1.png 1152x1512 pixels, 3x8 bits/pixel, RGB Input IDAT size = 496499 bytes Input file size = 497297 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 351214 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 = 351214 Output IDAT size = 351214 bytes (145285 bytes decrease) Output file size = 351292 bytes (146005 bytes = 29.36% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/CAESAR.Rcheck/vign_test/CAESAR/vignettes/XeniumBC_files/figure-html/unnamed-chunk-13-1.png 1152x1512 pixels, 3x8 bits/pixel, RGB Input IDAT size = 385496 bytes Input file size = 386138 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 270057 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 = 270057 Output IDAT size = 270057 bytes (115439 bytes decrease) Output file size = 270135 bytes (116003 bytes = 30.04% decrease) Quitting from lines 245-262 [unnamed-chunk-15] (XeniumBC.Rmd) Error: processing vignette 'XeniumBC.Rmd' failed with diagnostics: could not find function "%>%" --- 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: 2 ERRORs, 3 NOTEs