* using log directory ‘/srv/hornik/tmp/CRAN/ScitoSimulations.Rcheck’
* using R Under development (unstable) (2023-08-31 r85038)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 16.0.6 (10)
    GNU Fortran (Debian 13.2.0-1) 13.2.0
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘ScitoSimulations/DESCRIPTION’ ... OK
* this is package ‘ScitoSimulations’ version ‘1.0’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [2s/2s] NOTE
Maintainer: ‘Carter Hall <jchall@scitovation.com>’

New submission

Non-FOSS package license (use_mit_license())

Possibly misspelled words in DESCRIPTION:
  ScitoSim (2:8)

Found the following (possibly) invalid file URIs:
  URI: jchall@scitovation.com
    From: inst/doc/ScitoSimulations.html
  URI: tantonijevic@scitovation.com
    From: inst/doc/ScitoSimulations.html

DESCRIPTION fields with placeholder content:
  Description: what the package does (one paragraph).

Size of tarball: 8595817 bytes
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... NOTE
Found the following apparent object files/libraries:
  PBPKmodels/code/KMD_model_event_vedika.o
  PBPKmodels/code/KMD_model_event_vedika.so
  PBPKmodels/code/totalModel.o PBPKmodels/run/KMD_model_event_vedika.so
  PBPKmodels/run/totalModel.so inst/models/KMD_model_event_vedika.o
  inst/models/KMD_model_event_vedika.so inst/models/totalModel.o
  inst/models/totalModel.so
Object files/libraries should not be included in a source package.
* 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 ‘ScitoSimulations’ can be installed ... [5s/5s] WARNING
Found the following significant warnings:
  Warning: /srv/hornik/tmp/CRAN/ScitoSimulations.Rcheck/00_pkg_src/ScitoSimulations/man/postRunModel.Rd:12: unexpected TEXT 'as defined in the model database table modelNames', expecting ']'
  Warning: /srv/hornik/tmp/CRAN/ScitoSimulations.Rcheck/00_pkg_src/ScitoSimulations/man/postRunModel.Rd:13: unexpected TEXT 'modelParameters data.frame returned in the list of data.frames given by the
  Warning: /srv/hornik/tmp/CRAN/ScitoSimulations.Rcheck/00_pkg_src/ScitoSimulations/man/postRunModel.Rd:15: unexpected TEXT 'data.frame returned in the list of data.frames given by the
  Warning: /srv/hornik/tmp/CRAN/ScitoSimulations.Rcheck/00_pkg_src/ScitoSimulations/man/postRunModel.Rd:17: unexpected TEXT 'data.frame returned in the list of data.frames given by the
  Warning: replacing previous import ‘cowplot::get_legend’ by ‘ggpubr::get_legend’ when loading ‘ScitoSimulations’
  Warning: replacing previous import ‘deSolve::rk4’ by ‘pracma::rk4’ when loading ‘ScitoSimulations’
  Warning: replacing previous import ‘DT::dataTableOutput’ by ‘shiny::dataTableOutput’ when loading ‘ScitoSimulations’
  Warning: replacing previous import ‘jsonlite::validate’ by ‘shiny::validate’ when loading ‘ScitoSimulations’
  Warning: replacing previous import ‘DT::renderDataTable’ by ‘shiny::renderDataTable’ when loading ‘ScitoSimulations’
  Warning: replacing previous import ‘shiny::runExample’ by ‘shinyalert::runExample’ when loading ‘ScitoSimulations’
  Warning: replacing previous import ‘shinyalert::runExample’ by ‘shinyjs::runExample’ when loading ‘ScitoSimulations’
  Warning: replacing previous import ‘RSQLite::show’ by ‘shinyjs::show’ when loading ‘ScitoSimulations’
See ‘/srv/hornik/tmp/CRAN/ScitoSimulations.Rcheck/00install.out’ for details.
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... WARNING
Non-standard license specification:
  use_mit_license()
Standardizable: FALSE
* checking top-level files ... NOTE
Non-standard files/directories found at top level:
  ‘PBPKmodels’ ‘dev’ ‘temporary’
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... WARNING
Found the following files with non-ASCII characters:
  exposureSetUp.R
  unitConversion.R
Portable packages must use only ASCII characters in their R code,
except perhaps in comments.
Use \uxxxx escapes for other characters.
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [1s/1s] OK
* checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the package can be unloaded cleanly ... [1s/1s] OK
* checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
* checking loading without being on the library search path ... [1s/1s] OK
* checking whether startup messages can be suppressed ... [1s/1s] NOTE
'R' should not be used without a path -- see par. 1.6 of the manual
'R' should not be used without a path -- see par. 1.6 of the manual

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
'R' should not be used without a path -- see par. 1.6 of the manual
'R' should not be used without a path -- see par. 1.6 of the manual
* checking S3 generic/method consistency ... WARNING
'R' should not be used without a path -- see par. 1.6 of the manual
'R' should not be used without a path -- see par. 1.6 of the manual
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... WARNING
'R' should not be used without a path -- see par. 1.6 of the manual
'R' should not be used without a path -- see par. 1.6 of the manual
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
* checking foreign function calls ... NOTE
'R' should not be used without a path -- see par. 1.6 of the manual
'R' should not be used without a path -- see par. 1.6 of the manual
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... [8s/8s] NOTE
'R' should not be used without a path -- see par. 1.6 of the manual
'R' should not be used without a path -- see par. 1.6 of the manual
'R' should not be used without a path -- see par. 1.6 of the manual
'R' should not be used without a path -- see par. 1.6 of the manual
AUC_Cmax.calculateAUCinfinity: no visible global function definition
  for ‘tail’
AUC_Cmax.calculateAUCinfinity: no visible global function definition
  for ‘lm’
cdfPlot: no visible global function definition for ‘reorder’
cdfPlot: no visible binding for global variable ‘x’
cdfPlot: no visible binding for global variable ‘y’
getExamplePCData: no visible global function definition for
  ‘read.delim’
initialize.createParametersVector: no visible global function
  definition for ‘setNames’
initialize.createStatesVector: no visible global function definition
  for ‘setNames’
resultsViewerServer: no visible global function definition for ‘hist’
reverseDosimetryServer: no visible global function definition for
  ‘read.delim’
runMonteCarlo: no visible binding for '<<-' assignment to ‘ret’
userDatabase.writeBinary: no visible binding for global variable
  ‘result’
userDatabase.writeBinary: no visible binding for global variable
  ‘databaseConnection’
Undefined global functions or variables:
  databaseConnection hist lm read.delim reorder result setNames tail x
  y
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "lm", "reorder", "setNames")
  importFrom("utils", "read.delim", "tail")
to your NAMESPACE file.

Found the following calls to attach():
File ‘ScitoSimulations/R/userDatabase.R’:
  attach("x.rData", pos = 2)
See section ‘Good practice’ in ‘?attach’.

'R' should not be used without a path -- see par. 1.6 of the manual
'R' should not be used without a path -- see par. 1.6 of the manual
* checking Rd files ... [0s/0s] WARNING
checkRd: (7) freqPC.Rd:19-22: Tag \dontrun not recognized
prepare_Rd: ./man/postRunModel.Rd:12: unexpected TEXT 'as defined in the model database table modelNames', expecting ']'
prepare_Rd: ./man/postRunModel.Rd:13: unexpected TEXT 'modelParameters data.frame returned in the list of data.frames given by the
', expecting ']'
prepare_Rd: ./man/postRunModel.Rd:15: unexpected TEXT 'data.frame returned in the list of data.frames given by the
', expecting ']'
prepare_Rd: ./man/postRunModel.Rd:17: unexpected TEXT 'data.frame returned in the list of data.frames given by the
', expecting ']'
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'initialize.createParametersVector.Rd':
  \examples lines wider than 100 characters:
     modelParameters <- modelParameters[, !names(modelParameters) %in% c("monteCarloCV", "monteCarloDistribution", "parameterCSS")]

Rd file 'initialize.getParameters.Rd':
  \examples lines wider than 100 characters:
     modelParameters <- modelParameters[, !names(modelParameters) %in% c("monteCarloCV", "monteCarloDistribution", "parameterCSS")]

These lines will be truncated in the PDF manual.
* checking Rd cross-references ... NOTE
Unknown packages ‘as defined in the model database table modelNames’, ‘getLoadModelParameters function’ in Rd xrefs
* checking for missing documentation entries ... WARNING
'R' should not be used without a path -- see par. 1.6 of the manual
'R' should not be used without a path -- see par. 1.6 of the manual
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
'R' should not be used without a path -- see par. 1.6 of the manual
'R' should not be used without a path -- see par. 1.6 of the manual
'R' should not be used without a path -- see par. 1.6 of the manual
'R' should not be used without a path -- see par. 1.6 of the manual
'R' should not be used without a path -- see par. 1.6 of the manual
'R' should not be used without a path -- see par. 1.6 of the manual
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object ‘AUC_Cmax.calculateAUCinfinity’
  ‘resultsDataFrame’
Documented arguments not in \usage in documentation object ‘AUC_Cmax.calculateAUCinfinity’:
  ‘in_vivo_experiment_ids’ ‘inVivoData’

Undocumented arguments in documentation object ‘AUC_Cmax.computeAUC24hDR’
  ‘mcResults’ ‘dosingAmounts’
Documented arguments not in \usage in documentation object ‘AUC_Cmax.computeAUC24hDR’:
  ‘mainInput’

Undocumented arguments in documentation object ‘ForwardDosimetryMC.computeCmaxs’
  ‘mcResults’
Documented arguments not in \usage in documentation object ‘ForwardDosimetryMC.computeCmaxs’:
  ‘mainInput’

Undocumented arguments in documentation object ‘ForwardDosimetryMC.computeColumnMaxs’
  ‘x’
Documented arguments not in \usage in documentation object ‘ForwardDosimetryMC.computeColumnMaxs’:
  ‘mainInput’

Undocumented arguments in documentation object ‘ForwardDosimetryMC.computeMeans’
  ‘mcResults’
Documented arguments not in \usage in documentation object ‘ForwardDosimetryMC.computeMeans’:
  ‘mainInput’

Undocumented arguments in documentation object ‘exposureSetUp.bolusDermal’
  ‘exposureParameters’ ‘exposureSelected’ ‘modelUnits’ ‘modelOrder’
  ‘modelExposures’ ‘molecularWeight’ ‘bodyWeight’
Documented arguments not in \usage in documentation object ‘exposureSetUp.bolusDermal’:
  ‘mainInput’

Undocumented arguments in documentation object ‘exposureSetUp.bolusOral’
  ‘exposureParameters’ ‘exposureSelected’ ‘modelUnits’ ‘modelOrder’
  ‘modelExposures’ ‘molecularWeight’ ‘bodyWeight’
Documented arguments not in \usage in documentation object ‘exposureSetUp.bolusOral’:
  ‘mainInput’

Undocumented arguments in documentation object ‘exposureSetUp.getExposureLength’
  ‘modelName’
Documented arguments not in \usage in documentation object ‘exposureSetUp.getExposureLength’:
  ‘mainInput’

Undocumented arguments in documentation object ‘exposureSetUp.getExposureOrder’
  ‘modelName’ ‘exposureSelected’
Documented arguments not in \usage in documentation object ‘exposureSetUp.getExposureOrder’:
  ‘mainInput’

Undocumented arguments in documentation object ‘exposureSetUp.getExposureUnits’
  ‘modelName’ ‘exposureSelected’
Documented arguments not in \usage in documentation object ‘exposureSetUp.getExposureUnits’:
  ‘mainInput’

Undocumented arguments in documentation object ‘exposureSetUp.master’
  ‘exposureParameters’ ‘exposureSelected’ ‘modelName’ ‘molecularWeight’
  ‘bodyWeight’
Documented arguments not in \usage in documentation object ‘exposureSetUp.master’:
  ‘mainInput’

Undocumented arguments in documentation object ‘exposureSetUp.singleIV’
  ‘exposureParameters’ ‘exposureSelected’ ‘modelUnits’ ‘modelOrder’
  ‘modelExposures’ ‘molecularWeight’ ‘bodyWeight’
Documented arguments not in \usage in documentation object ‘exposureSetUp.singleIV’:
  ‘mainInput’

Undocumented arguments in documentation object ‘exposureSetUp.singleInhalation’
  ‘exposureParameters’ ‘exposureSelected’ ‘modelUnits’ ‘modelOrder’
  ‘modelExposures’ ‘molecularWeight’ ‘bodyWeight’
Documented arguments not in \usage in documentation object ‘exposureSetUp.singleInhalation’:
  ‘mainInput’

Undocumented arguments in documentation object ‘exposureSetUp.timedOral’
  ‘exposureParameters’ ‘exposureSelected’ ‘modelUnits’ ‘modelOrder’
  ‘modelExposures’ ‘molecularWeight’ ‘bodyWeight’
Documented arguments not in \usage in documentation object ‘exposureSetUp.timedOral’:
  ‘mainInput’

Undocumented arguments in documentation object ‘forwardDosimetry.createTable’
  ‘modelName’ ‘modelResults’

Undocumented arguments in documentation object ‘freqMC’
  ‘step’

Undocumented arguments in documentation object ‘freqPC’
  ‘step’

Undocumented arguments in documentation object ‘getFullResults’
  ‘userName’ ‘runName’
Documented arguments not in \usage in documentation object ‘getFullResults’:
  ‘query’ ‘databaseLocation’

Undocumented arguments in documentation object ‘getResults’
  ‘userName’ ‘monteCarlo’

Undocumented arguments in documentation object ‘initialize.createStatesVector’
  ‘initialStates’

Undocumented arguments in documentation object ‘initialize.getParametersMC’
  ‘modelName’ ‘modelParameters’

Undocumented arguments in documentation object ‘loadModelParameters2’
  ‘modelName’ ‘species’ ‘chemicalID’

Documented arguments not in \usage in documentation object ‘modelDatabase.Insert’:
  ‘databaseLocation’

Undocumented arguments in documentation object ‘modelOutputs’
  ‘modelName’

Undocumented arguments in documentation object ‘monteCarlo.CreateExposureLists’
  ‘exposureParameters’ ‘numberOfRuns’

Undocumented arguments in documentation object ‘monteCarlo.calculateMCdistributions’
  ‘maxValue’

Undocumented arguments in documentation object ‘monteCarlo.createDataFrame’
  ‘modelParameters’

Undocumented arguments in documentation object ‘postRunModel’
  ‘RunName’

Undocumented arguments in documentation object ‘runModel’
  ‘monteCarloRun’ ‘userName’ ‘userOptions’ ‘req’

Undocumented arguments in documentation object ‘runMonteCarlo’
  ‘modelParameters’ ‘exposureParameters’ ‘exposureClasses’ ‘modelName’
  ‘exposureSelected’

Undocumented arguments in documentation object ‘runPBPKmodel.initialStates’
  ‘Y’ ‘package’
Documented arguments not in \usage in documentation object ‘runPBPKmodel.initialStates’:
  ‘parms’ ‘newStates’

Undocumented arguments in documentation object ‘runReverseDosimetry’
  ‘mcNumTrials’

Documented arguments not in \usage in documentation object ‘runReverseDosimetryInterface’:
  ‘...’

Undocumented arguments in documentation object ‘runTimeCourse.run’
  ‘modelName’ ‘initialParameters’ ‘initialStates’ ‘outputParameters’
  ‘exposures’ ‘simulationDuration’
Documented arguments not in \usage in documentation object ‘runTimeCourse.run’:
  ‘input’

Undocumented arguments in documentation object ‘setUp.orderParameters’
  ‘parametersVector’ ‘modelName’

Undocumented arguments in documentation object ‘unitConversion’
  ‘value’ ‘currentUnits’ ‘newUnits’ ‘molecularWeight’ ‘bodyWeight’

Documented arguments not in \usage in documentation object ‘userDatabase.Insert’:
  ‘databaseLocation’

Undocumented arguments in documentation object ‘userDatabase.createUser’
  ‘newUser’
Documented arguments not in \usage in documentation object ‘userDatabase.createUser’:
  ‘query’ ‘databaseLocation’

Documented arguments not in \usage in documentation object ‘userDatabase.getUserNames’:
  ‘query’ ‘databaseLocation’

Undocumented arguments in documentation object ‘userDatabase.saveResults’
  ‘modelResultsPath’ ‘modelParametersFromInterfacePath’ ‘RunName’
Documented arguments not in \usage in documentation object ‘userDatabase.saveResults’:
  ‘databaseLocation’

Undocumented arguments in documentation object ‘userLogin’
  ‘userLoginType’ ‘req’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'R' should not be used without a path -- see par. 1.6 of the manual
'R' should not be used without a path -- see par. 1.6 of the manual
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... WARNING
Files not of a type allowed in a ‘data’ directory:
  ‘Examples’
Please use e.g. ‘inst/extdata’ for non-R data files

* checking data for non-ASCII characters ... [0s/0s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [3s/3s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking re-building of vignette outputs ... [1s/1s] OK
* checking PDF version of manual ... [4s/4s] WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! You can't use `macro parameter character #' in horizontal mode.
l.986 #
       # Not run:
Sorry, but I'm not programmed to handle this case;
I'll just pretend that you didn't ask for it.
! You can't use `macro parameter character #' in horizontal mode.
l.986 ##
         Not run:
Sorry, but I'm not programmed to handle this case;
I'll just pretend that you didn't ask for it.
! You can't use `macro parameter character #' in vertical mode.
l.990 #
       # End(Not run)
Sorry, but I'm not programmed to handle this case;
I'll just pretend that you didn't ask for it.
! You can't use `macro parameter character #' in vertical mode.
l.990 ##
         End(Not run)
Sorry, but I'm not programmed to handle this case;
I'll just pretend that you didn't ask for it.
* checking PDF version of manual without index ... ERROR
* checking HTML version of manual ... [1s/1s] OK
* checking for non-standard things in the check directory ... NOTE
Found the following files/directories:
  ‘ScitoSimulations-manual.tex’
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 ERROR, 11 WARNINGs, 10 NOTEs