* using log directory ‘/data/gannet/ripley/R/packages/tests-devel/CAESAR.Suite.Rcheck’ * 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 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-gcc/CAESAR.Suite-00install.html' 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 ... -> .local -> do.call -> -> 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