CRAN Package Check Results for Package ClinReport

Last updated on 2019-04-18 14:48:43 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.9.1.12 6.63 114.36 120.99 OK
r-devel-linux-x86_64-debian-gcc 0.9.1.12 5.81 101.94 107.75 OK
r-devel-linux-x86_64-fedora-clang 0.9.1.12 127.96 NOTE
r-devel-linux-x86_64-fedora-gcc 0.9.1.12 114.35 NOTE
r-devel-windows-ix86+x86_64 0.9.1.12 22.00 166.00 188.00 OK
r-patched-linux-x86_64 0.9.1.12 6.61 110.44 117.05 OK
r-patched-solaris-x86 0.9.1.12 142.10 WARN
r-release-linux-x86_64 0.9.1.12 5.27 102.81 108.08 OK
r-release-windows-ix86+x86_64 0.9.1.12 11.00 111.00 122.00 OK
r-release-osx-x86_64 0.9.1.12 WARN
r-oldrel-windows-ix86+x86_64 0.9.1.12 18.00 168.00 186.00 ERROR
r-oldrel-osx-x86_64 0.9.1.11 ERROR

Check Details

Version: 0.9.1.12
Check: dependencies in R code
Result: NOTE
    Namespaces in Imports field not imported from:
     ‘emmeans’ ‘utils’
     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-osx-x86_64

Version: 0.9.1.12
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building ‘clinreport_graphics.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.
    
    Attaching package: 'dplyr'
    
    The following object is masked from 'package:ClinReport':
    
     desc
    
    The following objects are masked from 'package:stats':
    
     filter, lag
    
    The following objects are masked from 'package:base':
    
     intersect, setdiff, setequal, union
    
    
    Attaching package: 'nlme'
    
    The following object is masked from 'package:dplyr':
    
     collapse
    
    Loading required package: carData
    
    Attaching package: 'car'
    
    The following object is masked from 'package:dplyr':
    
     recode
    
    --- finished re-building ‘clinreport_graphics.Rmd’
    
    --- re-building ‘clinreport_modify_outputs.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.
    
    Attaching package: 'dplyr'
    
    The following object is masked from 'package:ClinReport':
    
     desc
    
    The following objects are masked from 'package:stats':
    
     filter, lag
    
    The following objects are masked from 'package:base':
    
     intersect, setdiff, setequal, union
    
    
    Attaching package: 'nlme'
    
    The following object is masked from 'package:dplyr':
    
     collapse
    
    Loading required package: carData
    
    Attaching package: 'car'
    
    The following object is masked from 'package:dplyr':
    
     recode
    
    Quitting from lines 60-71 (clinreport_modify_outputs.Rmd)
    Error: processing vignette 'clinreport_modify_outputs.Rmd' failed with diagnostics:
    `render_flextable` needs to be used as a renderer for a knitr/rmarkdown R code chunk (render by rmarkdown)
    --- failed re-building ‘clinreport_modify_outputs.Rmd’
    
    --- re-building ‘clinreport_vignette_get_started.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.
    
    Attaching package: 'dplyr'
    
    The following object is masked from 'package:ClinReport':
    
     desc
    
    The following objects are masked from 'package:stats':
    
     filter, lag
    
    The following objects are masked from 'package:base':
    
     intersect, setdiff, setequal, union
    
    
    Attaching package: 'nlme'
    
    The following object is masked from 'package:dplyr':
    
     collapse
    
    Loading required package: carData
    
    Attaching package: 'car'
    
    The following object is masked from 'package:dplyr':
    
     recode
    
    Quitting from lines 82-84 (clinreport_vignette_get_started.Rmd)
    Error: processing vignette 'clinreport_vignette_get_started.Rmd' failed with diagnostics:
    `render_flextable` needs to be used as a renderer for a knitr/rmarkdown R code chunk (render by rmarkdown)
    --- failed re-building ‘clinreport_vignette_get_started.Rmd’
    
    SUMMARY: processing the following files failed:
     ‘clinreport_modify_outputs.Rmd’ ‘clinreport_vignette_get_started.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-patched-solaris-x86

Version: 0.9.1.12
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
    Fontconfig error: "/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/magick/etc/fonts/conf.d/65-nonlatin.conf", line 6: invalid attribute 'version'
    Fontconfig warning: "/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/magick/etc/fonts/conf.d/65-nonlatin.conf", line 8: unknown element "description"
    Fontconfig warning: "/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/magick/etc/fonts/conf.d/69-unifont.conf", line 4: unknown element "its:rules"
    Fontconfig warning: "/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/magick/etc/fonts/conf.d/69-unifont.conf", line 5: unknown element "its:translateRule"
    Fontconfig error: "/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/magick/etc/fonts/conf.d/69-unifont.conf", line 5: invalid attribute 'translate'
    Fontconfig error: "/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/magick/etc/fonts/conf.d/69-unifont.conf", line 5: invalid attribute 'selector'
    Fontconfig error: "/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/magick/etc/fonts/conf.d/69-unifont.conf", line 6: invalid attribute 'xmlns:its'
    Fontconfig error: "/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/magick/etc/fonts/conf.d/69-unifont.conf", line 6: invalid attribute 'version'
    Fontconfig warning: "/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/magick/etc/fonts/conf.d/80-delicious.conf", line 4: unknown element "its:rules"
    Fontconfig warning: "/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/magick/etc/fonts/conf.d/80-delicious.conf", line 5: unknown element "its:translateRule"
    Fontconfig error: "/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/magick/etc/fonts/conf.d/80-delicious.conf", line 5: invalid attribute 'translate'
    Fontconfig error: "/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/magick/etc/fonts/conf.d/80-delicious.conf", line 5: invalid attribute 'selector'
    Fontconfig error: "/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/magick/etc/fonts/conf.d/80-delicious.conf", line 6: invalid attribute 'xmlns:its'
    Fontconfig error: "/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/magick/etc/fonts/conf.d/80-delicious.conf", line 6: invalid attribute 'version'
    Fontconfig warning: "/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/magick/etc/fonts/conf.d/90-synthetic.conf", line 4: unknown element "its:rules"
    Fontconfig warning: "/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/magick/etc/fonts/conf.d/90-synthetic.conf", line 5: unknown element "its:translateRule"
    Fontconfig error: "/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/magick/etc/fonts/conf.d/90-synthetic.conf", line 5: invalid attribute 'translate'
    Fontconfig error: "/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/magick/etc/fonts/conf.d/90-synthetic.conf", line 5: invalid attribute 'selector'
    Fontconfig error: "/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/magick/etc/fonts/conf.d/90-synthetic.conf", line 6: invalid attribute 'xmlns:its'
    Fontconfig error: "/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/magick/etc/fonts/conf.d/90-synthetic.conf", line 6: invalid attribute 'version'
    Fontconfig error: Cannot load default config file
    Quitting from lines 60-71 (clinreport_modify_outputs.Rmd)
    Error: processing vignette 'clinreport_modify_outputs.Rmd' failed with diagnostics:
    `render_flextable` needs to be used as a renderer for a knitr/rmarkdown R code chunk (render by rmarkdown)
    Execution halted
Flavor: r-release-osx-x86_64

Version: 0.9.1.12
Check: examples
Result: ERROR
    Running examples in 'ClinReport-Ex.R' failed
    The error most likely occurred in:
    
    > ### Name: report.quali
    > ### Title: Descriptive "qualitative" statistics (frequencies and
    > ### percentages) reporting
    > ### Aliases: report.quali
    >
    > ### ** Examples
    >
    >
    >
    > data(data)
    >
    > # No explicative variable changing y labels (option y.levels.label)
    > report.quali(data=data,y="y_logistic",
    + y.label="Clinical cure",y.levels.label="Levels")
     Levels Statistics Clinical cure
    1 0 n (column %) 186(46.97%)
    2 1 n (column %) 200(50.51%)
    3 Missing n(%) 10(2.53%)
    >
    > # 1 explicative variable (option x1: levels in columns)
    > report.quali(data=data,y="y_logistic",x1="GROUP",y.levels.label="Clinical cure")
     Clinical cure Statistics A B C
    1 0 n (column %) 79(43.89%) 60(50.00%) 47(48.96%)
    2 1 n (column %) 97(53.89%) 59(49.17%) 44(45.83%)
    3 Missing n(%) 4(2.22%) 1(0.83%) 5(5.21%)
    >
    > # 2 explicative variables (x1, levels in columns, option x2, levels in rows),
    > # spcacing the results (option at.row)
    > report.quali(data=data,y="y_logistic",x1="GROUP",
    + x2="TIMEPOINT",y.levels.label="Clinical cure",x2.label="Days",at.row="Days")
     Days Clinical cure Statistics A B C
    1 D0 0 n (column %) 11(36.67%) 11(55.00%) 7(43.75%)
    2 D0 1 n (column %) 18(60.00%) 8(40.00%) 7(43.75%)
    3 D0 Missing n(%) 1(3.33%) 1(5.00%) 2(12.50%)
    4
    5 D1 0 n (column %) 7(23.33%) 13(65.00%) 8(50.00%)
    6 D1 1 n (column %) 21(70.00%) 7(35.00%) 7(43.75%)
    7 D1 Missing n(%) 2(6.67%) 0(0%) 1(6.25%)
    8
    9 D2 0 n (column %) 18(60.00%) 7(35.00%) 11(68.75%)
    10 D2 1 n (column %) 12(40.00%) 13(65.00%) 5(31.25%)
    11 D2 Missing n(%) 0(0%) 0(0%) 0(0%)
    12
    13 D3 0 n (column %) 11(36.67%) 10(50.00%) 7(43.75%)
    14 D3 1 n (column %) 19(63.33%) 10(50.00%) 9(56.25%)
    15 D3 Missing n(%) 0(0%) 0(0%) 0(0%)
    16
    17 D4 0 n (column %) 18(60.00%) 12(60.00%) 6(37.50%)
    18 D4 1 n (column %) 12(40.00%) 8(40.00%) 8(50.00%)
    19 D4 Missing n(%) 0(0%) 0(0%) 2(12.50%)
    20
    21 D5 0 n (column %) 14(46.67%) 7(35.00%) 8(50.00%)
    22 D5 1 n (column %) 15(50.00%) 13(65.00%) 8(50.00%)
    23 D5 Missing n(%) 1(3.33%) 0(0%) 0(0%)
    >
    > # 2 explicative variables with row percentages (option percent.col=F)
    > report.quali(data=data,y="y_logistic",x1="GROUP",
    + x2="TIMEPOINT",percent.col=FALSE,x2.label="Days",y.levels.label="Clinical cure")
     Days Clinical cure Statistics A B C
    1 D0 0 n (row %) 11(37.93%) 11(37.93%) 7(24.14%)
    2 D0 1 n (row %) 18(54.55%) 8(24.24%) 7(21.21%)
    3 D0 Missing n(%) 1(25.00%) 1(25.00%) 2(50.00%)
    4 D1 0 n (row %) 7(25.00%) 13(46.43%) 8(28.57%)
    5 D1 1 n (row %) 21(60.00%) 7(20.00%) 7(20.00%)
    6 D1 Missing n(%) 2(66.67%) 0(0%) 1(33.33%)
    7 D2 0 n (row %) 18(50.00%) 7(19.44%) 11(30.56%)
    8 D2 1 n (row %) 12(40.00%) 13(43.33%) 5(16.67%)
    9 D2 Missing n(%) 0 0 0
    10 D3 0 n (row %) 11(39.29%) 10(35.71%) 7(25.00%)
    11 D3 1 n (row %) 19(50.00%) 10(26.32%) 9(23.68%)
    12 D3 Missing n(%) 0 0 0
    13 D4 0 n (row %) 18(50.00%) 12(33.33%) 6(16.67%)
    14 D4 1 n (row %) 12(42.86%) 8(28.57%) 8(28.57%)
    15 D4 Missing n(%) 0(0%) 0(0%) 2(100.00%)
    16 D5 0 n (row %) 14(48.28%) 7(24.14%) 8(27.59%)
    17 D5 1 n (row %) 15(41.67%) 13(36.11%) 8(22.22%)
    18 D5 Missing n(%) 1(100.00%) 0(0%) 0(0%)
    >
    > # Add Total number of subjects in headers (option subjid="SUBJID")
    > report.quali(data=data,y="y_logistic",x1="GROUP",
    + x2="TIMEPOINT",at.row="TIMEPOINT",subjid="SUBJID")
     TIMEPOINT Levels Statistics A (N=30) B (N=21) C (N=17)
    1 D0 0 n (column %) 11(36.67%) 11(55.00%) 7(43.75%)
    2 D0 1 n (column %) 18(60.00%) 8(40.00%) 7(43.75%)
    3 D0 Missing n(%) 1(3.33%) 1(5.00%) 2(12.50%)
    4
    5 D1 0 n (column %) 7(23.33%) 13(65.00%) 8(50.00%)
    6 D1 1 n (column %) 21(70.00%) 7(35.00%) 7(43.75%)
    7 D1 Missing n(%) 2(6.67%) 0(0%) 1(6.25%)
    8
    9 D2 0 n (column %) 18(60.00%) 7(35.00%) 11(68.75%)
    10 D2 1 n (column %) 12(40.00%) 13(65.00%) 5(31.25%)
    11 D2 Missing n(%) 0(0%) 0(0%) 0(0%)
    12
    13 D3 0 n (column %) 11(36.67%) 10(50.00%) 7(43.75%)
    14 D3 1 n (column %) 19(63.33%) 10(50.00%) 9(56.25%)
    15 D3 Missing n(%) 0(0%) 0(0%) 0(0%)
    16
    17 D4 0 n (column %) 18(60.00%) 12(60.00%) 6(37.50%)
    18 D4 1 n (column %) 12(40.00%) 8(40.00%) 8(50.00%)
    19 D4 Missing n(%) 0(0%) 0(0%) 2(12.50%)
    20
    21 D5 0 n (column %) 14(46.67%) 7(35.00%) 8(50.00%)
    22 D5 1 n (column %) 15(50.00%) 13(65.00%) 8(50.00%)
    23 D5 Missing n(%) 1(3.33%) 0(0%) 0(0%)
    >
    > # Round percentages to 1 digit (option round=1)
    > report.quali(data=data,y="y_logistic",x1="GROUP",
    + x2="TIMEPOINT",at.row="TIMEPOINT",subjid="SUBJID",round=1)
     TIMEPOINT Levels Statistics A (N=30) B (N=21) C (N=17)
    1 D0 0 n (column %) 11(36.7%) 11(55.0%) 7(43.8%)
    2 D0 1 n (column %) 18(60.0%) 8(40.0%) 7(43.8%)
    3 D0 Missing n(%) 1(3.3%) 1(5.0%) 2(12.5%)
    4
    5 D1 0 n (column %) 7(23.3%) 13(65.0%) 8(50.0%)
    6 D1 1 n (column %) 21(70.0%) 7(35.0%) 7(43.8%)
    7 D1 Missing n(%) 2(6.7%) 0(0.0%) 1(6.2%)
    8
    9 D2 0 n (column %) 18(60.0%) 7(35.0%) 11(68.8%)
    10 D2 1 n (column %) 12(40.0%) 13(65.0%) 5(31.2%)
    11 D2 Missing n(%) 0(0.0%) 0(0.0%) 0(0.0%)
    12
    13 D3 0 n (column %) 11(36.7%) 10(50.0%) 7(43.8%)
    14 D3 1 n (column %) 19(63.3%) 10(50.0%) 9(56.2%)
    15 D3 Missing n(%) 0(0.0%) 0(0.0%) 0(0.0%)
    16
    17 D4 0 n (column %) 18(60.0%) 12(60.0%) 6(37.5%)
    18 D4 1 n (column %) 12(40.0%) 8(40.0%) 8(50.0%)
    19 D4 Missing n(%) 0(0.0%) 0(0.0%) 2(12.5%)
    20
    21 D5 0 n (column %) 14(46.7%) 7(35.0%) 8(50.0%)
    22 D5 1 n (column %) 15(50.0%) 13(65.0%) 8(50.0%)
    23 D5 Missing n(%) 1(3.3%) 0(0.0%) 0(0.0%)
    >
    >
    > # Qualitative statistics with a response with more than one levels
    > tab=report.quali(data=data,y="y_poisson",x1="GROUP",
    + x2="TIMEPOINT",at.row="TIMEPOINT",subjid="SUBJID",round=1)
    data[,'y_poisson']has been transformed into a factor
    Error in sort.list(y) : 'x' must be atomic for 'sort.list'
    Have you called 'sort' on a list?
    Calls: report.quali -> check.x -> as.factor -> factor -> sort.list
    Execution halted
Flavor: r-oldrel-windows-ix86+x86_64

Version: 0.9.1.11
Check: dependencies in R code
Result: NOTE
    Namespaces in Imports field not imported from:
     ‘emmeans’ ‘utils’
     All declared Imports should be used.
Flavor: r-oldrel-osx-x86_64

Version: 0.9.1.11
Check: examples
Result: ERROR
    Running examples in ‘ClinReport-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: report.quali
    > ### Title: Descriptive "qualitative" statistics (frequencies and
    > ### percentages) reporting
    > ### Aliases: report.quali
    >
    > ### ** Examples
    >
    >
    >
    > data(data)
    >
    > # No explicative variable changing y labels (option y.levels.label)
    > report.quali(data=data,y="y_logistic",
    + y.label="Clinical cure",y.levels.label="Levels")
     Levels Statistics Clinical cure
    1 0 n (column %) 186(46.97%)
    2 1 n (column %) 200(50.51%)
    3 Missing n(%) 10(2.53%)
    >
    > # 1 explicative variable (option x1: levels in columns)
    > report.quali(data=data,y="y_logistic",x1="GROUP",y.levels.label="Clinical cure")
     Clinical cure Statistics A B C
    1 0 n (column %) 79(43.89%) 60(50.00%) 47(48.96%)
    2 1 n (column %) 97(53.89%) 59(49.17%) 44(45.83%)
    3 Missing n(%) 4(2.22%) 1(0.83%) 5(5.21%)
    >
    > # 2 explicative variables (x1, levels in columns, option x2, levels in rows),
    > # spcacing the results (option at.row)
    > report.quali(data=data,y="y_logistic",x1="GROUP",
    + x2="TIMEPOINT",y.levels.label="Clinical cure",x2.label="Days",at.row="Days")
     Days Clinical cure Statistics A B C
    1 D0 0 n (column %) 11(36.67%) 11(55.00%) 7(43.75%)
    2 D0 1 n (column %) 18(60.00%) 8(40.00%) 7(43.75%)
    3 D0 Missing n(%) 1(3.33%) 1(5.00%) 2(12.50%)
    4
    5 D1 0 n (column %) 7(23.33%) 13(65.00%) 8(50.00%)
    6 D1 1 n (column %) 21(70.00%) 7(35.00%) 7(43.75%)
    7 D1 Missing n(%) 2(6.67%) 0(0%) 1(6.25%)
    8
    9 D2 0 n (column %) 18(60.00%) 7(35.00%) 11(68.75%)
    10 D2 1 n (column %) 12(40.00%) 13(65.00%) 5(31.25%)
    11 D2 Missing n(%) 0(0%) 0(0%) 0(0%)
    12
    13 D3 0 n (column %) 11(36.67%) 10(50.00%) 7(43.75%)
    14 D3 1 n (column %) 19(63.33%) 10(50.00%) 9(56.25%)
    15 D3 Missing n(%) 0(0%) 0(0%) 0(0%)
    16
    17 D4 0 n (column %) 18(60.00%) 12(60.00%) 6(37.50%)
    18 D4 1 n (column %) 12(40.00%) 8(40.00%) 8(50.00%)
    19 D4 Missing n(%) 0(0%) 0(0%) 2(12.50%)
    20
    21 D5 0 n (column %) 14(46.67%) 7(35.00%) 8(50.00%)
    22 D5 1 n (column %) 15(50.00%) 13(65.00%) 8(50.00%)
    23 D5 Missing n(%) 1(3.33%) 0(0%) 0(0%)
    >
    > # 2 explicative variables with row percentages (option percent.col=F)
    > report.quali(data=data,y="y_logistic",x1="GROUP",
    + x2="TIMEPOINT",percent.col=FALSE,x2.label="Days",y.levels.label="Clinical cure")
     Days Clinical cure Statistics A B C
    1 D0 0 n (row %) 11(37.93%) 11(37.93%) 7(24.14%)
    2 D0 1 n (row %) 18(54.55%) 8(24.24%) 7(21.21%)
    3 D0 Missing n(%) 1(25.00%) 1(25.00%) 2(50.00%)
    4 D1 0 n (row %) 7(25.00%) 13(46.43%) 8(28.57%)
    5 D1 1 n (row %) 21(60.00%) 7(20.00%) 7(20.00%)
    6 D1 Missing n(%) 2(66.67%) 0(0%) 1(33.33%)
    7 D2 0 n (row %) 18(50.00%) 7(19.44%) 11(30.56%)
    8 D2 1 n (row %) 12(40.00%) 13(43.33%) 5(16.67%)
    9 D2 Missing n(%) 0 0 0
    10 D3 0 n (row %) 11(39.29%) 10(35.71%) 7(25.00%)
    11 D3 1 n (row %) 19(50.00%) 10(26.32%) 9(23.68%)
    12 D3 Missing n(%) 0 0 0
    13 D4 0 n (row %) 18(50.00%) 12(33.33%) 6(16.67%)
    14 D4 1 n (row %) 12(42.86%) 8(28.57%) 8(28.57%)
    15 D4 Missing n(%) 0(0%) 0(0%) 2(100.00%)
    16 D5 0 n (row %) 14(48.28%) 7(24.14%) 8(27.59%)
    17 D5 1 n (row %) 15(41.67%) 13(36.11%) 8(22.22%)
    18 D5 Missing n(%) 1(100.00%) 0(0%) 0(0%)
    >
    > # Add Total number of subjects in headers (option subjid="SUBJID")
    > report.quali(data=data,y="y_logistic",x1="GROUP",
    + x2="TIMEPOINT",at.row="TIMEPOINT",subjid="SUBJID")
     TIMEPOINT Levels Statistics A (N=30) B (N=21) C (N=17)
    1 D0 0 n (column %) 11(36.67%) 11(55.00%) 7(43.75%)
    2 D0 1 n (column %) 18(60.00%) 8(40.00%) 7(43.75%)
    3 D0 Missing n(%) 1(3.33%) 1(5.00%) 2(12.50%)
    4
    5 D1 0 n (column %) 7(23.33%) 13(65.00%) 8(50.00%)
    6 D1 1 n (column %) 21(70.00%) 7(35.00%) 7(43.75%)
    7 D1 Missing n(%) 2(6.67%) 0(0%) 1(6.25%)
    8
    9 D2 0 n (column %) 18(60.00%) 7(35.00%) 11(68.75%)
    10 D2 1 n (column %) 12(40.00%) 13(65.00%) 5(31.25%)
    11 D2 Missing n(%) 0(0%) 0(0%) 0(0%)
    12
    13 D3 0 n (column %) 11(36.67%) 10(50.00%) 7(43.75%)
    14 D3 1 n (column %) 19(63.33%) 10(50.00%) 9(56.25%)
    15 D3 Missing n(%) 0(0%) 0(0%) 0(0%)
    16
    17 D4 0 n (column %) 18(60.00%) 12(60.00%) 6(37.50%)
    18 D4 1 n (column %) 12(40.00%) 8(40.00%) 8(50.00%)
    19 D4 Missing n(%) 0(0%) 0(0%) 2(12.50%)
    20
    21 D5 0 n (column %) 14(46.67%) 7(35.00%) 8(50.00%)
    22 D5 1 n (column %) 15(50.00%) 13(65.00%) 8(50.00%)
    23 D5 Missing n(%) 1(3.33%) 0(0%) 0(0%)
    >
    > # Round percentages to 1 digit (option round=1)
    > report.quali(data=data,y="y_logistic",x1="GROUP",
    + x2="TIMEPOINT",at.row="TIMEPOINT",subjid="SUBJID",round=1)
     TIMEPOINT Levels Statistics A (N=30) B (N=21) C (N=17)
    1 D0 0 n (column %) 11(36.7%) 11(55.0%) 7(43.8%)
    2 D0 1 n (column %) 18(60.0%) 8(40.0%) 7(43.8%)
    3 D0 Missing n(%) 1(3.3%) 1(5.0%) 2(12.5%)
    4
    5 D1 0 n (column %) 7(23.3%) 13(65.0%) 8(50.0%)
    6 D1 1 n (column %) 21(70.0%) 7(35.0%) 7(43.8%)
    7 D1 Missing n(%) 2(6.7%) 0(0.0%) 1(6.2%)
    8
    9 D2 0 n (column %) 18(60.0%) 7(35.0%) 11(68.8%)
    10 D2 1 n (column %) 12(40.0%) 13(65.0%) 5(31.2%)
    11 D2 Missing n(%) 0(0.0%) 0(0.0%) 0(0.0%)
    12
    13 D3 0 n (column %) 11(36.7%) 10(50.0%) 7(43.8%)
    14 D3 1 n (column %) 19(63.3%) 10(50.0%) 9(56.2%)
    15 D3 Missing n(%) 0(0.0%) 0(0.0%) 0(0.0%)
    16
    17 D4 0 n (column %) 18(60.0%) 12(60.0%) 6(37.5%)
    18 D4 1 n (column %) 12(40.0%) 8(40.0%) 8(50.0%)
    19 D4 Missing n(%) 0(0.0%) 0(0.0%) 2(12.5%)
    20
    21 D5 0 n (column %) 14(46.7%) 7(35.0%) 8(50.0%)
    22 D5 1 n (column %) 15(50.0%) 13(65.0%) 8(50.0%)
    23 D5 Missing n(%) 1(3.3%) 0(0.0%) 0(0.0%)
    >
    >
    > # Qualitative statistics with a response with more than one levels
    > tab=report.quali(data=data,y="y_poisson",x1="GROUP",
    + x2="TIMEPOINT",at.row="TIMEPOINT",subjid="SUBJID",round=1)
    data[,'y_poisson']has been transformed into a factor
    Error in sort.list(y) : 'x' must be atomic for 'sort.list'
    Have you called 'sort' on a list?
    Calls: report.quali -> check.x -> as.factor -> factor -> sort.list
    Execution halted
Flavor: r-oldrel-osx-x86_64

Version: 0.9.1.11
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
    Fontconfig error: "/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.4/magick/etc/fonts/conf.d/65-nonlatin.conf", line 6: invalid attribute 'version'
    Fontconfig warning: "/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.4/magick/etc/fonts/conf.d/65-nonlatin.conf", line 8: unknown element "description"
    Fontconfig warning: "/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.4/magick/etc/fonts/conf.d/69-unifont.conf", line 4: unknown element "its:rules"
    Fontconfig warning: "/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.4/magick/etc/fonts/conf.d/69-unifont.conf", line 5: unknown element "its:translateRule"
    Fontconfig error: "/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.4/magick/etc/fonts/conf.d/69-unifont.conf", line 5: invalid attribute 'translate'
    Fontconfig error: "/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.4/magick/etc/fonts/conf.d/69-unifont.conf", line 5: invalid attribute 'selector'
    Fontconfig error: "/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.4/magick/etc/fonts/conf.d/69-unifont.conf", line 6: invalid attribute 'xmlns:its'
    Fontconfig error: "/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.4/magick/etc/fonts/conf.d/69-unifont.conf", line 6: invalid attribute 'version'
    Fontconfig warning: "/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.4/magick/etc/fonts/conf.d/80-delicious.conf", line 4: unknown element "its:rules"
    Fontconfig warning: "/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.4/magick/etc/fonts/conf.d/80-delicious.conf", line 5: unknown element "its:translateRule"
    Fontconfig error: "/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.4/magick/etc/fonts/conf.d/80-delicious.conf", line 5: invalid attribute 'translate'
    Fontconfig error: "/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.4/magick/etc/fonts/conf.d/80-delicious.conf", line 5: invalid attribute 'selector'
    Fontconfig error: "/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.4/magick/etc/fonts/conf.d/80-delicious.conf", line 6: invalid attribute 'xmlns:its'
    Fontconfig error: "/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.4/magick/etc/fonts/conf.d/80-delicious.conf", line 6: invalid attribute 'version'
    Fontconfig warning: "/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.4/magick/etc/fonts/conf.d/90-synthetic.conf", line 4: unknown element "its:rules"
    Fontconfig warning: "/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.4/magick/etc/fonts/conf.d/90-synthetic.conf", line 5: unknown element "its:translateRule"
    Fontconfig error: "/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.4/magick/etc/fonts/conf.d/90-synthetic.conf", line 5: invalid attribute 'translate'
    Fontconfig error: "/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.4/magick/etc/fonts/conf.d/90-synthetic.conf", line 5: invalid attribute 'selector'
    Fontconfig error: "/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.4/magick/etc/fonts/conf.d/90-synthetic.conf", line 6: invalid attribute 'xmlns:its'
    Fontconfig error: "/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.4/magick/etc/fonts/conf.d/90-synthetic.conf", line 6: invalid attribute 'version'
    Fontconfig error: Cannot load default config file
    Quitting from lines 60-71 (clinreport_modify_outputs.Rmd)
    Error: processing vignette 'clinreport_modify_outputs.Rmd' failed with diagnostics:
    `render_flextable` needs to be used as a renderer for a knitr/rmarkdown R code chunk (render by rmarkdown)
    Execution halted
Flavor: r-oldrel-osx-x86_64