* using log directory ‘/srv/hornik/tmp/CRAN_pretest/solareclipser.Rcheck’ * using R Under development (unstable) (2025-04-02 r88102) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 19.1.7 (1+b1) Debian flang-new version 19.1.7 (1+b1) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘solareclipser/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘solareclipser’ version ‘0.3.3’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [4s/124s] NOTE Maintainer: ‘William Burroughs ’ New submission Possibly misspelled words in DESCRIPTION: QTLs (13:58) solareclipser (18:27) Suggests or Enhances not in mainstream repositories: rsnps Package CITATION file contains call(s) to old-style personList() or as.personList(). Please use c() on person objects instead. Package CITATION file contains call(s) to old-style citEntry(). Please use bibentry() instead. Found the following (possibly) invalid URLs: URL: http://bioinformatics.oxfordjournals.org/content/32/12/1901 From: inst/CITATION Status: 403 Message: Forbidden URL: http://cran.r-project.org/web/packages/solareclipser/ From: inst/doc/tutorial.html Status: 404 Message: Not Found CRAN URL not in canonical form URL: http://en.wikipedia.org/wiki/Huntington%27s_disease (moved to https://en.wikipedia.org/wiki/Huntington%27s_disease) From: inst/doc/tutorial.html Status: 301 Message: Moved Permanently URL: http://helix.nih.gov/Documentation/solar-6.6.2-doc/91.appendix_1_text.html From: README.md Status: Error Message: Timeout was reached [helix.nih.gov]: Connection timed out after 60000 milliseconds URL: http://helix.nih.gov/Documentation/solar-6.6.2-doc/91.appendix_1_text.html#mga From: inst/doc/tutorial.html README.md Status: Error Message: Timeout was reached [helix.nih.gov]: Operation timed out after 60000 milliseconds with 0 bytes received URL: http://helix.nih.gov/Documentation/solar-6.6.2-doc/91.appendix_1_text.html#multipoint From: inst/doc/tutorial.html README.md Status: Error Message: Timeout was reached [helix.nih.gov]: Operation timed out after 60000 milliseconds with 0 bytes received URL: http://helix.nih.gov/Documentation/solar-6.6.2-doc/91.appendix_1_text.html#polygenic From: README.md Status: Error Message: Timeout was reached [helix.nih.gov]: Operation timed out after 60000 milliseconds with 0 bytes received URL: http://mga.bionet.nsc.ru/soft/FFBSKAT/ (moved to https://mga.bionet.nsc.ru/soft/FFBSKAT/) From: man/dat50.Rd inst/doc/tutorial.html Status: 301 Message: Moved Permanently URL: http://solar.txbiomedgenetics.org/ From: inst/doc/tutorial.html Status: Error Message: Could not resolve hostname [solar.txbiomedgenetics.org]: Could not resolve host: solar.txbiomedgenetics.org URL: http://solar.txbiomedgenetics.org/doc/05.chapter.html From: man/solarMultipoint.Rd Status: Error Message: Could not resolve hostname [solar.txbiomedgenetics.org]: Could not resolve host: solar.txbiomedgenetics.org URL: http://solar.txbiomedgenetics.org/doc/91.appendix_1_text.html#chromosome From: man/solarMultipoint.Rd Status: Error Message: Timeout was reached [solar.txbiomedgenetics.org]: Operation timed out after 60000 milliseconds with 0 bytes received URL: http://solar.txbiomedgenetics.org/doc/91.appendix_1_text.html#ibd From: man/solarMultipoint.Rd Status: Error Message: Timeout was reached [solar.txbiomedgenetics.org]: Operation timed out after 60000 milliseconds with 0 bytes received URL: http://solar.txbiomedgenetics.org/doc/91.appendix_1_text.html#multipoint From: man/solarMultipoint.Rd Status: Error Message: Timeout was reached [solar.txbiomedgenetics.org]: Operation timed out after 60000 milliseconds with 0 bytes received URL: http://solar.txbiomedgenetics.org/doc/91.appendix_1_text.html#polygenic From: man/solarPolygenic.Rd Status: Error Message: Could not resolve hostname [solar.txbiomedgenetics.org]: Could not resolve host: solar.txbiomedgenetics.org URL: http://solar.txbiomedgenetics.org/solarlinux.html From: inst/doc/tutorial.html Status: Error Message: Timeout was reached [solar.txbiomedgenetics.org]: Resolving timed out after 60000 milliseconds URL: http://solar.txbiomedgenetics.org/solarwindows.html From: inst/doc/tutorial.html Status: Error Message: Timeout was reached [solar.txbiomedgenetics.org]: Operation timed out after 60000 milliseconds with 0 bytes received URL: http://ugcd.github.io/solareclipser/vignettes/tutorial.html#association-model-in-solar From: README.md Status: 404 Message: Not Found URL: http://ugcd.github.io/solareclipser/vignettes/tutorial.html#linkage-model-in-solar From: README.md Status: 404 Message: Not Found URL: http://ugcd.github.io/solareclipser/vignettes/tutorial.html#parallel-computation From: README.md Status: 404 Message: Not Found URL: http://ugcd.github.io/solareclipser/vignettes/tutorial.html#parallel-computation-1 From: README.md Status: 404 Message: Not Found URL: http://ugcd.github.io/solareclipser/vignettes/tutorial.html#polygenic-model-in-solar From: README.md Status: 404 Message: Not Found URL: http://www.biostat.wustl.edu/genetics/geneticssoft/manuals/solar210/08.chapter.html From: man/solarKinship2.Rd Status: 404 Message: Not Found URL: https://github.com/Rdatatable/data.table/blob/master/CRAN_Release.cmd From: inst/doc/tutorial.html Status: 404 Message: Not Found URL: https://github.com/enigma-1590c46634/solareclipser (moved to https://github.com/txbrain-org/solareclipser) From: DESCRIPTION Status: 301 Message: Moved Permanently URL: https://github.com/hadley/ggplot2 (moved to https://github.com/tidyverse/ggplot2) From: inst/doc/tutorial.html Status: 301 Message: Moved Permanently URL: https://github.com/ugcd/solareclipser/blob/master/DESCRIPTION From: inst/doc/tutorial.html Status: 404 Message: Not Found URL: https://solar-eclipse-genetics.org// From: DESCRIPTION Status: 404 Message: Not Found 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. Found the following (possibly) invalid file URIs: URI: ./release/solareclipser_0.3.3.tar.gz From: README.md URI: inst/doc/tutorial.md From: README.md The Date field is over a month old. This build time stamp is over a month old. Size of tarball: 77183241 bytes * checking package namespace information ... OK * checking package dependencies ... INFO Package suggested but not available for checking: ‘rsnps’ * checking if this is a source package ... NOTE Found the following apparent object files/libraries: lib/solar900/lib/libgpu-commands.so Object files/libraries should not be included in a source package. * checking if there is a namespace ... OK * checking for executable files ... WARNING Found the following executable files: inst/lib/solar900/bin/allfreq inst/lib/solar900/bin/genfreq inst/lib/solar900/bin/getmeans inst/lib/solar900/bin/homo inst/lib/solar900/bin/ibdmat inst/lib/solar900/bin/ibdmc inst/lib/solar900/bin/ibdprep inst/lib/solar900/bin/makeped inst/lib/solar900/bin/mlink inst/lib/solar900/bin/mrgibd inst/lib/solar900/bin/multipnt inst/lib/solar900/bin/relate inst/lib/solar900/bin/rlwrap inst/lib/solar900/bin/solarmain inst/lib/solar900/bin/unknown lib/solar900/bin/allfreq lib/solar900/bin/genfreq lib/solar900/bin/getmeans lib/solar900/bin/homo lib/solar900/bin/ibdmat lib/solar900/bin/ibdmc lib/solar900/bin/ibdprep lib/solar900/bin/makeped lib/solar900/bin/mlink lib/solar900/bin/mrgibd lib/solar900/bin/multipnt lib/solar900/bin/relate lib/solar900/bin/rlwrap lib/solar900/bin/solarmain lib/solar900/bin/unknown Source packages should not contain undeclared executable files. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking serialization versions ... OK * checking whether package ‘solareclipser’ can be installed ... [4s/4s] OK * checking package directory ... OK * checking for future file timestamps ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... NOTE Non-standard files/directories found at top level: ‘LICENSE.md’ ‘README.Rmd’ ‘TODO.md’ ‘docs’ ‘justfile’ ‘lib’ ‘misc’ ‘scratch.md’ * 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 ... [1s/1s] OK * checking whether the package can be loaded with stated dependencies ... [1s/1s] OK * checking whether the package can be unloaded cleanly ... [1s/1s] OK * checking whether the namespace can be loaded with stated dependencies ... [1s/1s] WARNING Warning: S4 exports specified in 'NAMESPACE' but not defined in package ‘solareclipser’ * checking whether the namespace can be unloaded cleanly ... [1s/1s] OK * checking loading without being on the library search path ... [1s/1s] 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 ... [8s/8s] NOTE extractVarCompFrame: no visible global function definition for ‘pchisq’ extractVarCompFrame: no visible binding for global variable ‘Z’ Undefined global functions or variables: Z pchisq Consider adding importFrom("stats", "pchisq") to your NAMESPACE file. Found if() conditions comparing class() to string: File ‘solareclipser/R/assoc.lib.R’: if (class(tab) == "try-error") ... File ‘solareclipser/R/plot.lib.R’: if (class(SEX) == "character" & all(c("1", "2") %in% SEX)) ... File ‘solareclipser/R/solarMultipoint.R’: if (class(num.passes) == "integer") ... Use inherits() (or maybe is()) instead. * checking Rd files ... [0s/0s] OK * checking Rd metadata ... NOTE Invalid package aliases in Rd file 'solareclipserPackage.Rd': ‘-package’ * 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 ... WARNING Documented arguments not in \usage in Rd file 'annotateSNPs.Rd': ‘...’ Undocumented arguments in Rd file 'plotPed.Rd' ‘affected’ Undocumented arguments in Rd file 'readPhen.Rd' ‘na.strings’ Documented arguments not in \usage in Rd file 'solarAssocClass.Rd': ‘object’ ‘y’ ‘alpha’ Documented arguments not in \usage in Rd file 'solarBaeysAvgPolygenicClass.Rd': ‘object’ Undocumented arguments in Rd file 'solarKinship2.Rd' ‘coef’ Documented arguments not in \usage in Rd file 'solarMultipointClass.Rd': ‘object’ ‘pass’ ‘LOD.thr’ ‘plot.null’ Documented arguments not in \usage in Rd file 'solarPolygenicClass.Rd': ‘object’ ‘trait’ Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... [0s/0s] OK * checking data for ASCII and uncompressed saves ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [4s/4s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [1s/1s] ERROR Running ‘testthat.R’ [1s/1s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > library(solareclipser) > > test_check("solareclipser") sh: 1: solar: not found Error in system("solar", input = cmd, intern = result, ignore.stdout = ignore.stdout, : error in running command sh: 1: solar: not found Error in system("solar", input = cmd, intern = result, ignore.stdout = ignore.stdout, : error in running command sh: 1: solar: not found Error in system("solar", input = cmd, intern = result, ignore.stdout = ignore.stdout, : error in running command [ FAIL 3 | WARN 0 | SKIP 0 | PASS 0 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-solarPar.R:5:3'): kurtosis ───────────────────────────────────── Error in `df2solar(data, dir)`: file.exists(file.path(dir, "phi2.gz")) is not TRUE Backtrace: ▆ 1. └─solareclipser::solarPolygenic(trait1 ~ 1, dat30) at test-solarPar.R:5:3 2. └─solareclipser::df2solar(data, dir) 3. └─base::stopifnot(file.exists(file.path(dir, "phi2.gz"))) ── Error ('test-solarPar.R:14:3'): covlist pvalue ────────────────────────────── Error in `df2solar(data, dir)`: file.exists(file.path(dir, "phi2.gz")) is not TRUE Backtrace: ▆ 1. └─solareclipser::solarPolygenic(trait1 ~ sex, dat30) at test-solarPar.R:14:3 2. └─solareclipser::df2solar(data, dir) 3. └─base::stopifnot(file.exists(file.path(dir, "phi2.gz"))) ── Error ('test-solarPar.R:38:3'): function explainedVarProp ─────────────────── Error in `df2solar(data, dir)`: file.exists(file.path(dir, "phi2.gz")) is not TRUE Backtrace: ▆ 1. └─solareclipser::solarPolygenic(trait1 ~ 1, dat30) at test-solarPar.R:38:3 2. └─solareclipser::df2solar(data, dir) 3. └─base::stopifnot(file.exists(file.path(dir, "phi2.gz"))) [ FAIL 3 | WARN 0 | SKIP 0 | PASS 0 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [1s/1s] ERROR Error(s) in re-building vignettes: ... --- re-building ‘tutorial.Rmd’ using rmarkdown sh: 1: solar: not found Quitting from tutorial.Rmd:648-671 [minimal] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `df2solar()`: ! file.exists(file.path(dir, "phi2.gz")) is not TRUE --- Backtrace: ▆ 1. └─solareclipser::solarPolygenic(trait1 ~ 1, dat30) 2. └─solareclipser::df2solar(data, dir) 3. └─base::stopifnot(file.exists(file.path(dir, "phi2.gz"))) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'tutorial.Rmd' failed with diagnostics: file.exists(file.path(dir, "phi2.gz")) is not TRUE --- failed re-building ‘tutorial.Rmd’ SUMMARY: processing the following file failed: ‘tutorial.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... [4s/4s] OK * checking HTML version of manual ... [1s/1s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 2 ERRORs, 3 WARNINGs, 5 NOTEs