* using log directory ‘/srv/hornik/tmp/CRAN_pretest/CAESAR.Suite.Rcheck’ * using R Under development (unstable) (2024-09-05 r87100) * 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.Suite/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘CAESAR.Suite’ version ‘0.1.0’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [3s/4s] NOTE Maintainer: ‘Xiao Zhang ’ New submission Possibly misspelled words in DESCRIPTION: Omics (4:17) omics (14:30, 14:174, 14:644) scRNA (14:324, 14:588) Found the following (possibly) invalid URLs: URL: https://XiaoZhangryy.github.io/CAESAR/index.html From: README.md Status: 404 Message: Not Found Size of tarball: 7449892 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.Suite’ can be installed ... [60s/60s] 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 ... 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 ... [42s/42s] OK * checking Rd files ... [0s/0s] NOTE checkRd: (-1) toydata.Rd:12: Lost braces in \itemize; meant \describe ? checkRd: (-1) toydata.Rd:13: Lost braces in \itemize; meant \describe ? checkRd: (-1) toydata.Rd:14: Lost braces in \itemize; meant \describe ? checkRd: (-1) toydata.Rd:15: Lost braces in \itemize; meant \describe ? checkRd: (-1) toydata.Rd:16: 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 ... [83s/82s] NOTE Examples with CPU (user + system) or elapsed time > 5s user system elapsed CAESAR.coembedding.image 11.369 0.096 11.472 CoUMAP.plot 7.153 0.238 7.361 CAESAR.CTDEP 5.725 1.635 6.646 CoUMAP 6.826 0.199 6.995 CAESAR.coembedding 5.417 0.055 5.477 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [193s/161s] OK * 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: 3 NOTEs