* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/ClinReport.Rcheck’
* using R Under development (unstable) (2020-03-29 r78100)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘ClinReport/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ClinReport’ version ‘0.9.1.14’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ClinReport’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
  ‘car’ ‘emmeans’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [11s/11s] OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘ClinReport-Ex.R’ failed
The error most likely occurred in:

> ### Name: report.quali.hlev
> ### Title: 'Hierarchical Qualitative' statistics reporting (experimental)
> ### Aliases: report.quali.hlev
> 
> ### ** Examples
> 
> 
> data(adverse_event)
> 
> test=report.quali.hlev(data=adverse_event,subjid="SUBJID",var_upper="PTNAME",
+ var_lower="SOCNAME",lower.levels="System Organ Class",upper.levels="Prefered Terms",x1="randtrt")
Error in match.names(clabs, names(xi)) : 
  names do not match previous names
Calls: report.quali.hlev -> report.quali.hlev -> rbind -> rbind -> match.names
Execution halted
* checking examples with --run-donttest ... ERROR
Running examples in ‘ClinReport-Ex.R’ failed
The error most likely occurred in:

> ### Name: report.doc
> ### Title: Export a statistical table into a 'Microsoft Word' or a R
> ###   markdown document
> ### Aliases: report.doc report.doc.desc report.doc.anova
> ###   report.doc.anova.lme
> 
> ### ** Examples
> 
> ## Don't show: 
> 
> 
> library(officer)
> library(flextable)
> library(reshape2)
> library(emmeans)
> library(lme4)
Loading required package: Matrix
> library(nlme)

Attaching package: ‘nlme’

The following object is masked from ‘package:lme4’:

    lmList

> 
> data(datafake)
> 
> tab=report.quanti(data=datafake,y="y_numeric",
+ 	x1="GROUP",x2="TIMEPOINT",at.row="TIMEPOINT",subjid="SUBJID")
> 
> mod=glm(y_logistic~GROUP+TIMEPOINT+GROUP*TIMEPOINT,
+ family=binomial,data=datafake,na.action=na.omit)
> 
> test=emmeans(mod,~GROUP|TIMEPOINT)
> 
> tab.mod=report.lsmeans(lsm=test)
> 
> 
> doc=read_docx()
> 
> doc=body_add_par(doc,"A statistical report using ClinReport", style = "heading 1")
> 
> doc=report.doc(tab,title="Quantitative statistics",
+ 	colspan.value="Treatment group",doc=doc,init.numbering=TRUE)
> 
> 
> doc=report.doc(tab.mod,title="Generalized Linear Mixed Model LS-Means results using lme",
+ 	colspan.value="Treatment group",doc=doc)
> 
> ## End(Don't show)
> 
> 
> ## No test: 
> 
> #####################
> # Import libraries
> #####################
> 
> library(officer)
> library(flextable)
> library(reshape2)
> library(emmeans)
> library(lme4)
> library(nlme)
> library(ggplot2)
> library(car) 
Loading required package: carData
> library(xtable)

Attaching package: ‘xtable’

The following objects are masked from ‘package:flextable’:

    align, display

> 
> #####################
> # Load data
> #####################
> 
> data(datafake) 
> head(datafake)
   y_numeric y_logistic y_poisson   baseline   VAR GROUP TIMEPOINT SUBJID
1 -0.4203490          1         5 -0.4203490 Cat 1     A        D0 Subj 1
2 -0.1570941          1         5 -0.1570941 Cat 2     A        D0 Subj 1
3         NA          0         3 -2.0853720 Cat 2     A        D0 Subj 1
4 -0.4728527          0         5 -0.4728527 Cat 1     A        D0 Subj 1
5 -0.8651713          1         4 -0.8651713 Cat 1     A        D0 Subj 1
6 -1.5476907          1         3 -1.5476907 Cat 1     A        D0 Subj 1
> 
> # Removing baseline data for the model
> 
> data.mod=droplevels(datafake[datafake$TIMEPOINT!="D0",])
> 
> #####################
> # Create your stats tables and graphics
> #####################
> 
> # Quatitative stats (2 explicative variables) ##################################
> # since it's a big enough table, we don't want it to overlap 2 pasges
> # so we split it in two with split.desc function
> 
> tab1=report.quanti(data=datafake,y="y_numeric",
+ 	x1="GROUP",x2="TIMEPOINT",at.row="TIMEPOINT",subjid="SUBJID")
> 
> 
> s=split(tab1,variable="TIMEPOINT",at=3)
> 
> tab1.1=s$x1
> tab1.2=s$x2
> 
> 
> gg=plot(tab1,title="Mean response evolution as a function of time by treatment group",
+ legend.label="Treatment groups",ylab="Y mean")
> 
> # Qualitative stats (2 explicative variables) ##################################
> 
> tab2=report.quali(data=datafake,y="y_logistic",
+ 	x1="GROUP",x2="TIMEPOINT",at.row="TIMEPOINT",total=TRUE,subjid="SUBJID")
> 
> gg2=plot(tab2,title="Response distribution (%) by day and treatment group",
+ legend.label="Y levels")
> 
> # Qualitative stats (no explicative variable)  ###################################
> 
> tab3=report.quali(data=datafake,y="VAR",y.label="Whatever")
> 
> # Qualitative stats (no explicative variables ; add number of subjects in header)#
> 
> tab4=report.quali(data=datafake,y="VAR",y.label="Whatever",
+ 	subjid="SUBJID")
> 
> # Qualitative stats (1 explicative variable)#######################################
> 
> tab5=report.quali(data=datafake,y="VAR",y.label="Whatever",x1="GROUP",
+ 	subjid="SUBJID")
> 
> 
> # Quantitative stats (1 explicative variable)#######################################
> 
> tab6=report.quanti(data=datafake,y="y_numeric",y.label="Whatever 2",x1="GROUP",
+ 	subjid="SUBJID")
> 
> # Quali-Quanti table
> 
> tab5.6=regroup(tab5,tab6)
> 
> 
> # Linear model (order 2 interaction): Anova and LS-Means reporting ################
> 
> mod1=lm(y_numeric~baseline+GROUP+TIMEPOINT+GROUP*TIMEPOINT,data=data.mod)
> test1=emmeans(mod1,~GROUP|TIMEPOINT)
> 
> anov1=Anova(mod1)
> 
> tab.mod1=report.lsmeans(lsm=test1)
> 
> gg.mod1=plot(tab.mod1,title="LS-Means response evolution as a function of time\n
+ by treatment group (95% CI)",
+ legend.label="Treatment groups",ylab="Y mean",add.ci=TRUE)
> 
> # Linear model (1 group only): Anova and LS-Means and graph reporting ################
> 
> mod2=lm(y_numeric~baseline+GROUP,data=data.mod)
> 
> anov2=Anova(mod2,type=3)
> 
> test2=emmeans(mod2,~GROUP)
> tab.mod2=report.lsmeans(lsm=test2)
> 
> 
> gg.mod2=plot(tab.mod2,title="LS-Means response\nby treatment group (95% CI)",
+ 	legend.label="Treatment groups",ylab="Y mean",add.ci=TRUE)
> 
> # Linear mixed model (order 2 interaction):
> # Anova and LS-Means and graph reporting #################
> 
> mod3=lme(y_numeric~baseline+GROUP+TIMEPOINT+GROUP*TIMEPOINT,
+ random=~1|SUBJID,data=data.mod,na.action=na.omit)
> 
> anov3=Anova(mod3,3)
> 
> test3=emmeans(mod3,~GROUP|TIMEPOINT)
> 
> tab.mod3=report.lsmeans(lsm=test3)
> 
> gg.mod3=plot(tab.mod3,title="LS-Means response evolution as a function of time\n
+ by treatment group (95% CI Mixed model)",
+ 	legend.label="Treatment groups",ylab="Y mean",add.ci=TRUE)
> 
> # Contrast example
> 
> contr=contrast(test3, "trt.vs.ctrl", ref = "A")
> 
> tab.mod3.contr=report.lsmeans(lsm=contr)
> 
> gg.mod3.contr=plot(tab.mod3.contr,title="LS-Means contrast versus reference A\n
+ 			(95% CI Mixed model)",
+ 	legend.label="Treatment groups",ylab="Y mean",add.ci=TRUE,add.line=FALSE)
> 
> 
> ############################################################
> # Generalized Logistic Linear model (order 2 interaction):
> ############################################################
> 
> # Anova LS-Means and graph reporting ##########
> 
> mod4=glm(y_logistic~baseline+GROUP+TIMEPOINT+GROUP*TIMEPOINT,
+ family=binomial,data=data.mod,na.action=na.omit)
> 
> anov4=Anova(mod4,3)
> 
> test4=emmeans(mod4,~GROUP|TIMEPOINT)
> 
> tab.mod4=report.lsmeans(lsm=test4,at.row="TIMEPOINT")
> 
> gg.mod4=plot(tab.mod4,title="LS-Means response evolution as a function of time\n
+ by treatment group (95% CI Logistic model)",
+ 	legend.label="Treatment groups",ylab="Y mean",add.ci=TRUE)
> 
> # Generalized Poisson Linear model (order 2 interaction):
> # Anova LS-Means and graph reporting #'
> 
> 
> mod5=glm(y_poisson~baseline+GROUP+TIMEPOINT+GROUP*TIMEPOINT,
+ family=poisson,data=data.mod,na.action=na.omit)
> 
> anov5=Anova(mod5,3)
> 
> 
> test5=emmeans(mod5,~GROUP|TIMEPOINT)
> 
> tab.mod5=report.lsmeans(lsm=test5,at.row="TIMEPOINT")
> 
> 
> gg.mod5=plot(tab.mod5,title="LS-Means response evolution as a function of time\n
+ by treatment group (95% CI Poisson model)",
+ 	legend.label="Treatment groups",ylab="Y mean",add.ci=TRUE)
> 
> #####################
> # Create your report
> #####################
> 
> 
> doc=read_docx()
> doc=body_add_toc(doc)
> 
> 
> doc=body_add_par(doc,"A beautiful reporting using ClinReport", style = "heading 1")
> 
> doc=body_add_par(doc,"Descriptive statistics", style = "heading 2")
> 
> doc=report.doc(tab1.1,title="Quantitative statistics (2 explicative variables) (Table 1/2)",
+ 	colspan.value="Treatment group",doc=doc,init.numbering=TRUE,
+ page.break=FALSE)
> 
> doc=report.doc(tab1.2,title="Quantitative statistics (2 explicative variables) (Table 2/2)",
+ 	colspan.value="Treatment group",doc=doc)
> 
> doc=body_add_par(doc,"Corresponding graphic of outputs 1 & 2", style ="Normal") 
> 
> doc=body_add_gg(doc, value = gg, style = "centered" )
> 
> doc=body_add_break(doc)
> 
> doc=report.doc(tab2,title="Qualitative statistics (2 explicative variables)",
+ 	colspan.value="Treatment group",doc=doc)
> 
> 
> doc=report.doc(tab2,title="The same with smaller font size",
+ 	colspan.value="Treatment group",doc=doc,font.size=8)
> 
> doc=body_add_par(doc,"Corresponding graphic of output 3", style ="Normal") 
> 
> doc=body_add_gg(doc, value = gg2, style = "centered" )
> 
> doc=body_add_break(doc)
> 
> doc=body_add_par(doc,"Example of mixing qualitative and quantitative
+ statistics with the function regroup", style ="Normal") 
> 
> doc=report.doc(tab5.6,title="Quali-Qanti statistics (1 variable only)",doc=doc)
> 
> doc=body_add_par(doc,"Statistical model results", style = "heading 2")
> 
> doc=body_add_par(doc,"Model 1", style = "heading 3")
> 
> doc=body_add_par(doc,"Anova table example", style = "Normal")
> 
> doc=report.doc(anov1,doc=doc)
> 
> doc=body_add_par(doc,"LS-Means example", style = "Normal")
> 
> doc=report.doc(tab.mod1,title="Linear Model LS-Means results using lm with interactions",
+ 	colspan.value="Treatment group",doc=doc)
> 
> doc=body_add_gg(doc, value = gg.mod1, style = "centered" )
> 
> doc=body_add_break(doc)
> 
> 
> doc=body_add_par(doc,"Model 2", style = "heading 3")
> 
> 
> doc=report.doc(anov2,doc=doc)
> 
> 
> doc=report.doc(tab.mod2,title="Linear Model LS-Means results using lm without interaction",
+ 	colspan.value="Treatment group",doc=doc)
> 
> doc=body_add_gg(doc, value = gg.mod2, style = "centered" )
> 
> doc=body_add_break(doc)
> 
> 
> doc=body_add_par(doc,"Model 3", style = "heading 3")
> 
> doc=report.doc(anov3,doc=doc)
> 
> 
> doc=report.doc(tab.mod3,title="Linear Mixed Model LS-Means results using lme",
+ 	colspan.value="Treatment group",doc=doc)
> 
> doc=body_add_gg(doc, value = gg.mod3, style = "centered" )
> 
> doc=body_add_break(doc)
> 
> 
> doc=report.doc(tab.mod3.contr,title="LS-Means Contrast example",
+ 	colspan.value="Timepoints",doc=doc)
> 
> doc=body_add_gg(doc, value = gg.mod3.contr, style = "centered" )
> 
> doc=body_add_break(doc)
> 
> 
> 
> 
> doc=body_add_par(doc,"Model 4", style = "heading 3")
> 
> doc=report.doc(anov4,doc=doc)
> 
> 
> doc=report.doc(tab.mod4,title="Generalized Linear Mixed Model LS-Means results using glm",
+ 	colspan.value="Treatment group",doc=doc)
> 
> doc=body_add_gg(doc, value = gg.mod4, style = "centered" )
> 
> doc=body_add_break(doc)
> 
> 
> doc=body_add_par(doc,"Model 5", style = "heading 3")
> 
> doc=report.doc(anov5,doc=doc)
> 
> doc=report.doc(tab.mod5,title="Poisson Model LS-Means results",
+ 	colspan.value="Treatment group",doc=doc)
> 
> doc=body_add_gg(doc, value = gg.mod5, style = "centered" )
> 
> 
> 
> file=paste(tempfile(),".docx",sep="")
> print(doc, target =file)
> shell.exec(file)
Error in shell.exec(file) : could not find function "shell.exec"
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking re-building of vignette outputs ... [21s/20s] WARNING
Error(s) in re-building vignettes:
  ...
--- re-building ‘clinreport_graphics.Rmd’ using knitr

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 knitr
--- finished re-building ‘clinreport_modify_outputs.Rmd’

--- re-building ‘clinreport_vignette_get_started.Rmd’ using knitr

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 202-220 (clinreport_vignette_get_started.Rmd) 
Error: processing vignette 'clinreport_vignette_get_started.Rmd' failed with diagnostics:
names do not match previous names
--- failed re-building ‘clinreport_vignette_get_started.Rmd’

--- re-building ‘clinreport_vignette_standard.Rmd’ using knitr

Attaching package: 'dplyr'

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_vignette_standard.Rmd’

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

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 2 ERRORs, 1 WARNING, 1 NOTE
See
  ‘/data/blackswan/ripley/R/packages/tests-devel/ClinReport.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 1:44.27, 99.03 + 6.57