* using log directory ‘/srv/hornik/tmp/CRAN_pretest/solareclipser.Rcheck’
* using R Under development (unstable) (2025-06-23 r88348)
* 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 ‘solareclipser/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘solareclipser’ version ‘1.0.0’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [4s/5s] NOTE
Maintainer: ‘William Burroughs <wilbura009@gmail.com>’

New submission

Possibly misspelled words in DESCRIPTION:
  QTLs (13:58)
  solareclipser (18:27)

Found the following (possibly) invalid URLs:
  URL: https://github.com/enigma-1590c46634/solareclipser (moved to https://github.com/txbrain-org/solareclipser)
    From: DESCRIPTION
    Status: 301
    Message: Moved Permanently
  URL: https://solar-eclipse-genetics.org//
    From: DESCRIPTION
    Status: 404
    Message: Not Found
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 URI:
  URI: doc/solareclipser.pdf
    From: README.md

The Date field is over a month old.
* 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 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’
* 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 whether startup messages can be suppressed ... [0s/0s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... WARNING
'library' or 'require' call not declared from: ‘stringr’
'library' or 'require' call to ‘stringr’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [2s/2s] NOTE
File ‘solareclipser/R/zzz.R’:
  .onLoad calls:
    library(stringr, quietly = TRUE)

Package startup functions should not change the search path.
See section ‘Good practice’ in '?.onAttach'.
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... WARNING
Missing link(s) in Rd file 'Covariate.Rd':
  ‘,3...’ ‘trait’

Missing link(s) in Rd file 'Load.Rd':
  ‘-sample | -allow’ ‘-nosave’ ‘-xlinked’ ‘-haldane | -kosambi’

Missing link(s) in Rd file 'Polygenic.Rd':
  ‘-screen’ ‘-all’ ‘-testrhoe’ ‘-testrhog’ ‘-testrhoc’ ‘-sporadic’
  ‘-keephouse’ ‘-testrhop’ ‘-rhopse’ ‘-fphi’

See section 'Cross-references' in the 'Writing R Extensions' manual.

Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Covariate.Rd: ,3..., trait
  Load.Rd: -sample | -allow, -nosave, -xlinked, -haldane | -kosambi
  Polygenic.Rd: -screen, -all, -testrhoe, -testrhog, -testrhoc,
    -sporadic, -keephouse, -testrhop, -rhopse, -fphi
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in Rd file 'testbench_init.Rd'
  ‘tmp’

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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [0s/0s] OK
* checking for unstated dependencies in vignettes ... NOTE
'::' or ':::' import not declared from: ‘rprojroot’
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [1s/1s] ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘solareclipser.Rmd’ using rmarkdown

Quitting from solareclipser.Rmd:14-20 [unnamed-chunk-1]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! No root directory found in /srv/hornik/tmp/CRAN_pretest/solareclipser.Rcheck/vign_test/solareclipser/vignettes or its parent directories. Root criterion: contains a file matching "[.]Rproj$" with contents matching "^Version: " in the first line
---
Backtrace:
    ▆
 1. ├─knitr::opts_knit$set(root.dir = rprojroot::find_rstudio_root_file())
 2. │ ├─knitr (local) set2(resolve(...))
 3. │ │ └─knitr (local) get(names(values), drop = FALSE)
 4. │ │   └─stats::setNames(defaults[name], name)
 5. │ └─knitr (local) resolve(...)
 6. └─rprojroot::find_rstudio_root_file()
 7.   └─rprojroot::find_root_file(..., criterion = criterion, path = path)
 8.     └─rprojroot::find_root(criterion = criterion, path = path)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'solareclipser.Rmd' failed with diagnostics:
No root directory found in /srv/hornik/tmp/CRAN_pretest/solareclipser.Rcheck/vign_test/solareclipser/vignettes or its parent directories. Root criterion: contains a file matching "[.]Rproj$" with contents matching "^Version: " in the first line
--- failed re-building ‘solareclipser.Rmd’

SUMMARY: processing the following file failed:
  ‘solareclipser.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... [3s/3s] OK
* checking HTML version of manual ... [1s/1s] NOTE
Found the following HTML validation problems:
Covariate.html:32:11 (Covariate.Rd:13): Error: <variable> is not recognized!
Covariate.html:32:11 (Covariate.Rd:13): Warning: discarding unexpected <variable>
Covariate.html:32:42 (Covariate.Rd:13): Error: <variable> is not recognized!
Covariate.html:32:42 (Covariate.Rd:13): Warning: discarding unexpected <variable>
Covariate.html:32:56 (Covariate.Rd:13): Error: <variable> is not recognized!
Covariate.html:32:56 (Covariate.Rd:13): Warning: discarding unexpected <variable>
Covariate.html:37:18 (Covariate.Rd:18): Error: <string> is not recognized!
Covariate.html:37:18 (Covariate.Rd:18): Warning: discarding unexpected <string>
Covariate.html:40:11 (Covariate.Rd:21): Error: <variable> is not recognized!
Covariate.html:40:11 (Covariate.Rd:21): Warning: discarding unexpected <variable>
CreateEvdData.html:36:14 (CreateEvdData.Rd:17): Error: <plink> is not recognized!
CreateEvdData.html:36:14 (CreateEvdData.Rd:17): Warning: discarding unexpected <plink>
CreateEvdData.html:35:26 (CreateEvdData.Rd:16): Warning: missing </output> before </p>
CreateEvdData.html:38:1 (CreateEvdData.Rd:19): Warning: inserting implicit <output>
CreateEvdData.html:38:1 (CreateEvdData.Rd:19): Warning: missing </output> before <p>
CreateEvdData.html:38:4 (CreateEvdData.Rd:19): Warning: inserting implicit <output>
CreateEvdData.html:45:1 (CreateEvdData.Rd:26): Warning: inserting implicit <output>
CreateEvdData.html:45:1 (CreateEvdData.Rd:26): Warning: missing </output> before <p>
CreateEvdData.html:45:4 (CreateEvdData.Rd:26): Warning: inserting implicit <output>
CreateEvdData.html:50:1 (CreateEvdData.Rd:31): Warning: missing </output> before </p>
CreateEvdData.html:49:1 (CreateEvdData.Rd:30): Warning: missing </output> before </p>
CreateEvdData.html:48:1 (CreateEvdData.Rd:29): Warning: missing </output> before </p>
CreateEvdData.html:47:1 (CreateEvdData.Rd:28): Warning: missing </output> before </p>
CreateEvdData.html:54:1 (CreateEvdData.Rd:33): Warning: inserting implicit <output>
CreateEvdData.html:54:1 (CreateEvdData.Rd:33): Warning: missing </output> before <h3>
CreateEvdData.html:54:5 (CreateEvdData.Rd:33): Warning: inserting implicit <output>
CreateEvdData.html:58:5 (CreateEvdData.Rd:34): Warning: inserting implicit <output>
CreateEvdData.html:62:5 (CreateEvdData.Rd:36): Warning: inserting implicit <output>
CreateEvdData.html:62:5 (CreateEvdData.Rd:36): Warning: missing </output> before <p>
CreateEvdData.html:62:9 (CreateEvdData.Rd:36): Warning: inserting implicit <output>
CreateEvdData.html:64:1 (CreateEvdData.Rd:37): Warning: inserting implicit <output>
CreateEvdData.html:65:5 (CreateEvdData.Rd:37): Warning: inserting implicit <output>
CreateEvdData.html:65:5 (CreateEvdData.Rd:37): Warning: missing </output> before <p>
CreateEvdData.html:65:9 (CreateEvdData.Rd:37): Warning: inserting implicit <output>
CreateEvdData.html:67:1 (CreateEvdData.Rd:38): Warning: inserting implicit <output>
CreateEvdData.html:68:5 (CreateEvdData.Rd:38): Warning: inserting implicit <output>
CreateEvdData.html:68:5 (CreateEvdData.Rd:38): Warning: missing </output> before <p>
CreateEvdData.html:68:9 (CreateEvdData.Rd:38): Warning: inserting implicit <output>
CreateEvdData.html:70:1 (CreateEvdData.Rd:39): Warning: inserting implicit <output>
CreateEvdData.html:71:5 (CreateEvdData.Rd:39): Warning: inserting implicit <output>
CreateEvdData.html:71:5 (CreateEvdData.Rd:39): Warning: missing </output> before <p>
CreateEvdData.html:71:9 (CreateEvdData.Rd:39): Warning: inserting implicit <output>
CreateEvdData.html:73:1 (CreateEvdData.Rd:40): Warning: inserting implicit <output>
CreateEvdData.html:74:5 (CreateEvdData.Rd:40): Warning: inserting implicit <output>
CreateEvdData.html:74:5 (CreateEvdData.Rd:40): Warning: missing </output> before <p>
CreateEvdData.html:74:9 (CreateEvdData.Rd:40): Warning: inserting implicit <output>
CreateEvdData.html:76:1 (CreateEvdData.Rd:41): Warning: inserting implicit <output>
CreateEvdData.html:77:5 (CreateEvdData.Rd:41): Warning: inserting implicit <output>
CreateEvdData.html:77:5 (CreateEvdData.Rd:41): Warning: missing </output> before <p>
CreateEvdData.html:77:9 (CreateEvdData.Rd:41): Warning: inserting implicit <output>
CreateEvdData.html:79:1 (CreateEvdData.Rd:42): Warning: inserting implicit <output>
CreateEvdData.html:80:5 (CreateEvdData.Rd:42): Warning: inserting implicit <output>
CreateEvdData.html:80:5 (CreateEvdData.Rd:42): Warning: missing </output> before <p>
CreateEvdData.html:80:9 (CreateEvdData.Rd:42): Warning: inserting implicit <output>
CreateEvdData.html:82:1 (CreateEvdData.Rd:42): Warning: inserting implicit <output>
CreateEvdData.html:86:1 (CreateEvdData.Rd:46): Warning: inserting implicit <output>
CreateEvdData.html:86:1 (CreateEvdData.Rd:46): Warning: missing </output> before <h4>
CreateEvdData.html:90:5 (CreateEvdData.Rd:48): Warning: inserting implicit <output>
CreateEvdData.html:94:5 (CreateEvdData.Rd:49): Warning: inserting implicit <output>
CreateEvdData.html:96:16 (CreateEvdData.Rd:50): Warning: inserting implicit <output>
CreateEvdData.html:96:16 (CreateEvdData.Rd:50): Warning: missing </output> before <pre>
CreateEvdData.html:104:1 (CreateEvdData.Rd:59): Warning: inserting implicit <output>
CreateEvdData.html:104:1 (CreateEvdData.Rd:59): Warning: missing </output> before <h4>
CreateEvdData.html:108:5 (CreateEvdData.Rd:61): Warning: inserting implicit <output>
CreateEvdData.html:112:5 (CreateEvdData.Rd:62): Warning: inserting implicit <output>
CreateEvdData.html:114:16 (CreateEvdData.Rd:63): Warning: inserting implicit <output>
CreateEvdData.html:114:16 (CreateEvdData.Rd:63): Warning: missing </output> before <pre>
CreateEvdData.html:118:1 (CreateEvdData.Rd:68): Warning: inserting implicit <output>
CreateEvdData.html:118:1 (CreateEvdData.Rd:68): Warning: missing </output> before <h4>
CreateEvdData.html:122:5 (CreateEvdData.Rd:70): Warning: inserting implicit <output>
CreateEvdData.html:126:5 (CreateEvdData.Rd:71): Warning: inserting implicit <output>
CreateEvdData.html:128:16 (CreateEvdData.Rd:72): Warning: inserting implicit <output>
CreateEvdData.html:128:16 (CreateEvdData.Rd:72): Warning: missing </output> before <pre>
CreateEvdData.html:132:1 (CreateEvdData.Rd:77): Warning: inserting implicit <output>
CreateEvdData.html:132:1 (CreateEvdData.Rd:77): Warning: missing </output> before <h4>
CreateEvdData.html:136:5 (CreateEvdData.Rd:79): Warning: inserting implicit <output>
CreateEvdData.html:140:5 (CreateEvdData.Rd:80): Warning: inserting implicit <output>
CreateEvdData.html:142:16 (CreateEvdData.Rd:81): Warning: inserting implicit <output>
CreateEvdData.html:142:16 (CreateEvdData.Rd:81): Warning: missing </output> before <pre>
CreateEvdData.html:146:1 (CreateEvdData.Rd:86): Warning: inserting implicit <output>
CreateEvdData.html:146:1 (CreateEvdData.Rd:86): Warning: missing </output> before <h4>
CreateEvdData.html:150:5 (CreateEvdData.Rd:88): Warning: inserting implicit <output>
CreateEvdData.html:154:5 (CreateEvdData.Rd:89): Warning: inserting implicit <output>
CreateEvdData.html:156:16 (CreateEvdData.Rd:90): Warning: inserting implicit <output>
CreateEvdData.html:156:16 (CreateEvdData.Rd:90): Warning: missing </output> before <pre>
CreateEvdData.html:160:1 (CreateEvdData.Rd:95): Warning: inserting implicit <output>
CreateEvdData.html:160:1 (CreateEvdData.Rd:95): Warning: missing </output> before <h4>
CreateEvdData.html:164:5 (CreateEvdData.Rd:97): Warning: inserting implicit <output>
CreateEvdData.html:168:5 (CreateEvdData.Rd:98): Warning: inserting implicit <output>
CreateEvdData.html:170:16 (CreateEvdData.Rd:99): Warning: inserting implicit <output>
CreateEvdData.html:170:16 (CreateEvdData.Rd:99): Warning: missing </output> before <pre>
CreateEvdData.html:174:1 (CreateEvdData.Rd:104): Warning: inserting implicit <output>
CreateEvdData.html:174:1 (CreateEvdData.Rd:104): Warning: missing </output> before <h4>
CreateEvdData.html:178:5 (CreateEvdData.Rd:106): Warning: inserting implicit <output>
CreateEvdData.html:180:4 (CreateEvdData.Rd:107): Warning: inserting implicit <output>
CreateEvdData.html:184:1 (CreateEvdData.Rd:108): Warning: inserting implicit <output>
CreateEvdData.html:184:1 (CreateEvdData.Rd:108): Warning: missing </output> before <h5>
CreateEvdData.html:184:5 (CreateEvdData.Rd:108): Warning: inserting implicit <output>
CreateEvdData.html:186:16 (CreateEvdData.Rd:109): Warning: inserting implicit <output>
CreateEvdData.html:186:16 (CreateEvdData.Rd:109): Warning: missing </output> before <pre>
CreateEvdData.html:190:5 (CreateEvdData.Rd:112): Warning: inserting implicit <output>
CreateEvdData.html:193:1 (CreateEvdData.Rd:113): Warning: inserting implicit <output>
CreateEvdData.html:193:1 (CreateEvdData.Rd:113): Warning: missing </output> before <dl>
CreateEvdData.html:195:5 (CreateEvdData.Rd:115): Warning: inserting implicit <output>
CreateEvdData.html:195:31 (CreateEvdData.Rd:115): Warning: inserting implicit <output>
CreateEvdData.html:195:31 (CreateEvdData.Rd:115): Warning: missing </output> before <p>
CreateEvdData.html:195:34 (CreateEvdData.Rd:115): Warning: inserting implicit <output>
CreateEvdData.html:38:1 (CreateEvdData.Rd:19): Warning: trimming empty <output>
CreateEvdData.html:45:1 (CreateEvdData.Rd:26): Warning: trimming empty <output>
CreateEvdData.html:54:1 (CreateEvdData.Rd:33): Warning: trimming empty <output>
CreateEvdData.html:62:5 (CreateEvdData.Rd:36): Warning: trimming empty <output>
CreateEvdData.html:64:1 (CreateEvdData.Rd:37): Warning: trimming empty <output>
CreateEvdData.html:65:5 (CreateEvdData.Rd:37): Warning: trimming empty <output>
CreateEvdData.html:67:1 (CreateEvdData.Rd:38): Warning: trimming empty <output>
CreateEvdData.html:68:5 (CreateEvdData.Rd:38): Warning: trimming empty <output>
CreateEvdData.html:70:1 (CreateEvdData.Rd:39): Warning: trimming empty <output>
CreateEvdData.html:71:5 (CreateEvdData.Rd:39): Warning: trimming empty <output>
CreateEvdData.html:73:1 (CreateEvdData.Rd:40): Warning: trimming empty <output>
CreateEvdData.html:74:5 (CreateEvdData.Rd:40): Warning: trimming empty <output>
CreateEvdData.html:76:1 (CreateEvdData.Rd:41): Warning: trimming empty <output>
CreateEvdData.html:77:5 (CreateEvdData.Rd:41): Warning: trimming empty <output>
CreateEvdData.html:79:1 (CreateEvdData.Rd:42): Warning: trimming empty <output>
CreateEvdData.html:80:5 (CreateEvdData.Rd:42): Warning: trimming empty <output>
CreateEvdData.html:82:1 (CreateEvdData.Rd:42): Warning: trimming empty <output>
CreateEvdData.html:96:16 (CreateEvdData.Rd:50): Warning: trimming empty <output>
CreateEvdData.html:114:16 (CreateEvdData.Rd:63): Warning: trimming empty <output>
CreateEvdData.html:128:16 (CreateEvdData.Rd:72): Warning: trimming empty <output>
CreateEvdData.html:142:16 (CreateEvdData.Rd:81): Warning: trimming empty <output>
CreateEvdData.html:156:16 (CreateEvdData.Rd:90): Warning: trimming empty <output>
CreateEvdData.html:170:16 (CreateEvdData.Rd:99): Warning: trimming empty <output>
CreateEvdData.html:184:1 (CreateEvdData.Rd:108): Warning: trimming empty <output>
CreateEvdData.html:186:16 (CreateEvdData.Rd:109): Warning: trimming empty <output>
CreateEvdData.html:193:1 (CreateEvdData.Rd:113): Warning: trimming empty <output>
CreateEvdData.html:195:31 (CreateEvdData.Rd:115): Warning: trimming empty <output>
CreateEvdData.html:35:26 (CreateEvdData.Rd:16): Warning: <output> proprietary attribute "base"
CreateEvdData.html:35:26 (CreateEvdData.Rd:16): Warning: <output> proprietary attribute "filename"
CreateEvdData.html:38:4 (CreateEvdData.Rd:19): Warning: <output> proprietary attribute "base"
CreateEvdData.html:38:4 (CreateEvdData.Rd:19): Warning: <output> proprietary attribute "filename"
CreateEvdData.html:45:4 (CreateEvdData.Rd:26): Warning: <output> proprietary attribute "base"
CreateEvdData.html:45:4 (CreateEvdData.Rd:26): Warning: <output> proprietary attribute "filename"
CreateEvdData.html:47:1 (CreateEvdData.Rd:28): Warning: <output> proprietary attribute "base"
CreateEvdData.html:47:1 (CreateEvdData.Rd:28): Warning: <output> proprietary attribute "filename"
CreateEvdData.html:48:1 (CreateEvdData.Rd:29): Warning: <output> proprietary attribute "base"
CreateEvdData.html:48:1 (CreateEvdData.Rd:29): Warning: <output> proprietary attribute "filename"
CreateEvdData.html:49:1 (CreateEvdData.Rd:30): Warning: <output> proprietary attribute "base"
CreateEvdData.html:49:1 (CreateEvdData.Rd:30): Warning: <output> proprietary attribute "filename"
CreateEvdData.html:50:1 (CreateEvdData.Rd:31): Warning: <output> proprietary attribute "base"
CreateEvdData.html:50:1 (CreateEvdData.Rd:31): Warning: <output> proprietary attribute "filename"
CreateEvdData.html:54:5 (CreateEvdData.Rd:33): Warning: <output> proprietary attribute "base"
CreateEvdData.html:54:5 (CreateEvdData.Rd:33): Warning: <output> proprietary attribute "filename"
CreateEvdData.html:58:5 (CreateEvdData.Rd:34): Warning: <output> proprietary attribute "base"
CreateEvdData.html:58:5 (CreateEvdData.Rd:34): Warning: <output> proprietary attribute "filename"
CreateEvdData.html:62:9 (CreateEvdData.Rd:36): Warning: <output> proprietary attribute "base"
CreateEvdData.html:62:9 (CreateEvdData.Rd:36): Warning: <output> proprietary attribute "filename"
CreateEvdData.html:65:9 (CreateEvdData.Rd:37): Warning: <output> proprietary attribute "base"
CreateEvdData.html:65:9 (CreateEvdData.Rd:37): Warning: <output> proprietary attribute "filename"
CreateEvdData.html:68:9 (CreateEvdData.Rd:38): Warning: <output> proprietary attribute "base"
CreateEvdData.html:68:9 (CreateEvdData.Rd:38): Warning: <output> proprietary attribute "filename"
CreateEvdData.html:71:9 (CreateEvdData.Rd:39): Warning: <output> proprietary attribute "base"
CreateEvdData.html:71:9 (CreateEvdData.Rd:39): Warning: <output> proprietary attribute "filename"
CreateEvdData.html:74:9 (CreateEvdData.Rd:40): Warning: <output> proprietary attribute "base"
CreateEvdData.html:74:9 (CreateEvdData.Rd:40): Warning: <output> proprietary attribute "filename"
CreateEvdData.html:77:9 (CreateEvdData.Rd:41): Warning: <output> proprietary attribute "base"
CreateEvdData.html:77:9 (CreateEvdData.Rd:41): Warning: <output> proprietary attribute "filename"
CreateEvdData.html:80:9 (CreateEvdData.Rd:42): Warning: <output> proprietary attribute "base"
CreateEvdData.html:80:9 (CreateEvdData.Rd:42): Warning: <output> proprietary attribute "filename"
CreateEvdData.html:86:1 (CreateEvdData.Rd:46): Warning: <output> proprietary attribute "base"
CreateEvdData.html:86:1 (CreateEvdData.Rd:46): Warning: <output> proprietary attribute "filename"
CreateEvdData.html:90:5 (CreateEvdData.Rd:48): Warning: <output> proprietary attribute "base"
CreateEvdData.html:90:5 (CreateEvdData.Rd:48): Warning: <output> proprietary attribute "filename"
CreateEvdData.html:94:5 (CreateEvdData.Rd:49): Warning: <output> proprietary attribute "base"
CreateEvdData.html:94:5 (CreateEvdData.Rd:49): Warning: <output> proprietary attribute "filename"
CreateEvdData.html:96:21 (CreateEvdData.Rd:50): Warning: <output> proprietary attribute "base"
CreateEvdData.html:96:21 (CreateEvdData.Rd:50): Warning: <output> proprietary attribute "filename"
CreateEvdData.html:104:1 (CreateEvdData.Rd:59): Warning: <output> proprietary attribute "base"
CreateEvdData.html:104:1 (CreateEvdData.Rd:59): Warning: <output> proprietary attribute "filename"
CreateEvdData.html:108:5 (CreateEvdData.Rd:61): Warning: <output> proprietary attribute "base"
CreateEvdData.html:108:5 (CreateEvdData.Rd:61): Warning: <output> proprietary attribute "filename"
CreateEvdData.html:112:5 (CreateEvdData.Rd:62): Warning: <output> proprietary attribute "base"
CreateEvdData.html:112:5 (CreateEvdData.Rd:62): Warning: <output> proprietary attribute "filename"
CreateEvdData.html:114:21 (CreateEvdData.Rd:63): Warning: <output> proprietary attribute "base"
CreateEvdData.html:114:21 (CreateEvdData.Rd:63): Warning: <output> proprietary attribute "filename"
CreateEvdData.html:118:1 (CreateEvdData.Rd:68): Warning: <output> proprietary attribute "base"
CreateEvdData.html:118:1 (CreateEvdData.Rd:68): Warning: <output> proprietary attribute "filename"
CreateEvdData.html:122:5 (CreateEvdData.Rd:70): Warning: <output> proprietary attribute "base"
CreateEvdData.html:122:5 (CreateEvdData.Rd:70): Warning: <output> proprietary attribute "filename"
CreateEvdData.html:126:5 (CreateEvdData.Rd:71): Warning: <output> proprietary attribute "base"
CreateEvdData.html:126:5 (CreateEvdData.Rd:71): Warning: <output> proprietary attribute "filename"
CreateEvdData.html:128:21 (CreateEvdData.Rd:72): Warning: <output> proprietary attribute "base"
CreateEvdData.html:128:21 (CreateEvdData.Rd:72): Warning: <output> proprietary attribute "filename"
CreateEvdData.html:132:1 (CreateEvdData.Rd:77): Warning: <output> proprietary attribute "base"
CreateEvdData.html:132:1 (CreateEvdData.Rd:77): Warning: <output> proprietary attribute "filename"
CreateEvdData.html:136:5 (CreateEvdData.Rd:79): Warning: <output> proprietary attribute "base"
CreateEvdData.html:136:5 (CreateEvdData.Rd:79): Warning: <output> proprietary attribute "filename"
CreateEvdData.html:140:5 (CreateEvdData.Rd:80): Warning: <output> proprietary attribute "base"
CreateEvdData.html:140:5 (CreateEvdData.Rd:80): Warning: <output> proprietary attribute "filename"
CreateEvdData.html:142:21 (CreateEvdData.Rd:81): Warning: <output> proprietary attribute "base"
CreateEvdData.html:142:21 (CreateEvdData.Rd:81): Warning: <output> proprietary attribute "filename"
CreateEvdData.html:146:1 (CreateEvdData.Rd:86): Warning: <output> proprietary attribute "base"
CreateEvdData.html:146:1 (CreateEvdData.Rd:86): Warning: <output> proprietary attribute "filename"
CreateEvdData.html:150:5 (CreateEvdData.Rd:88): Warning: <output> proprietary attribute "base"
CreateEvdData.html:150:5 (CreateEvdData.Rd:88): Warning: <output> proprietary attribute "filename"
CreateEvdData.html:154:5 (CreateEvdData.Rd:89): Warning: <output> proprietary attribute "base"
CreateEvdData.html:154:5 (CreateEvdData.Rd:89): Warning: <output> proprietary attribute "filename"
CreateEvdData.html:156:21 (CreateEvdData.Rd:90): Warning: <output> proprietary attribute "base"
CreateEvdData.html:156:21 (CreateEvdData.Rd:90): Warning: <output> proprietary attribute "filename"
CreateEvdData.html:160:1 (CreateEvdData.Rd:95): Warning: <output> proprietary attribute "base"
CreateEvdData.html:160:1 (CreateEvdData.Rd:95): Warning: <output> proprietary attribute "filename"
CreateEvdData.html:164:5 (CreateEvdData.Rd:97): Warning: <output> proprietary attribute "base"
CreateEvdData.html:164:5 (CreateEvdData.Rd:97): Warning: <output> proprietary attribute "filename"
CreateEvdData.html:168:5 (CreateEvdData.Rd:98): Warning: <output> proprietary attribute "base"
CreateEvdData.html:168:5 (CreateEvdData.Rd:98): Warning: <output> proprietary attribute "filename"
CreateEvdData.html:170:21 (CreateEvdData.Rd:99): Warning: <output> proprietary attribute "base"
CreateEvdData.html:170:21 (CreateEvdData.Rd:99): Warning: <output> proprietary attribute "filename"
CreateEvdData.html:174:1 (CreateEvdData.Rd:104): Warning: <output> proprietary attribute "base"
CreateEvdData.html:174:1 (CreateEvdData.Rd:104): Warning: <output> proprietary attribute "filename"
CreateEvdData.html:178:5 (CreateEvdData.Rd:106): Warning: <output> proprietary attribute "base"
CreateEvdData.html:178:5 (CreateEvdData.Rd:106): Warning: <output> proprietary attribute "filename"
CreateEvdData.html:180:4 (CreateEvdData.Rd:107): Warning: <output> proprietary attribute "base"
CreateEvdData.html:180:4 (CreateEvdData.Rd:107): Warning: <output> proprietary attribute "filename"
CreateEvdData.html:184:5 (CreateEvdData.Rd:108): Warning: <output> proprietary attribute "base"
CreateEvdData.html:184:5 (CreateEvdData.Rd:108): Warning: <output> proprietary attribute "filename"
CreateEvdData.html:186:21 (CreateEvdData.Rd:109): Warning: <output> proprietary attribute "base"
CreateEvdData.html:186:21 (CreateEvdData.Rd:109): Warning: <output> proprietary attribute "filename"
CreateEvdData.html:190:5 (CreateEvdData.Rd:112): Warning: <output> proprietary attribute "base"
CreateEvdData.html:190:5 (CreateEvdData.Rd:112): Warning: <output> proprietary attribute "filename"
CreateEvdData.html:195:5 (CreateEvdData.Rd:115): Warning: <output> proprietary attribute "base"
CreateEvdData.html:195:5 (CreateEvdData.Rd:115): Warning: <output> proprietary attribute "filename"
CreateEvdData.html:195:34 (CreateEvdData.Rd:115): Warning: <output> proprietary attribute "base"
CreateEvdData.html:195:34 (CreateEvdData.Rd:115): Warning: <output> proprietary attribute "filename"
FPHI.html:37:20 (FPHI.Rd:18): Error: <file> is not recognized!
FPHI.html:37:20 (FPHI.Rd:18): Warning: discarding unexpected <file>
FPHI.html:39:7 (FPHI.Rd:20): Error: <name> is not recognized!
FPHI.html:39:7 (FPHI.Rd:20): Warning: discarding unexpected <name>
FPHI.html:41:1 (FPHI.Rd:22): Warning: replacing </p> with <br>
FPHI.html:38:12 (FPHI.Rd:19): Warning: missing </h2> before <p>
FPHI.html:38:12 (FPHI.Rd:19): Warning: <h2> proprietary attribute "decimal"
FPHI.html:38:12 (FPHI.Rd:19): Warning: <h2> proprietary attribute "count"
Load.html:31:16 (Load.Rd:12): Error: <object-type> is not recognized! Did you mean to enable the custom-tags option?
Load.html:31:16 (Load.Rd:12): Warning: discarding unexpected <object-type>
Load.html:31:31 (Load.Rd:12): Error: <args> is not recognized!
Load.html:31:31 (Load.Rd:12): Warning: discarding unexpected <args>
Load.html:34:18 (Load.Rd:15): Error: <filename> is not recognized!
Load.html:34:18 (Load.Rd:15): Warning: discarding unexpected <filename>
Load.html:35:18 (Load.Rd:16): Error: <filename> is not recognized!
Load.html:35:18 (Load.Rd:16): Warning: discarding unexpected <filename>
Load.html:36:35 (Load.Rd:17): Error: <filename> is not recognized!
Load.html:36:35 (Load.Rd:17): Warning: discarding unexpected <filename>
PedifromSNPs.html:36:13 (PedifromSNPs.Rd:17): Error: <file> is not recognized!
PedifromSNPs.html:36:13 (PedifromSNPs.Rd:17): Warning: discarding unexpected <file>
PedifromSNPs.html:38:7 (PedifromSNPs.Rd:19): Error: <alpha> is not recognized!
PedifromSNPs.html:38:7 (PedifromSNPs.Rd:19): Warning: discarding unexpected <alpha>
PedifromSNPs.html:40:13 (PedifromSNPs.Rd:21): Error: <batch> is not recognized!
PedifromSNPs.html:40:13 (PedifromSNPs.Rd:21): Warning: discarding unexpected <batch>
PedifromSNPs.html:42:12 (PedifromSNPs.Rd:23): Error: <number> is not recognized!
PedifromSNPs.html:42:12 (PedifromSNPs.Rd:23): Warning: discarding unexpected <number>
PedifromSNPs.html:35:4 (PedifromSNPs.Rd:16): Warning: missing </output> before </p>
PedifromSNPs.html:44:1 (PedifromSNPs.Rd:25): Warning: inserting implicit <output>
PedifromSNPs.html:44:1 (PedifromSNPs.Rd:25): Warning: missing </output> before <p>
PedifromSNPs.html:44:4 (PedifromSNPs.Rd:25): Warning: inserting implicit <output>
PedifromSNPs.html:45:4 (PedifromSNPs.Rd:26): Error: <file> is not recognized!
PedifromSNPs.html:45:4 (PedifromSNPs.Rd:26): Warning: discarding unexpected <file>
Trait.html:33:7 (Trait.Rd:14): Error: <trait1> is not recognized!
Trait.html:33:7 (Trait.Rd:14): Warning: discarding unexpected <trait1>
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 ERROR, 3 WARNINGs, 5 NOTEs