CRAN Package Check Results for Package konfound

Last updated on 2021-01-16 06:51:11 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.3.0 6.56 73.50 80.06 ERROR
r-devel-linux-x86_64-debian-gcc 0.3.0 5.73 58.37 64.10 ERROR
r-devel-linux-x86_64-fedora-clang 0.3.0 103.07 ERROR
r-devel-linux-x86_64-fedora-gcc 0.3.0 103.42 ERROR
r-devel-windows-ix86+x86_64 0.3.0 11.00 78.00 89.00 ERROR
r-patched-linux-x86_64 0.3.0 7.68 68.92 76.60 ERROR
r-patched-solaris-x86 0.3.0 138.30 ERROR
r-release-linux-x86_64 0.3.0 7.21 72.49 79.70 ERROR
r-release-macos-x86_64 0.3.0 NOTE
r-release-windows-ix86+x86_64 0.3.0 12.00 74.00 86.00 ERROR
r-oldrel-macos-x86_64 0.3.0 NOTE
r-oldrel-windows-ix86+x86_64 0.3.0 12.00 70.00 82.00 ERROR

Check Details

Version: 0.3.0
Check: examples
Result: ERROR
    Running examples in 'konfound-Ex.R' failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: mkonfound
    > ### Title: Perform meta-analyses including sensitivity analysis
    > ### Aliases: mkonfound
    >
    > ### ** Examples
    >
    > d <- read.csv("https://msu.edu/~kenfrank/example%20dataset%20for%20mkonfound.csv")
    > d <- d[1:3, ] # this is only so that the example runs more quickly
    > str(d)
    'data.frame': 3 obs. of 906 variables:
     $ X..DOCTYPE.html..html.lang.en.US.itemscope.itemtype.http...schema.org.WebPage..head..meta.charset.utf.8..script.nonce.RN7uwIJHuS2V.xg.gaxfYA.var.DOCS_timing.....DOCS_timing..sl...new.Date...getTime.....script..script.nonce.RN7uwIJHuS2V.xg.gaxfYA.function._DumpException.e...throw.e....script..script.nonce.RN7uwIJHuS2V.xg.gaxfYA._docs_flag_initialData..atari.eiicg.false : chr "]" "" ""
     $ atari.eiitev.false : chr "" "null" "null"
     $ docs.sup. : chr "" "null" "null"
     $ docs.eea.false : chr "" "null" "null"
     $ docs.ecci.false : chr "" "null" "null"
     $ docs.ipmmp.true : chr "" "0" "null"
     $ docs.esi.false : chr "" "null" "null"
     $ docs.liap..logImpressions : chr "" "null" "null"
     $ ilcm..eui.AHKXmL2goufb2Mm06QI.s4TNOdX9ZzSduPw9IxbBhdbJwDQKlOF.shG70VOzWygM3Z4C.gK8HCUV : chr "" "null" "null"
     $ je.1 : chr "" "null" "null"
     $ sstu.1610701380856000 : chr "" "null" "null"
     $ si.CIzTlJ3Kne4CFRNPyAodrYIDCg : chr "" "null" "null"
     $ gsc.null : chr "" "null" "null"
     $ ei..5713211 : chr "" "null" "null"
     $ X14101430 : chr "" "null" "null"
     $ X5719651 : chr "" "https://drive.google.com" "null"
     $ X14101510 : chr "" "null" "null"
     $ X5715290 : chr "" "null" "null"
     $ X5714628 : chr "" "null" "null"
     $ X5711808 : chr "" "null" "null"
     $ X5712211 : chr "" "null" "null"
     $ X5713049 : chr "" "null" "null"
     $ X14100854 : chr "" "1" "null"
     $ X5704621 : chr "" "1" "null"
     $ X5714550 : chr "" "null" "null"
     $ X5708870 : chr "" "0" "null"
     $ X5711850 : chr "" "1" "null"
     $ X5703022 : chr "" "null" "null"
     $ X14101552 : chr "" "null" "null"
     $ X5720060 : chr "" "null" "null"
     $ X5706836 : chr "" "null" "null"
     $ X5709892 : chr "" "null" "null"
     $ X14101514 : chr "" "null" "null"
     $ X14101538 : chr "" "null" "null"
     $ X5703839 : chr "" "null" "null"
     $ X14101454 : chr "" "null" "null"
     $ X14101442 : chr "" "null" "null"
     $ X5706832 : chr "" "null" "https://www.gstatic.com/atari/embeds/5de913a2354e93acf4d43c4db53928e5/intermediate-frame-minified.html"
     $ X5713207 : chr "" "null" "0"
     $ X5721004 : chr "" "null" "null"
     $ X5707711 : chr "" "null" "v2beta"
     $ X14101462 : chr "" "null" "null"
     $ X14100834 : chr "" "null" "null"
     $ X5722301 : chr "" "null" "null"
     $ X5720925 : chr "" "null" "null"
     $ X14101254 : chr "" "null" "null"
     $ X14101502. : chr "" "null" "null"
     $ crc.0 : chr "" "null" "4"
     $ cvi.... : chr "" "null" "https://accounts.google.com/o/oauth2/iframe"
     $ docs.ccdil.false : chr "" "null" "null"
     $ docs.eil.true : chr "" "null" "null"
     $ docs.eoi.false : chr "" "null" "null"
     $ info_params... : chr "" "null" "null"
     $ docs.enpf.false : chr "" "null" "null"
     $ atari.jefp.._.view.jserror : chr "" "null" "null"
     $ docs.jern.view : chr "" "null" "https://482666924-atari-embeds.googleusercontent.com/embeds/16cb204cf3a9d4d223a0a3fd8b0eec5d/inner-frame-minified.html"
     $ atari.rhpp.._.view..._docs_flag_cek..null...if..window..DOCS_timing.....DOCS_timing..ifdld...new.Date...getTime......script..meta.name.viewport.content.width.device.width..initial.scale.1..maximum.scale.1.0..user.scalable.no..meta.http.equiv.X.UA.Compatible.content.IE.edge..meta.name.referrer.content.origin..link.rel.icon.href.https...ssl.gstatic.com.atari.images.favicon_2.ico..meta.property.og.type.content.website..meta.property.og.title.content.Ken.Frank.site..meta.itemprop.url.property.og.url.content.https...sites.google.com.msu.edu.kenfrank..meta.itemprop.thumbnailUrl.content.https...ssl.gstatic.com.atari.images.atari.logo.png..meta.itemprop.image.content.https...ssl.gstatic.com.atari.images.atari.logo.png..link.href.https...fonts.googleapis.com.css.family.Lato.3A300.2C300italic.2C400.2C400italic.2C700.2C700italic.display.swap.rel.stylesheet..link.href.https...fonts.googleapis.com.css.family.Google.Sans.400.500.Roboto.300.400.500.700.Source.Code.Pro.400.700.display.swap.rel.stylesheet..style.nonce.RN7uwIJHuS2V.xg.gaxfYA..media.only.screen.and..max.width..479px...CGqCRe.font.size..27.0pt....media.only.screen.and..min.width..480px..and..max.width..767px...CGqCRe.font.size..32.0pt....media.only.screen.and..min.width..768px..and..max.width..1279px...CGqCRe.font.size..36.0pt....media.only.screen.and..min.width..1280px...CGqCRe.font.size..36.0pt.....style..link.rel.stylesheet.href.https...www.gstatic.com._.atari._.ss.k.atari.vw.TuYBvO8_f2Y.L.X.O.d.1.ct.zgms.rs.AGEqA5nZjyfiuRtO8BcMuTlI35MwWPiqJw..title.itemprop.name.Ken.Frank.site..title..style.jsname.ptDGoc.nonce.RN7uwIJHuS2V.xg.gaxfYA..M63kCb.background.color..rgba.255 : chr "" "null" "null"
     $ X255 : chr "" "null" "null"
     $ X255.1 : chr "" "null" "null"
     $ X1....OUGEr.color..rgba.33 : chr "" "null" "null"
     $ X33 : chr "" "null" "null"
     $ X33.1 : chr "" "null" "null"
     $ X1....duRjpb..OUGEr.color..rgba.34 : chr "" "null" "null"
     $ X110 : chr "" "null" "null"
     $ X147 : chr "" "null" "null"
     $ X1....JYVBee..OUGEr.color..rgba.34 : chr "" "null" "null"
     $ X110.1 : chr "" "null" "null"
     $ X147.1 : chr "" "null" "null"
     $ X1....OmQG5e..OUGEr.color..rgba.33 : chr "" "null" "null"
     $ X33.2 : chr "" "null" "null"
     $ X33.3 : chr "" "null" "null"
     $ X1....iwQgFb.background.color..rgba.0 : chr "" "null" "null"
     $ X0 : chr "" "0" "null"
     $ X0.1 : chr "" "v2internal" "null"
     $ X0.150000006....ySLm4c.font.family..Lato : chr "" "https://docs.google.com" "null"
     $ sans.serif...CbiMKe.background.color..rgba.30 : chr "" "null" "null"
     $ X108 : chr "" "null" "null"
     $ X147.2 : chr "" "null" "null"
     $ X1....qeLZfd..zfr3Q.color..rgba.33 : chr "" "null" "null"
     $ X33.4 : chr "" "null" "null"
     $ X33.5 : chr "" "null" "null"
     $ X1....qeLZfd..qnVSj.color..rgba.33 : chr "" "https://sites.google.com/new/" "null"
     $ X33.6 : chr "" "null" "null"
     $ X33.7 : chr "" "null" "null"
     $ X1....qeLZfd..Glwbz.color..rgba.33 : chr "" "null" "null"
     $ X33.8 : chr "" "null" "null"
     $ X33.9 : chr "" "null" "null"
     $ X1....qeLZfd..duRjpb.color..rgba.34 : chr "" "0" "null"
     $ X110.2 : chr "" "null" "null"
     $ X147.3 : chr "" "null" "null"
     $ X1....qeLZfd..qLrapd.color..rgba.34 : chr "" "null" "null"
     $ X110.3 : chr "" "null" "null"
     $ X147.4 : chr "" "null" "null"
     $ X1....qeLZfd..JYVBee.color..rgba.34 : chr "" "null" "null"
     $ X110.4 : chr "" "null" "null"
     $ X147.5 : chr "" "null" "null"
     $ X1....qeLZfd..aHM7ed.color..rgba.34 : chr "" "null" "null"
     $ X110.5 : chr "" "null" "null"
     $ X147.6 : chr "" "null" "null"
     [list output truncated]
    > mkonfound(d, t, df)
    Error: Can't subset columns that don't exist.
    x Column `t` doesn't exist.
    Backtrace:
     x
     1. \-konfound::mkonfound(d, t, df)
     2. +-dplyr::pull(select(d, !!t_enquo))
     3. +-dplyr::select(d, !!t_enquo)
     4. \-dplyr:::select.data.frame(d, !!t_enquo)
     5. \-tidyselect::eval_select(expr(c(...)), .data)
     6. \-tidyselect:::eval_select_impl(...)
     7. +-tidyselect:::with_subscript_errors(...)
     8. | +-base::tryCatch(...)
     9. | | \-base:::tryCatchList(expr, classes, parentenv, handlers)
     10. | | \-base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
     11. | | \-base:::doTryCatch(return(expr), name, parentenv, handler)
     12. | \-tidyselect:::instrument_base_errors(expr)
     13. | \-base::withCallingHandlers(...)
     14. \-tidyselect:::vars_select_eval(...)
     15. \-tidyselect:::walk_data_tree(expr, data_mask, context_mask)
     16. \-tidyselect:::eval_c(expr, data_mask, context_mask)
     17. \-tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
     18. \-tidyselect:::walk_data_tree(new, data_mask, context_mask)
     19. \-tidyselect:::as_indices_sel_impl(...)
     20. \-tidyselect:::as_indices_impl(x, vars, strict = strict)
     21. \-tidyselect:::chr_as_locations(x, vars)
     22. \-vctrs::vec_as_location(x, n = length(vars), names = vars)
     23. \-(function () ...
     24. \-vctrs:::stop_subscript_oob(...)
     25. \-vctrs:::stop_subscript(...)
    Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 0.3.0
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building 'introduction-to-konfound.Rmd' using rmarkdown
    Loading required namespace: forcats
    Note that for a non-linear model, impact threshold should not be interpreted.
    Note that this is only an approximation. For exact results in terms of the number of cases that must be switched from treatment success to treatment failure to invalidate the inference see: https://msu.edu/~kenfrank/non%20linear%20replacement%20treatment.xlsm
    If a dichotomous independent variable is used, consider using the 2X2 table approach enabled with the argument two_by_two = TRUE
    Quitting from lines 204-207 (introduction-to-konfound.Rmd)
    Error: processing vignette 'introduction-to-konfound.Rmd' failed with diagnostics:
    Can't subset columns that don't exist.
    x Column `t` doesn't exist.
    --- failed re-building 'introduction-to-konfound.Rmd'
    
    SUMMARY: processing the following file failed:
     'introduction-to-konfound.Rmd'
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 0.3.0
Check: examples
Result: ERROR
    Running examples in ‘konfound-Ex.R’ failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: mkonfound
    > ### Title: Perform meta-analyses including sensitivity analysis
    > ### Aliases: mkonfound
    >
    > ### ** Examples
    >
    > d <- read.csv("https://msu.edu/~kenfrank/example%20dataset%20for%20mkonfound.csv")
    > d <- d[1:3, ] # this is only so that the example runs more quickly
    > str(d)
    'data.frame': 3 obs. of 904 variables:
     $ X..DOCTYPE.html..html.lang.en.US.itemscope.itemtype.http...schema.org.WebPage..head..meta.charset.utf.8..script.nonce.KW9OHw5j1FoXKz2RUEdciA.var.DOCS_timing.....DOCS_timing..sl...new.Date...getTime.....script..script.nonce.KW9OHw5j1FoXKz2RUEdciA.function._DumpException.e...throw.e....script..script.nonce.KW9OHw5j1FoXKz2RUEdciA._docs_flag_initialData..atari.eiicg.false : chr "]" "" ""
     $ atari.eiitev.false : chr "" "null" "null"
     $ docs.sup. : chr "" "null" "null"
     $ docs.eea.false : chr "" "null" "null"
     $ docs.ecci.false : chr "" "null" "null"
     $ docs.ipmmp.true : chr "" "0" "null"
     $ docs.esi.false : chr "" "null" "null"
     $ docs.liap..logImpressions : chr "" "null" "null"
     $ ilcm..eui.AHKXmL3xicuAZFYMfrk5rEQeYiiHX7W2BomNAbyYa5_cEMeS3Ybu_Ae6oPbwSpYNZUusq25yzVlW : chr "" "null" "null"
     $ je.1 : chr "" "null" "null"
     $ sstu.1610747291988000 : chr "" "null" "null"
     $ si.CJTmpaH1nu4CFREENwodn5QCvQ : chr "" "null" "null"
     $ gsc.null : chr "" "null" "null"
     $ ei..5713211 : chr "" "null" "null"
     $ X14101454 : chr "" "null" "null"
     $ X5720060 : chr "" "https://drive.google.com" "null"
     $ X14101552 : chr "" "null" "null"
     $ X5706836 : chr "" "null" "null"
     $ X5703839 : chr "" "null" "null"
     $ X14101502 : chr "" "null" "null"
     $ X5703022 : chr "" "null" "null"
     $ X5715290 : chr "" "null" "null"
     $ X14101442 : chr "" "1" "null"
     $ X5709892 : chr "" "1" "null"
     $ X14100854 : chr "" "null" "null"
     $ X5714550 : chr "" "0" "null"
     $ X5721004 : chr "" "1" "null"
     $ X14101462 : chr "" "null" "null"
     $ X14101430 : chr "" "null" "null"
     $ X5708870 : chr "" "null" "null"
     $ X5713049 : chr "" "null" "null"
     $ X14101254 : chr "" "null" "null"
     $ X5712211 : chr "" "null" "null"
     $ X5704621 : chr "" "null" "null"
     $ X5719651 : chr "" "null" "null"
     $ X5706832 : chr "" "null" "null"
     $ X14100834 : chr "" "null" "null"
     $ X5720925 : chr "" "null" "https://www.gstatic.com/atari/embeds/5de913a2354e93acf4d43c4db53928e5/intermediate-frame-minified.html"
     $ X5714628 : chr "" "null" "0"
     $ X14101514 : chr "" "null" "null"
     $ X5711850 : chr "" "null" "v2beta"
     $ X5711808 : chr "" "null" "null"
     $ X14101538 : chr "" "null" "null"
     $ X5713207 : chr "" "null" "null"
     $ X14101510 : chr "" "null" "null"
     $ X5707711. : chr "" "null" "null"
     $ crc.0 : chr "" "null" "null"
     $ cvi.... : chr "" "null" "4"
     $ docs.ccdil.false : chr "" "null" "https://accounts.google.com/o/oauth2/iframe"
     $ docs.eil.true : chr "" "null" "null"
     $ docs.eoi.false : chr "" "null" "null"
     $ info_params... : chr "" "null" "null"
     $ docs.enpf.false : chr "" "null" "null"
     $ atari.jefp.._.view.jserror : chr "" "null" "null"
     $ docs.jern.view : chr "" "null" "null"
     $ atari.rhpp.._.view..._docs_flag_cek..null...if..window..DOCS_timing.....DOCS_timing..ifdld...new.Date...getTime......script..meta.name.viewport.content.width.device.width..initial.scale.1..maximum.scale.1.0..user.scalable.no..meta.http.equiv.X.UA.Compatible.content.IE.edge..meta.name.referrer.content.origin..link.rel.icon.href.https...ssl.gstatic.com.atari.images.favicon_2.ico..meta.property.og.type.content.website..meta.property.og.title.content.Ken.Frank.site..meta.itemprop.url.property.og.url.content.https...sites.google.com.msu.edu.kenfrank..meta.itemprop.thumbnailUrl.content.https...ssl.gstatic.com.atari.images.atari.logo.png..meta.itemprop.image.content.https...ssl.gstatic.com.atari.images.atari.logo.png..link.href.https...fonts.googleapis.com.css.family.Lato.3A300.2C300italic.2C400.2C400italic.2C700.2C700italic.display.swap.rel.stylesheet..link.href.https...fonts.googleapis.com.css.family.Google.Sans.400.500.Roboto.300.400.500.700.Source.Code.Pro.400.700.display.swap.rel.stylesheet..style.nonce.KW9OHw5j1FoXKz2RUEdciA..media.only.screen.and..max.width..479px...CGqCRe.font.size..27.0pt....media.only.screen.and..min.width..480px..and..max.width..767px...CGqCRe.font.size..32.0pt....media.only.screen.and..min.width..768px..and..max.width..1279px...CGqCRe.font.size..36.0pt....media.only.screen.and..min.width..1280px...CGqCRe.font.size..36.0pt.....style..link.rel.stylesheet.href.https...www.gstatic.com._.atari._.ss.k.atari.vw.TuYBvO8_f2Y.L.X.O.d.1.ct.zgms.rs.AGEqA5nZjyfiuRtO8BcMuTlI35MwWPiqJw..title.itemprop.name.Ken.Frank.site..title..style.jsname.ptDGoc.nonce.KW9OHw5j1FoXKz2RUEdciA..M63kCb.background.color..rgba.255 : chr "" "null" "https://757282399-atari-embeds.googleusercontent.com/embeds/16cb204cf3a9d4d223a0a3fd8b0eec5d/inner-frame-minified.html"
     $ X255 : chr "" "null" "null"
     $ X255.1 : chr "" "null" "null"
     $ X1....OUGEr.color..rgba.33 : chr "" "null" "null"
     $ X33 : chr "" "null" "null"
     $ X33.1 : chr "" "null" "null"
     $ X1....duRjpb..OUGEr.color..rgba.34 : chr "" "null" "null"
     $ X110 : chr "" "null" "null"
     $ X147 : chr "" "null" "null"
     $ X1....JYVBee..OUGEr.color..rgba.34 : chr "" "null" "null"
     $ X110.1 : chr "" "null" "null"
     $ X147.1 : chr "" "null" "null"
     $ X1....OmQG5e..OUGEr.color..rgba.33 : chr "" "null" "null"
     $ X33.2 : chr "" "null" "null"
     $ X33.3 : chr "" "null" "null"
     $ X1....iwQgFb.background.color..rgba.0 : chr "" "null" "null"
     $ X0 : chr "" "null" "null"
     $ X0.1 : chr "" "0" "null"
     $ X0.150000006....ySLm4c.font.family..Lato : chr "" "v2internal" "null"
     $ sans.serif...CbiMKe.background.color..rgba.30 : chr "" "https://docs.google.com" "null"
     $ X108 : chr "" "null" "null"
     $ X147.2 : chr "" "null" "null"
     $ X1....qeLZfd..zfr3Q.color..rgba.33 : chr "" "null" "null"
     $ X33.4 : chr "" "null" "null"
     $ X33.5 : chr "" "null" "null"
     $ X1....qeLZfd..qnVSj.color..rgba.33 : chr "" "null" "null"
     $ X33.6 : chr "" "https://sites.google.com/new/" "null"
     $ X33.7 : chr "" "null" "null"
     $ X1....qeLZfd..Glwbz.color..rgba.33 : chr "" "null" "null"
     $ X33.8 : chr "" "null" "null"
     $ X33.9 : chr "" "null" "null"
     $ X1....qeLZfd..duRjpb.color..rgba.34 : chr "" "null" "null"
     $ X110.2 : chr "" "0" "null"
     $ X147.3 : chr "" "null" "null"
     $ X1....qeLZfd..qLrapd.color..rgba.34 : chr "" "null" "null"
     $ X110.3 : chr "" "null" "null"
     $ X147.4 : chr "" "null" "null"
     $ X1....qeLZfd..JYVBee.color..rgba.34 : chr "" "null" "null"
     $ X110.4 : chr "" "null" "null"
     $ X147.5 : chr "" "null" "null"
     $ X1....qeLZfd..aHM7ed.color..rgba.34 : chr "" "null" "null"
     $ X110.5 : chr "" "null" "null"
     $ X147.6 : chr "" "null" "null"
     $ X1....qeLZfd..OmQG5e.color..rgba.33 : chr "" "null" "null"
     [list output truncated]
    > mkonfound(d, t, df)
    Error: Can't subset columns that don't exist.
    ✖ Column `t` doesn't exist.
    Backtrace:
     █
     1. └─konfound::mkonfound(d, t, df)
     2. ├─dplyr::pull(select(d, !!t_enquo))
     3. ├─dplyr::select(d, !!t_enquo)
     4. └─dplyr:::select.data.frame(d, !!t_enquo)
     5. └─tidyselect::eval_select(expr(c(...)), .data)
     6. └─tidyselect:::eval_select_impl(...)
     7. ├─tidyselect:::with_subscript_errors(...)
     8. │ ├─base::tryCatch(...)
     9. │ │ └─base:::tryCatchList(expr, classes, parentenv, handlers)
     10. │ │ └─base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
     11. │ │ └─base:::doTryCatch(return(expr), name, parentenv, handler)
     12. │ └─tidyselect:::instrument_base_errors(expr)
     13. │ └─base::withCallingHandlers(...)
     14. └─tidyselect:::vars_select_eval(...)
     15. └─tidyselect:::walk_data_tree(expr, data_mask, context_mask)
     16. └─tidyselect:::eval_c(expr, data_mask, context_mask)
     17. └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
     18. └─tidyselect:::walk_data_tree(new, data_mask, context_mask)
     19. └─tidyselect:::as_indices_sel_impl(...)
     20. └─tidyselect:::as_indices_impl(x, vars, strict = strict)
     21. └─tidyselect:::chr_as_locations(x, vars)
     22. └─vctrs::vec_as_location(x, n = length(vars), names = vars)
     23. └─(function () ...
     24. └─vctrs:::stop_subscript_oob(...)
     25. └─vctrs:::stop_subscript(...)
    Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 0.3.0
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building ‘introduction-to-konfound.Rmd’ using rmarkdown
    Loading required namespace: forcats
    Note that for a non-linear model, impact threshold should not be interpreted.
    Note that this is only an approximation. For exact results in terms of the number of cases that must be switched from treatment success to treatment failure to invalidate the inference see: https://msu.edu/~kenfrank/non%20linear%20replacement%20treatment.xlsm
    If a dichotomous independent variable is used, consider using the 2X2 table approach enabled with the argument two_by_two = TRUE
    Quitting from lines 204-207 (introduction-to-konfound.Rmd)
    Error: processing vignette 'introduction-to-konfound.Rmd' failed with diagnostics:
    Can't subset columns that don't exist.
    ✖ Column `t` doesn't exist.
    --- failed re-building ‘introduction-to-konfound.Rmd’
    
    SUMMARY: processing the following file failed:
     ‘introduction-to-konfound.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavors: r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64

Version: 0.3.0
Check: dependencies in R code
Result: NOTE
    Namespaces in Imports field not imported from:
     ‘mice’ ‘tibble’
     All declared Imports should be used.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-solaris-x86, r-release-macos-x86_64, r-oldrel-macos-x86_64

Version: 0.3.0
Check: examples
Result: ERROR
    Running examples in ‘konfound-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: mkonfound
    > ### Title: Perform meta-analyses including sensitivity analysis
    > ### Aliases: mkonfound
    >
    > ### ** Examples
    >
    > d <- read.csv("https://msu.edu/~kenfrank/example%20dataset%20for%20mkonfound.csv")
    > d <- d[1:3, ] # this is only so that the example runs more quickly
    > str(d)
     chr [1:3] "<html lang=en>" " <head>" " <meta charset=utf-8>"
    > mkonfound(d, t, df)
    Warning: `select_()` is deprecated as of dplyr 0.7.0.
    Please use `select()` instead.
    This warning is displayed once every 8 hours.
    Call `lifecycle::last_warnings()` to see where this warning was generated.
    Error in UseMethod("select_") :
     no applicable method for 'select_' applied to an object of class "character"
    Calls: mkonfound -> pull -> select -> select.default -> select_
    Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 0.3.0
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building ‘introduction-to-konfound.Rmd’ using rmarkdown
    Loading required namespace: forcats
    Note that for a non-linear model, impact threshold should not be interpreted.
    Note that this is only an approximation. For exact results in terms of the number of cases that must be switched from treatment success to treatment failure to invalidate the inference see: https://msu.edu/~kenfrank/non%20linear%20replacement%20treatment.xlsm
    If a dichotomous independent variable is used, consider using the 2X2 table approach enabled with the argument two_by_two = TRUE
    Quitting from lines 204-207 (introduction-to-konfound.Rmd)
    Error: processing vignette 'introduction-to-konfound.Rmd' failed with diagnostics:
    Can't subset columns that don't exist.
    ✖ Column `t` doesn't exist.
    --- failed re-building ‘introduction-to-konfound.Rmd’
    
    SUMMARY: processing the following file failed:
     ‘introduction-to-konfound.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 0.3.0
Check: examples
Result: ERROR
    Running examples in ‘konfound-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: mkonfound
    > ### Title: Perform meta-analyses including sensitivity analysis
    > ### Aliases: mkonfound
    >
    > ### ** Examples
    >
    > d <- read.csv("https://msu.edu/~kenfrank/example%20dataset%20for%20mkonfound.csv")
    > d <- d[1:3, ] # this is only so that the example runs more quickly
    > str(d)
    'data.frame': 3 obs. of 904 variables:
     $ X..DOCTYPE.html..html.lang.en.US.itemscope.itemtype.http...schema.org.WebPage..head..meta.charset.utf.8..script.nonce.ptZnJL4fdJEgThOuXAEPgg.var.DOCS_timing.....DOCS_timing..sl...new.Date...getTime.....script..script.nonce.ptZnJL4fdJEgThOuXAEPgg.function._DumpException.e...throw.e....script..script.nonce.ptZnJL4fdJEgThOuXAEPgg._docs_flag_initialData..atari.eiicg.false : chr "]" "" ""
     $ atari.eiitev.false : chr "" "null" "null"
     $ docs.sup. : chr "" "null" "null"
     $ docs.eea.false : chr "" "null" "null"
     $ docs.ecci.false : chr "" "null" "null"
     $ docs.ipmmp.true : chr "" "0" "null"
     $ docs.esi.false : chr "" "null" "null"
     $ docs.liap..logImpressions : chr "" "null" "null"
     $ ilcm..eui.AHKXmL125xftp59270Vyy6O5LtH8SDNLC_25SRLoTX3sJaXKHjExYUlCYqtxkVPY7jSsS40B1hjX : chr "" "null" "null"
     $ je.1 : chr "" "null" "null"
     $ sstu.1610765020865000 : chr "" "null" "null"
     $ si.COrIiqe3n.4CFUucNwod8igF4Q : chr "" "null" "null"
     $ gsc.null : chr "" "null" "null"
     $ ei..5707711 : chr "" "null" "null"
     $ X5719651 : chr "" "null" "null"
     $ X5708870 : chr "" "https://drive.google.com" "null"
     $ X14101502 : chr "" "null" "null"
     $ X14100834 : chr "" "null" "null"
     $ X14101538 : chr "" "null" "null"
     $ X14101552 : chr "" "null" "null"
     $ X14101514 : chr "" "null" "null"
     $ X5713049 : chr "" "null" "null"
     $ X14101454 : chr "" "1" "null"
     $ X14101510 : chr "" "1" "null"
     $ X5711850 : chr "" "null" "null"
     $ X14101462 : chr "" "0" "null"
     $ X5713211 : chr "" "1" "null"
     $ X14101254 : chr "" "null" "null"
     $ X14101442 : chr "" "null" "null"
     $ X5720060 : chr "" "null" "null"
     $ X14101430 : chr "" "null" "null"
     $ X5714550 : chr "" "null" "null"
     $ X5712211 : chr "" "null" "null"
     $ X5709892 : chr "" "null" "null"
     $ X5706832 : chr "" "null" "null"
     $ X5721004 : chr "" "null" "null"
     $ X14100854 : chr "" "null" "null"
     $ X5703022 : chr "" "null" "https://www.gstatic.com/atari/embeds/5de913a2354e93acf4d43c4db53928e5/intermediate-frame-minified.html"
     $ X5715290 : chr "" "null" "0"
     $ X5706836 : chr "" "null" "null"
     $ X5711808 : chr "" "null" "v2beta"
     $ X5714628 : chr "" "null" "null"
     $ X5704621 : chr "" "null" "null"
     $ X5713207 : chr "" "null" "null"
     $ X5720925 : chr "" "null" "null"
     $ X5703839. : chr "" "null" "null"
     $ crc.0 : chr "" "null" "null"
     $ cvi.... : chr "" "null" "4"
     $ docs.ccdil.false : chr "" "null" "https://accounts.google.com/o/oauth2/iframe"
     $ docs.eil.true : chr "" "null" "null"
     $ docs.eoi.false : chr "" "null" "null"
     $ info_params... : chr "" "null" "null"
     $ docs.enpf.false : chr "" "null" "null"
     $ atari.jefp.._.view.jserror : chr "" "null" "null"
     $ docs.jern.view : chr "" "null" "null"
     $ atari.rhpp.._.view..._docs_flag_cek..null...if..window..DOCS_timing.....DOCS_timing..ifdld...new.Date...getTime......script..meta.name.viewport.content.width.device.width..initial.scale.1..maximum.scale.1.0..user.scalable.no..meta.http.equiv.X.UA.Compatible.content.IE.edge..meta.name.referrer.content.origin..link.rel.icon.href.https...ssl.gstatic.com.atari.images.favicon_2.ico..meta.property.og.type.content.website..meta.property.og.title.content.Ken.Frank.site..meta.itemprop.url.property.og.url.content.https...sites.google.com.msu.edu.kenfrank..meta.itemprop.thumbnailUrl.content.https...ssl.gstatic.com.atari.images.atari.logo.png..meta.itemprop.image.content.https...ssl.gstatic.com.atari.images.atari.logo.png..link.href.https...fonts.googleapis.com.css.family.Lato.3A300.2C300italic.2C400.2C400italic.2C700.2C700italic.display.swap.rel.stylesheet..link.href.https...fonts.googleapis.com.css.family.Google.Sans.400.500.Roboto.300.400.500.700.Source.Code.Pro.400.700.display.swap.rel.stylesheet..style.nonce.ptZnJL4fdJEgThOuXAEPgg..media.only.screen.and..max.width..479px...CGqCRe.font.size..27.0pt....media.only.screen.and..min.width..480px..and..max.width..767px...CGqCRe.font.size..32.0pt....media.only.screen.and..min.width..768px..and..max.width..1279px...CGqCRe.font.size..36.0pt....media.only.screen.and..min.width..1280px...CGqCRe.font.size..36.0pt.....style..link.rel.stylesheet.href.https...www.gstatic.com._.atari._.ss.k.atari.vw.TuYBvO8_f2Y.L.X.O.d.1.ct.zgms.rs.AGEqA5nZjyfiuRtO8BcMuTlI35MwWPiqJw..title.itemprop.name.Ken.Frank.site..title..style.jsname.ptDGoc.nonce.ptZnJL4fdJEgThOuXAEPgg..M63kCb.background.color..rgba.255 : chr "" "null" "https://1753628788-atari-embeds.googleusercontent.com/embeds/16cb204cf3a9d4d223a0a3fd8b0eec5d/inner-frame-minified.html"
     $ X255 : chr "" "null" "null"
     $ X255.1 : chr "" "null" "null"
     $ X1....OUGEr.color..rgba.33 : chr "" "null" "null"
     $ X33 : chr "" "null" "null"
     $ X33.1 : chr "" "null" "null"
     $ X1....duRjpb..OUGEr.color..rgba.34 : chr "" "null" "null"
     $ X110 : chr "" "null" "null"
     $ X147 : chr "" "null" "null"
     $ X1....JYVBee..OUGEr.color..rgba.34 : chr "" "null" "null"
     $ X110.1 : chr "" "null" "null"
     $ X147.1 : chr "" "null" "null"
     $ X1....OmQG5e..OUGEr.color..rgba.33 : chr "" "null" "null"
     $ X33.2 : chr "" "null" "null"
     $ X33.3 : chr "" "null" "null"
     $ X1....iwQgFb.background.color..rgba.0 : chr "" "null" "null"
     $ X0 : chr "" "null" "null"
     $ X0.1 : chr "" "0" "null"
     $ X0.150000006....ySLm4c.font.family..Lato : chr "" "v2internal" "null"
     $ sans.serif...CbiMKe.background.color..rgba.30 : chr "" "https://docs.google.com" "null"
     $ X108 : chr "" "null" "null"
     $ X147.2 : chr "" "null" "null"
     $ X1....qeLZfd..zfr3Q.color..rgba.33 : chr "" "null" "null"
     $ X33.4 : chr "" "null" "null"
     $ X33.5 : chr "" "null" "null"
     $ X1....qeLZfd..qnVSj.color..rgba.33 : chr "" "null" "null"
     $ X33.6 : chr "" "https://sites.google.com/new/" "null"
     $ X33.7 : chr "" "null" "null"
     $ X1....qeLZfd..Glwbz.color..rgba.33 : chr "" "null" "null"
     $ X33.8 : chr "" "null" "null"
     $ X33.9 : chr "" "null" "null"
     $ X1....qeLZfd..duRjpb.color..rgba.34 : chr "" "null" "null"
     $ X110.2 : chr "" "0" "null"
     $ X147.3 : chr "" "null" "null"
     $ X1....qeLZfd..qLrapd.color..rgba.34 : chr "" "null" "null"
     $ X110.3 : chr "" "null" "null"
     $ X147.4 : chr "" "null" "null"
     $ X1....qeLZfd..JYVBee.color..rgba.34 : chr "" "null" "null"
     $ X110.4 : chr "" "null" "null"
     $ X147.5 : chr "" "null" "null"
     $ X1....qeLZfd..aHM7ed.color..rgba.34 : chr "" "null" "null"
     $ X110.5 : chr "" "null" "null"
     $ X147.6 : chr "" "null" "null"
     $ X1....qeLZfd..OmQG5e.color..rgba.33 : chr "" "null" "null"
     [list output truncated]
    > mkonfound(d, t, df)
    Error: Can't subset columns that don't exist.
    ✖ Column `t` doesn't exist.
    Backtrace:
     █
     1. └─konfound::mkonfound(d, t, df)
     2. ├─dplyr::pull(select(d, !!t_enquo))
     3. ├─dplyr::select(d, !!t_enquo)
     4. └─dplyr:::select.data.frame(d, !!t_enquo)
     5. └─tidyselect::eval_select(expr(c(...)), .data)
     6. └─tidyselect:::eval_select_impl(...)
     7. ├─tidyselect:::with_subscript_errors(...)
     8. │ ├─base::tryCatch(...)
     9. │ │ └─base:::tryCatchList(expr, classes, parentenv, handlers)
     10. │ │ └─base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
     11. │ │ └─base:::doTryCatch(return(expr), name, parentenv, handler)
     12. │ └─tidyselect:::instrument_base_errors(expr)
     13. │ └─base::withCallingHandlers(...)
     14. └─tidyselect:::vars_select_eval(...)
     15. └─tidyselect:::walk_data_tree(expr, data_mask, context_mask)
     16. └─tidyselect:::eval_c(expr, data_mask, context_mask)
     17. └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
     18. └─tidyselect:::walk_data_tree(new, data_mask, context_mask)
     19. └─tidyselect:::as_indices_sel_impl(...)
     20. └─tidyselect:::as_indices_impl(x, vars, strict = strict)
     21. └─tidyselect:::chr_as_locations(x, vars)
     22. └─vctrs::vec_as_location(x, n = length(vars), names = vars)
     23. └─(function () ...
     24. └─vctrs:::stop_subscript_oob(...)
     25. └─vctrs:::stop_subscript(...)
    Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 0.3.0
Check: examples
Result: ERROR
    Running examples in 'konfound-Ex.R' failed
    The error most likely occurred in:
    
    > ### Name: mkonfound
    > ### Title: Perform meta-analyses including sensitivity analysis
    > ### Aliases: mkonfound
    >
    > ### ** Examples
    >
    > d <- read.csv("https://msu.edu/~kenfrank/example%20dataset%20for%20mkonfound.csv")
    Warning in file(file, "rt") :
     cannot open URL 'https://msu.edu/~kenfrank/example%20dataset%20for%20mkonfound.csv': HTTP status was '308 Permanent Redirect'
    Error in file(file, "rt") : cannot open the connection
    Calls: read.csv -> read.table -> file
    Execution halted
Flavors: r-devel-windows-ix86+x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 0.3.0
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building 'introduction-to-konfound.Rmd' using rmarkdown
    Loading required namespace: forcats
    Note that for a non-linear model, impact threshold should not be interpreted.
    Note that this is only an approximation. For exact results in terms of the number of cases that must be switched from treatment success to treatment failure to invalidate the inference see: https://msu.edu/~kenfrank/non%20linear%20replacement%20treatment.xlsm
    If a dichotomous independent variable is used, consider using the 2X2 table approach enabled with the argument two_by_two = TRUE
    Quitting from lines 204-207 (introduction-to-konfound.Rmd)
    Error: processing vignette 'introduction-to-konfound.Rmd' failed with diagnostics:
    cannot open the connection
    --- failed re-building 'introduction-to-konfound.Rmd'
    
    SUMMARY: processing the following file failed:
     'introduction-to-konfound.Rmd'
    
    Error: Vignette re-building failed.
    Execution halted
Flavors: r-devel-windows-ix86+x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 0.3.0
Check: examples
Result: ERROR
    Running examples in ‘konfound-Ex.R’ failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: mkonfound
    > ### Title: Perform meta-analyses including sensitivity analysis
    > ### Aliases: mkonfound
    >
    > ### ** Examples
    >
    > d <- read.csv("https://msu.edu/~kenfrank/example%20dataset%20for%20mkonfound.csv")
    > d <- d[1:3, ] # this is only so that the example runs more quickly
    > str(d)
    'data.frame': 3 obs. of 906 variables:
     $ X..DOCTYPE.html..html.lang.en.US.itemscope.itemtype.http...schema.org.WebPage..head..meta.charset.utf.8..script.nonce.YAar425u64bdVzQchjeR7g.var.DOCS_timing.....DOCS_timing..sl...new.Date...getTime.....script..script.nonce.YAar425u64bdVzQchjeR7g.function._DumpException.e...throw.e....script..script.nonce.YAar425u64bdVzQchjeR7g._docs_flag_initialData..atari.eiicg.false : chr "]" "" ""
     $ atari.eiitev.false : chr "" "null" "null"
     $ docs.sup. : chr "" "null" "null"
     $ docs.eea.false : chr "" "null" "null"
     $ docs.ecci.false : chr "" "null" "null"
     $ docs.ipmmp.true : chr "" "0" "null"
     $ docs.esi.false : chr "" "null" "null"
     $ docs.liap..logImpressions : chr "" "null" "null"
     $ ilcm..eui.AHKXmL09gslUY0y.Sg2pDVfb0pSqK6sRLG2k4PpcMt3hSuF16OP5dou779Bgb.qlR0YfpbfCWiDo : chr "" "null" "null"
     $ je.1 : chr "" "null" "null"
     $ sstu.1610642056208000 : chr "" "null" "null"
     $ si.CNrD.5ztm.4CFSaUTwkdxK4IvQ : chr "" "null" "null"
     $ gsc.null : chr "" "null" "null"
     $ ei..14101552 : chr "" "null" "null"
     $ X5721004 : chr "" "null" "null"
     $ X5720925 : chr "" "https://drive.google.com" "null"
     $ X5704621 : chr "" "null" "null"
     $ X14101454 : chr "" "null" "null"
     $ X14101254 : chr "" "null" "null"
     $ X5703022 : chr "" "null" "null"
     $ X5713207 : chr "" "null" "null"
     $ X14101514 : chr "" "null" "null"
     $ X5708870 : chr "" "1" "null"
     $ X14101442 : chr "" "1" "null"
     $ X14101538 : chr "" "null" "null"
     $ X5713211 : chr "" "0" "null"
     $ X14101510 : chr "" "1" "null"
     $ X14100834 : chr "" "null" "null"
     $ X5709892 : chr "" "null" "null"
     $ X5715290 : chr "" "null" "null"
     $ X5711808 : chr "" "null" "null"
     $ X5712211 : chr "" "null" "null"
     $ X5711850 : chr "" "null" "null"
     $ X14101502 : chr "" "null" "null"
     $ X14101430 : chr "" "null" "null"
     $ X5714550 : chr "" "null" "null"
     $ X5722301 : chr "" "null" "null"
     $ X5706836 : chr "" "null" "https://www.gstatic.com/atari/embeds/5de913a2354e93acf4d43c4db53928e5/intermediate-frame-minified.html"
     $ X5703839 : chr "" "null" "0"
     $ X5719651 : chr "" "null" "null"
     $ X5720060 : chr "" "null" "v2beta"
     $ X5713049 : chr "" "null" "null"
     $ X5707711 : chr "" "null" "null"
     $ X14101462 : chr "" "null" "null"
     $ X14100854 : chr "" "null" "null"
     $ X5706832 : chr "" "null" "null"
     $ X5714628. : chr "" "null" "null"
     $ crc.0 : chr "" "null" "4"
     $ cvi.... : chr "" "null" "https://accounts.google.com/o/oauth2/iframe"
     $ docs.ccdil.false : chr "" "null" "null"
     $ docs.eil.true : chr "" "null" "null"
     $ docs.eoi.false : chr "" "null" "null"
     $ info_params... : chr "" "null" "null"
     $ docs.enpf.false : chr "" "null" "null"
     $ atari.jefp.._.view.jserror : chr "" "null" "null"
     $ docs.jern.view : chr "" "null" "https://1506463312-atari-embeds.googleusercontent.com/embeds/16cb204cf3a9d4d223a0a3fd8b0eec5d/inner-frame-minified.html"
     $ atari.rhpp.._.view..._docs_flag_cek..null...if..window..DOCS_timing.....DOCS_timing..ifdld...new.Date...getTime......script..meta.name.viewport.content.width.device.width..initial.scale.1..maximum.scale.1.0..user.scalable.no..meta.http.equiv.X.UA.Compatible.content.IE.edge..meta.name.referrer.content.origin..link.rel.icon.href.https...ssl.gstatic.com.atari.images.favicon_2.ico..meta.property.og.type.content.website..meta.property.og.title.content.Ken.Frank.site..meta.itemprop.url.property.og.url.content.https...sites.google.com.msu.edu.kenfrank..meta.itemprop.thumbnailUrl.content.https...ssl.gstatic.com.atari.images.atari.logo.png..meta.itemprop.image.content.https...ssl.gstatic.com.atari.images.atari.logo.png..link.href.https...fonts.googleapis.com.css.family.Lato.3A300.2C300italic.2C400.2C400italic.2C700.2C700italic.display.swap.rel.stylesheet..link.href.https...fonts.googleapis.com.css.family.Google.Sans.400.500.Roboto.300.400.500.700.Source.Code.Pro.400.700.display.swap.rel.stylesheet..style.nonce.YAar425u64bdVzQchjeR7g..media.only.screen.and..max.width..479px...CGqCRe.font.size..27.0pt....media.only.screen.and..min.width..480px..and..max.width..767px...CGqCRe.font.size..32.0pt....media.only.screen.and..min.width..768px..and..max.width..1279px...CGqCRe.font.size..36.0pt....media.only.screen.and..min.width..1280px...CGqCRe.font.size..36.0pt.....style..link.rel.stylesheet.href.https...www.gstatic.com._.atari._.ss.k.atari.vw.TuYBvO8_f2Y.L.X.O.d.1.ct.zgms.rs.AGEqA5nZjyfiuRtO8BcMuTlI35MwWPiqJw..title.itemprop.name.Ken.Frank.site..title..style.jsname.ptDGoc.nonce.YAar425u64bdVzQchjeR7g..M63kCb.background.color..rgba.255 : chr "" "null" "null"
     $ X255 : chr "" "null" "null"
     $ X255.1 : chr "" "null" "null"
     $ X1....OUGEr.color..rgba.33 : chr "" "null" "null"
     $ X33 : chr "" "null" "null"
     $ X33.1 : chr "" "null" "null"
     $ X1....duRjpb..OUGEr.color..rgba.34 : chr "" "null" "null"
     $ X110 : chr "" "null" "null"
     $ X147 : chr "" "null" "null"
     $ X1....JYVBee..OUGEr.color..rgba.34 : chr "" "null" "null"
     $ X110.1 : chr "" "null" "null"
     $ X147.1 : chr "" "null" "null"
     $ X1....OmQG5e..OUGEr.color..rgba.33 : chr "" "null" "null"
     $ X33.2 : chr "" "null" "null"
     $ X33.3 : chr "" "null" "null"
     $ X1....iwQgFb.background.color..rgba.0 : chr "" "null" "null"
     $ X0 : chr "" "0" "null"
     $ X0.1 : chr "" "v2internal" "null"
     $ X0.150000006....ySLm4c.font.family..Lato : chr "" "https://docs.google.com" "null"
     $ sans.serif...CbiMKe.background.color..rgba.30 : chr "" "null" "null"
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     $ X147.2 : chr "" "null" "null"
     $ X1....qeLZfd..zfr3Q.color..rgba.33 : chr "" "null" "null"
     $ X33.4 : chr "" "null" "null"
     $ X33.5 : chr "" "null" "null"
     $ X1....qeLZfd..qnVSj.color..rgba.33 : chr "" "https://sites.google.com/new/" "null"
     $ X33.6 : chr "" "null" "null"
     $ X33.7 : chr "" "null" "null"
     $ X1....qeLZfd..Glwbz.color..rgba.33 : chr "" "null" "null"
     $ X33.8 : chr "" "null" "null"
     $ X33.9 : chr "" "null" "null"
     $ X1....qeLZfd..duRjpb.color..rgba.34 : chr "" "0" "null"
     $ X110.2 : chr "" "null" "null"
     $ X147.3 : chr "" "null" "null"
     $ X1....qeLZfd..qLrapd.color..rgba.34 : chr "" "null" "null"
     $ X110.3 : chr "" "null" "null"
     $ X147.4 : chr "" "null" "null"
     $ X1....qeLZfd..JYVBee.color..rgba.34 : chr "" "null" "null"
     $ X110.4 : chr "" "null" "null"
     $ X147.5 : chr "" "null" "null"
     $ X1....qeLZfd..aHM7ed.color..rgba.34 : chr "" "null" "null"
     $ X110.5 : chr "" "null" "null"
     $ X147.6 : chr "" "null" "null"
     [list output truncated]
    > mkonfound(d, t, df)
    Error: Can't subset columns that don't exist.
    ✖ Column `t` doesn't exist.
    Backtrace:
     █
     1. └─konfound::mkonfound(d, t, df)
     2. ├─dplyr::pull(select(d, !!t_enquo))
     3. ├─dplyr::select(d, !!t_enquo)
     4. └─dplyr:::select.data.frame(d, !!t_enquo)
     5. └─tidyselect::eval_select(expr(c(...)), .data)
     6. └─tidyselect:::eval_select_impl(...)
     7. ├─tidyselect:::with_subscript_errors(...)
     8. │ ├─base::tryCatch(...)
     9. │ │ └─base:::tryCatchList(expr, classes, parentenv, handlers)
     10. │ │ └─base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
     11. │ │ └─base:::doTryCatch(return(expr), name, parentenv, handler)
     12. │ └─tidyselect:::instrument_base_errors(expr)
     13. │ └─base::withCallingHandlers(...)
     14. └─tidyselect:::vars_select_eval(...)
     15. └─tidyselect:::walk_data_tree(expr, data_mask, context_mask)
     16. └─tidyselect:::eval_c(expr, data_mask, context_mask)
     17. └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
     18. └─tidyselect:::walk_data_tree(new, data_mask, context_mask)
     19. └─tidyselect:::as_indices_sel_impl(...)
     20. └─tidyselect:::as_indices_impl(x, vars, strict = strict)
     21. └─tidyselect:::chr_as_locations(x, vars)
     22. └─vctrs::vec_as_location(x, n = length(vars), names = vars)
     23. └─(function () ...
     24. └─vctrs:::stop_subscript_oob(...)
     25. └─vctrs:::stop_subscript(...)
    Execution halted
Flavor: r-patched-linux-x86_64

Version: 0.3.0
Check: examples
Result: ERROR
    Running examples in ‘konfound-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: mkonfound
    > ### Title: Perform meta-analyses including sensitivity analysis
    > ### Aliases: mkonfound
    >
    > ### ** Examples
    >
    > d <- read.csv("https://msu.edu/~kenfrank/example%20dataset%20for%20mkonfound.csv")
    > d <- d[1:3, ] # this is only so that the example runs more quickly
    > str(d)
    'data.frame': 3 obs. of 906 variables:
     $ X..DOCTYPE.html..html.lang.en.US.itemscope.itemtype.http...schema.org.WebPage..head..meta.charset.utf.8..script.nonce.skATzEoYFDPtpba51YjwRg.var.DOCS_timing.....DOCS_timing..sl...new.Date...getTime.....script..script.nonce.skATzEoYFDPtpba51YjwRg.function._DumpException.e...throw.e....script..script.nonce.skATzEoYFDPtpba51YjwRg._docs_flag_initialData..atari.eiicg.false : chr "]" "" ""
     $ atari.eiitev.false : chr "" "null" "null"
     $ docs.sup. : chr "" "null" "null"
     $ docs.eea.false : chr "" "null" "null"
     $ docs.ecci.false : chr "" "null" "null"
     $ docs.ipmmp.true : chr "" "0" "null"
     $ docs.esi.false : chr "" "null" "null"
     $ docs.liap..logImpressions : chr "" "null" "null"
     $ ilcm..eui.AHKXmL1RJNMbPMSa42.3s15tC6S_ti1y05ukQrC.6c6S.dDi60dxCg7QFSVJ.aG0k0j0Bc5FHdRF : chr "" "null" "null"
     $ je.1 : chr "" "null" "null"
     $ sstu.1610751394118000 : chr "" "null" "null"
     $ si.CNnzq8WEn.4CFcYLNwodTDcNFg : chr "" "null" "null"
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     $ ei..14100834 : chr "" "null" "null"
     $ X5711850 : chr "" "null" "null"
     $ X5704621 : chr "" "https://drive.google.com" "null"
     $ X5711808 : chr "" "null" "null"
     $ X14100854 : chr "" "null" "null"
     $ X5719651 : chr "" "null" "null"
     $ X14101430 : chr "" "null" "null"
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     $ X5706832 : chr "" "null" "null"
     $ X5703839 : chr "" "1" "null"
     $ X14101254 : chr "" "1" "null"
     $ X14101514 : chr "" "null" "null"
     $ X14101510 : chr "" "0" "null"
     $ X5707711 : chr "" "1" "null"
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     $ X5722301 : chr "" "null" "null"
     $ X5713211 : chr "" "null" "null"
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     $ X5720060 : chr "" "null" "null"
     $ X14101538 : chr "" "null" "null"
     $ X5714628 : chr "" "null" "null"
     $ X5709892 : chr "" "null" "null"
     $ X5706836 : chr "" "null" "null"
     $ X14101442. : chr "" "null" "null"
     $ crc.0 : chr "" "null" "4"
     $ cvi.... : chr "" "null" "https://accounts.google.com/o/oauth2/iframe"
     $ docs.ccdil.false : chr "" "null" "null"
     $ docs.eil.true : chr "" "null" "null"
     $ docs.eoi.false : chr "" "null" "null"
     $ info_params... : chr "" "null" "null"
     $ docs.enpf.false : chr "" "null" "null"
     $ atari.jefp.._.view.jserror : chr "" "null" "null"
     $ docs.jern.view : chr "" "null" "https://265042616-atari-embeds.googleusercontent.com/embeds/16cb204cf3a9d4d223a0a3fd8b0eec5d/inner-frame-minified.html"
     $ atari.rhpp.._.view..._docs_flag_cek..null...if..window..DOCS_timing.....DOCS_timing..ifdld...new.Date...getTime......script..meta.name.viewport.content.width.device.width..initial.scale.1..maximum.scale.1.0..user.scalable.no..meta.http.equiv.X.UA.Compatible.content.IE.edge..meta.name.referrer.content.origin..link.rel.icon.href.https...ssl.gstatic.com.atari.images.favicon_2.ico..meta.property.og.type.content.website..meta.property.og.title.content.Ken.Frank.site..meta.itemprop.url.property.og.url.content.https...sites.google.com.msu.edu.kenfrank..meta.itemprop.thumbnailUrl.content.https...ssl.gstatic.com.atari.images.atari.logo.png..meta.itemprop.image.content.https...ssl.gstatic.com.atari.images.atari.logo.png..link.href.https...fonts.googleapis.com.css.family.Lato.3A300.2C300italic.2C400.2C400italic.2C700.2C700italic.display.swap.rel.stylesheet..link.href.https...fonts.googleapis.com.css.family.Google.Sans.400.500.Roboto.300.400.500.700.Source.Code.Pro.400.700.display.swap.rel.stylesheet..style.nonce.skATzEoYFDPtpba51YjwRg..media.only.screen.and..max.width..479px...CGqCRe.font.size..27.0pt....media.only.screen.and..min.width..480px..and..max.width..767px...CGqCRe.font.size..32.0pt....media.only.screen.and..min.width..768px..and..max.width..1279px...CGqCRe.font.size..36.0pt....media.only.screen.and..min.width..1280px...CGqCRe.font.size..36.0pt.....style..link.rel.stylesheet.href.https...www.gstatic.com._.atari._.ss.k.atari.vw.TuYBvO8_f2Y.L.X.O.d.1.ct.zgms.rs.AGEqA5nZjyfiuRtO8BcMuTlI35MwWPiqJw..title.itemprop.name.Ken.Frank.site..title..style.jsname.ptDGoc.nonce.skATzEoYFDPtpba51YjwRg..M63kCb.background.color..rgba.255 : chr "" "null" "null"
     $ X255 : chr "" "null" "null"
     $ X255.1 : chr "" "null" "null"
     $ X1....OUGEr.color..rgba.33 : chr "" "null" "null"
     $ X33 : chr "" "null" "null"
     $ X33.1 : chr "" "null" "null"
     $ X1....duRjpb..OUGEr.color..rgba.34 : chr "" "null" "null"
     $ X110 : chr "" "null" "null"
     $ X147 : chr "" "null" "null"
     $ X1....JYVBee..OUGEr.color..rgba.34 : chr "" "null" "null"
     $ X110.1 : chr "" "null" "null"
     $ X147.1 : chr "" "null" "null"
     $ X1....OmQG5e..OUGEr.color..rgba.33 : chr "" "null" "null"
     $ X33.2 : chr "" "null" "null"
     $ X33.3 : chr "" "null" "null"
     $ X1....iwQgFb.background.color..rgba.0 : chr "" "null" "null"
     $ X0 : chr "" "0" "null"
     $ X0.1 : chr "" "v2internal" "null"
     $ X0.150000006....ySLm4c.font.family..Lato : chr "" "https://docs.google.com" "null"
     $ sans.serif...CbiMKe.background.color..rgba.30 : chr "" "null" "null"
     $ X108 : chr "" "null" "null"
     $ X147.2 : chr "" "null" "null"
     $ X1....qeLZfd..zfr3Q.color..rgba.33 : chr "" "null" "null"
     $ X33.4 : chr "" "null" "null"
     $ X33.5 : chr "" "null" "null"
     $ X1....qeLZfd..qnVSj.color..rgba.33 : chr "" "https://sites.google.com/new/" "null"
     $ X33.6 : chr "" "null" "null"
     $ X33.7 : chr "" "null" "null"
     $ X1....qeLZfd..Glwbz.color..rgba.33 : chr "" "null" "null"
     $ X33.8 : chr "" "null" "null"
     $ X33.9 : chr "" "null" "null"
     $ X1....qeLZfd..duRjpb.color..rgba.34 : chr "" "0" "null"
     $ X110.2 : chr "" "null" "null"
     $ X147.3 : chr "" "null" "null"
     $ X1....qeLZfd..qLrapd.color..rgba.34 : chr "" "null" "null"
     $ X110.3 : chr "" "null" "null"
     $ X147.4 : chr "" "null" "null"
     $ X1....qeLZfd..JYVBee.color..rgba.34 : chr "" "null" "null"
     $ X110.4 : chr "" "null" "null"
     $ X147.5 : chr "" "null" "null"
     $ X1....qeLZfd..aHM7ed.color..rgba.34 : chr "" "null" "null"
     $ X110.5 : chr "" "null" "null"
     $ X147.6 : chr "" "null" "null"
     [list output truncated]
    > mkonfound(d, t, df)
    Error: Can't subset columns that don't exist.
    ✖ Column `t` doesn't exist.
    Backtrace:
     █
     1. └─konfound::mkonfound(d, t, df)
     2. ├─dplyr::pull(select(d, !!t_enquo))
     3. ├─dplyr::select(d, !!t_enquo)
     4. └─dplyr:::select.data.frame(d, !!t_enquo)
     5. └─tidyselect::eval_select(expr(c(...)), .data)
     6. └─tidyselect:::eval_select_impl(...)
     7. ├─tidyselect:::with_subscript_errors(...)
     8. │ ├─base::tryCatch(...)
     9. │ │ └─base:::tryCatchList(expr, classes, parentenv, handlers)
     10. │ │ └─base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
     11. │ │ └─base:::doTryCatch(return(expr), name, parentenv, handler)
     12. │ └─tidyselect:::instrument_base_errors(expr)
     13. │ └─base::withCallingHandlers(...)
     14. └─tidyselect:::vars_select_eval(...)
     15. └─tidyselect:::walk_data_tree(expr, data_mask, context_mask)
     16. └─tidyselect:::eval_c(expr, data_mask, context_mask)
     17. └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
     18. └─tidyselect:::walk_data_tree(new, data_mask, context_mask)
     19. └─tidyselect:::as_indices_sel_impl(...)
     20. └─tidyselect:::as_indices_impl(x, vars, strict = strict)
     21. └─tidyselect:::chr_as_locations(x, vars)
     22. └─vctrs::vec_as_location(x, n = length(vars), names = vars)
     23. └─(function () ...
     24. └─vctrs:::stop_subscript_oob(...)
     25. └─vctrs:::stop_subscript(...)
    Execution halted
Flavor: r-patched-solaris-x86

Version: 0.3.0
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building ‘introduction-to-konfound.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    Loading required namespace: forcats
    Note that for a non-linear model, impact threshold should not be interpreted.
    Note that this is only an approximation. For exact results in terms of the number of cases that must be switched from treatment success to treatment failure to invalidate the inference see: https://msu.edu/~kenfrank/non%20linear%20replacement%20treatment.xlsm
    If a dichotomous independent variable is used, consider using the 2X2 table approach enabled with the argument two_by_two = TRUE
    Quitting from lines 204-207 (introduction-to-konfound.Rmd)
    Error: processing vignette 'introduction-to-konfound.Rmd' failed with diagnostics:
    Can't subset columns that don't exist.
    ✖ Column `t` doesn't exist.
    --- failed re-building ‘introduction-to-konfound.Rmd’
    
    SUMMARY: processing the following file failed:
     ‘introduction-to-konfound.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-patched-solaris-x86

Version: 0.3.0
Check: examples
Result: ERROR
    Running examples in ‘konfound-Ex.R’ failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: mkonfound
    > ### Title: Perform meta-analyses including sensitivity analysis
    > ### Aliases: mkonfound
    >
    > ### ** Examples
    >
    > d <- read.csv("https://msu.edu/~kenfrank/example%20dataset%20for%20mkonfound.csv")
    > d <- d[1:3, ] # this is only so that the example runs more quickly
    > str(d)
    'data.frame': 3 obs. of 904 variables:
     $ X..DOCTYPE.html..html.lang.en.US.itemscope.itemtype.http...schema.org.WebPage..head..meta.charset.utf.8..script.nonce.W5dUpeb91nX5SqKdctpNbg.var.DOCS_timing.....DOCS_timing..sl...new.Date...getTime.....script..script.nonce.W5dUpeb91nX5SqKdctpNbg.function._DumpException.e...throw.e....script..script.nonce.W5dUpeb91nX5SqKdctpNbg._docs_flag_initialData..atari.eiicg.false : chr "]" "" ""
     $ atari.eiitev.false : chr "" "null" "null"
     $ docs.sup. : chr "" "null" "null"
     $ docs.eea.false : chr "" "null" "null"
     $ docs.ecci.false : chr "" "null" "null"
     $ docs.ipmmp.true : chr "" "0" "null"
     $ docs.esi.false : chr "" "null" "null"
     $ docs.liap..logImpressions : chr "" "null" "null"
     $ ilcm..eui.AHKXmL3dkcHd1yXSWCyPOeQDOUtcKKrBopQ7nNCDgkp69xHF6ptCNYEbZHwhgGp59KjbuTPzrqcx : chr "" "null" "null"
     $ je.1 : chr "" "null" "null"
     $ sstu.1610757638055000 : chr "" "null" "null"
     $ si.CNjO1.abn.4CFeNDqwIdwU8Jjw : chr "" "null" "null"
     $ gsc.null : chr "" "null" "null"
     $ ei..5721004 : chr "" "null" "null"
     $ X5704621 : chr "" "null" "null"
     $ X14101502 : chr "" "https://drive.google.com" "null"
     $ X14101462 : chr "" "null" "null"
     $ X14101430 : chr "" "null" "null"
     $ X5706836 : chr "" "null" "null"
     $ X5703839 : chr "" "null" "null"
     $ X5719651 : chr "" "null" "null"
     $ X5708870 : chr "" "null" "null"
     $ X14101442 : chr "" "1" "null"
     $ X14101254 : chr "" "1" "null"
     $ X5715290 : chr "" "null" "null"
     $ X14100834 : chr "" "0" "null"
     $ X5713211 : chr "" "1" "null"
     $ X5714550 : chr "" "null" "null"
     $ X5712211 : chr "" "null" "null"
     $ X14101510 : chr "" "null" "null"
     $ X5720925 : chr "" "null" "null"
     $ X5720060 : chr "" "null" "null"
     $ X5703022 : chr "" "null" "null"
     $ X5711808 : chr "" "null" "null"
     $ X14101552 : chr "" "null" "null"
     $ X5706832 : chr "" "null" "null"
     $ X14100854 : chr "" "null" "null"
     $ X5713049 : chr "" "null" "https://www.gstatic.com/atari/embeds/5de913a2354e93acf4d43c4db53928e5/intermediate-frame-minified.html"
     $ X14101538 : chr "" "null" "0"
     $ X5714628 : chr "" "null" "null"
     $ X5711850 : chr "" "null" "v2beta"
     $ X14101454 : chr "" "null" "null"
     $ X14101514 : chr "" "null" "null"
     $ X5713207 : chr "" "null" "null"
     $ X5709892 : chr "" "null" "null"
     $ X5707711. : chr "" "null" "null"
     $ crc.0 : chr "" "null" "null"
     $ cvi.... : chr "" "null" "4"
     $ docs.ccdil.false : chr "" "null" "https://accounts.google.com/o/oauth2/iframe"
     $ docs.eil.true : chr "" "null" "null"
     $ docs.eoi.false : chr "" "null" "null"
     $ info_params... : chr "" "null" "null"
     $ docs.enpf.false : chr "" "null" "null"
     $ atari.jefp.._.view.jserror