• using R Under development (unstable) (2025-02-21 r87787)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)     GNU Fortran (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
• running under: Fedora Linux 40 (Workstation Edition)
• using session charset: UTF-8
• using option ‘--no-stop-on-test-error’
• checking for file ‘CAESAR.Suite/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘CAESAR.Suite’ version ‘0.1.0’
• 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 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 ... [196s/184s] OK See the install log for details.
• used C++ compiler: ‘g++ (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)’
• 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 ... [33s/40s] OK
• checking whether the package can be loaded with stated dependencies ... [31s/38s] OK
• checking whether the package can be unloaded cleanly ... [31s/37s] OK
• checking whether the namespace can be loaded with stated dependencies ... [32s/38s] OK
• checking whether the namespace can be unloaded cleanly ... [33s/41s] OK
• checking loading without being on the library search path ... [33s/40s] 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 ... [104s/112s] OK
• checking Rd files ... 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 ... 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 $(LAPACK_LIBS) ... OK
• checking use of PKG_*FLAGS in Makefiles ... OK
• checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
• checking pragmas in C/C++ headers and code ... OK
• checking compilation flags used ... OK
• checking compiled code ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [32s/32s] ERROR Running examples in ‘CAESAR.Suite-Ex.R’ failed The error most likely occurred in: > ### Name: CoUMAP > ### Title: Co-embedding UMAP for Genes and Cells in a Seurat Object > ### Aliases: CoUMAP > > ### ** Examples > > data(toydata) > > seu <- toydata$seu > > seu <- CoUMAP(seu, gene.set = rownames(seu)) Error in min(nrow(X), na.rm = col(X)) :   'length = 40100' in coercion to 'logical(1)' Calls: CoUMAP ... <Anonymous> -> .local -> do.call -> <Anonymous> -> uwot Execution halted
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [246s/206s] 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%  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: /data/gannet/ripley/R/packages/tests-devel/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 = 126368 bytes Input file size = 126626 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 92863   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 = 92863 Output IDAT size = 92863 bytes (33505 bytes decrease) Output file size = 92941 bytes (33685 bytes = 26.60% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-devel/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 = 127839 bytes Input file size = 128097 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 93814   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 = 93814 Output IDAT size = 93814 bytes (34025 bytes decrease) Output file size = 93892 bytes (34205 bytes = 26.70% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-devel/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 = 127839 bytes Input file size = 128097 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 93814   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 = 93814 Output IDAT size = 93814 bytes (34025 bytes decrease) Output file size = 93892 bytes (34205 bytes = 26.70% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-devel/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 = 91989 bytes Input file size = 92199 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 66560   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 = 66560 Output IDAT size = 66560 bytes (25429 bytes decrease) Output file size = 66638 bytes (25561 bytes = 27.72% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-devel/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 = 188968 bytes Input file size = 189322 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 168348   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 = 168348 Output IDAT size = 168348 bytes (20620 bytes decrease) Output file size = 168426 bytes (20896 bytes = 11.04% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-devel/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 = 49375 bytes Input file size = 49525 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 38960   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 = 38960 Output IDAT size = 38960 bytes (10415 bytes decrease) Output file size = 39038 bytes (10487 bytes = 21.18% decrease) Quitting from lines 267-282 [unnamed-chunk-20] (STMOB.Rmd) Error: processing vignette 'STMOB.Rmd' failed with diagnostics: 'length = 14600' in coercion to 'logical(1)' --- failed 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%  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%** Processing: /data/gannet/ripley/R/packages/tests-devel/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 = 527131 bytes Input file size = 527977 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 365220   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 = 365220 Output IDAT size = 365220 bytes (161911 bytes decrease) Output file size = 365298 bytes (162679 bytes = 30.81% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-devel/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 = 404815 bytes Input file size = 405481 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 284971   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 = 284971 Output IDAT size = 284971 bytes (119844 bytes decrease) Output file size = 285049 bytes (120432 bytes = 29.70% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-devel/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 = 137347 bytes Input file size = 137617 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 109537   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 = 109537 Output IDAT size = 109537 bytes (27810 bytes decrease) Output file size = 109615 bytes (28002 bytes = 20.35% decrease) Quitting from lines 287-306 [unnamed-chunk-17] (XeniumBC.Rmd) Error: processing vignette 'XeniumBC.Rmd' failed with diagnostics: 'length = 151350' in coercion to 'logical(1)' --- failed re-building ‘XeniumBC.Rmd’ SUMMARY: processing the following files failed:   ‘STMOB.Rmd’ ‘XeniumBC.Rmd’ Error: Vignette re-building failed. Execution halted
• checking PDF version of manual ... OK
• checking HTML version of manual ... OK
• checking for non-standard things in the check directory ... OK
• checking for detritus in the temp directory ... OK
• DONE

Status: 2 ERRORs