* using log directory 'd:/RCompile/CRANincoming/R-devel/immunarch.Rcheck' * using R Under development (unstable) (2025-10-08 r88906 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * checking for file 'immunarch/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'immunarch' version '0.10.0' * package encoding: UTF-8 * checking CRAN incoming feasibility ... [18s] NOTE Maintainer: 'Vadim I. Nazarov ' New maintainer: Vadim I. Nazarov Old maintainer(s): Vadim I. Nazarov Possibly misspelled words in DESCRIPTION: AbSeq (15:72) Immunotherapy (3:52) Scanpy (20:11) VDJ (20:92, 21:5) immunogenicity (15:88) tcR (21:67) Found the following (possibly) invalid URLs: URL: http://friedmanlab.weizmann.ac.il/McPAS-TCR/ From: man/dbLoad.Rd Status: Error Message: Could not connect to server [friedmanlab.weizmann.ac.il]: Failed to connect to friedmanlab.weizmann.ac.il port 80 after 2378 ms: Could not connect to server URL: https://immunomind.github.io/docs/tutorials/ From: inst/doc/immunarch.html Status: 404 Message: Not Found URL: https://immunomind.github.io/immunarch/reference (moved to https://immunarch.com/reference/) From: inst/doc/immunarch.html README.md Status: 301 Message: Moved Permanently For content that is 'Moved Permanently', please change http to https, add trailing slashes, or replace the old by the new URL. * 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 hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'immunarch' can be installed ... OK * used C++ compiler: 'g++.exe (GCC) 14.2.0' * checking installed package size ... OK * 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 ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... 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 ... [36s] 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 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 ... [212s] NOTE Examples with CPU (user + system) or elapsed time > 10s user system elapsed inc_overlap 17.06 3.13 7.11 vis.immunr_gene_usage 13.89 0.28 14.19 airr_diversity 11.11 2.97 9.12 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... [17s] WARNING LaTeX errors when creating PDF version. This typically indicates Rd problems. LaTeX errors found: ! LaTeX Error: Unicode character ≥ (U+2265) not set up for use with LaTeX. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ! LaTeX Error: Unicode character ≥ (U+2265) not set up for use with LaTeX. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ! LaTeX Error: Unicode character ≥ (U+2265) not set up for use with LaTeX. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ! LaTeX Error: Unicode character ∈ (U+2208) not set up for use with LaTeX. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ! LaTeX Error: Unicode character ≤ (U+2264) not set up for use with LaTeX. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ! LaTeX Error: Unicode character ∩ (U+2229) not set up for use with LaTeX. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ! LaTeX Error: Unicode character ∪ (U+222A) not set up for use with LaTeX. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. * checking PDF version of manual without index ... ERROR * checking HTML version of manual ... [17s] OK * DONE Status: 1 ERROR, 1 WARNING, 2 NOTEs