* using log directory ‘/srv/hornik/tmp/CRAN_pretest/smartsnp.Rcheck’ * using R Under development (unstable) (2025-06-08 r88288) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 19.1.7 (3) Debian flang-new version 19.1.7 (3) * running under: Debian GNU/Linux 13 (trixie) * using session charset: UTF-8 * checking for file ‘smartsnp/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘smartsnp’ version ‘1.2.0’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [5s/8s] NOTE Maintainer: ‘Christian Huber ’ Found the following (possibly) invalid URLs: URL: https://cran.r-project.org/web/packages/data.table/vignettes/datatable-intro.html From: inst/doc/aDNA_smartpca_analysis.html Status: 200 Message: OK CRAN URL not in canonical form URL: https://cran.r-project.org/web/packages/ggrepel/vignettes/ggrepel.html From: inst/doc/aDNA_smartpca_analysis.html Status: 200 Message: OK CRAN URL not in canonical form URL: https://datadryad.org/stash/dataset/doi:10.5061/dryad.1bq39 (moved to https://datadryad.org/dataset/doi:10.5061/dryad.1bq39) From: inst/doc/mallard_smartpca_analysis.html Status: 301 Message: Moved Permanently URL: https://reich.hms.harvard.edu/datasets From: inst/doc/aDNA_smartpca_analysis.html Status: Error Message: SSL peer certificate or SSH remote key was not OK [reich.hms.harvard.edu]: server verification failed: certificate has expired. (CAfile: /etc/ssl/certs/ca-certificates.crt CRLfile: none) URL: https://reich.hms.harvard.edu/software From: man/smart_mva.Rd man/smart_pca.Rd man/smart_permanova.Rd man/smart_permdisp.Rd Status: Error Message: SSL peer certificate or SSH remote key was not OK [reich.hms.harvard.edu]: server verification failed: certificate has expired. (CAfile: /etc/ssl/certs/ca-certificates.crt CRLfile: none) URL: https://stats.stackexchange.com/questions/88880/does-the-sign-of-scores-or-of-loadings-in-pca-or-fa-have-a-meaning-may-i-revers From: inst/doc/aDNA_smartpca_analysis.html Status: 403 Message: Forbidden The canonical URL of the CRAN page for a package is https://CRAN.R-project.org/package=pkgname 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 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 ‘smartsnp’ can be installed ... [10s/10s] OK * used C++ compiler: ‘Debian clang version 19.1.7 (3)’ * 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 ... [0s/0s] OK * checking whether the package can be loaded with stated dependencies ... [0s/0s] OK * checking whether the package can be unloaded cleanly ... [0s/0s] OK * checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK * checking whether the namespace can be unloaded cleanly ... [0s/0s] OK * checking loading without being on the library search path ... [0s/0s] 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 ... [4s/4s] OK * checking Rd files ... [0s/0s] NOTE checkRd: (-1) read_packedancestrymap.Rd:15: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) smart_mva.Rd:7-11: Lost braces 7 | \item{snp_data}{snp_data}{File name read from working directory. | ^ checkRd: (-1) smart_mva.Rd:100-101: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) smart_mva.Rd:102-103: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) smart_mva.Rd:104-105: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) smart_mva.Rd:106-109: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) smart_mva.Rd:110: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) smart_mva.Rd:111: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) smart_mva.Rd:112: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) smart_mva.Rd:113-114: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) smart_mva.Rd:115: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) smart_mva.Rd:116: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) smart_mva.Rd:117: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) smart_mva.Rd:118: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) smart_mva.Rd:119: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) smart_pca.Rd:62: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) smart_pca.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) smart_pca.Rd:64-67: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) smart_permanova.Rd:71-73: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) smart_permanova.Rd:74: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) smart_permanova.Rd:75-76: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) smart_permanova.Rd:77: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) smart_permanova.Rd:78: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) smart_permanova.Rd:79: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) smart_permdisp.Rd:79-82: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) smart_permdisp.Rd:83: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) smart_permdisp.Rd:84: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) smart_permdisp.Rd:85: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) smart_permdisp.Rd:86-87: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) smart_permdisp.Rd:88: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) smart_permdisp.Rd:89: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) smart_permdisp.Rd:90: Lost braces in \itemize; \value handles \item{}{} directly * 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 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 ... [8s/8s] OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [2s/2s] 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: 2 NOTEs