CRAN Package Check Results for Maintainer ‘Elizabeth Freeman <eafreeman at fs.fed.us>’

Last updated on 2020-08-07 01:50:18 CEST.

Package ModelMap

Current CRAN status: FAIL: 1, NOTE: 7, OK: 4

Version: 3.4.0.1
Flags: --no-vignettes
Check: for non-standard things in the check directory
Result: NOTE
    Found the following files/directories:
     'BIO_TCandNLCD_NLCD.jpg' 'BIO_TCandNLCD_TCB.jpg'
     'BIO_TCandNLCD_TCG.jpg' 'BIO_TCandNLCD_TCW.jpg'
     'BIO_TCandNLCD_corrplot.jpg' 'BIO_TCandNLCD_mask_all_predictors.jpg'
     'BIO_TCandNLCD_projections.txt' 'RF_BIO_TCandNLCD_01.img'
     'RF_BIO_TCandNLCD_01.img.aux.xml'
     'RF_BIO_TCandNLCD_01_mapmake_arguments.txt'
     'RF_BIO_TCandNLCD_01_projections.txt' 'RF_BIO_TCandNLCD_OOB.csv'
     'RF_BIO_TCandNLCD_OOB_corrplot.jpg'
     'RF_BIO_TCandNLCD_OOB_corrplot.pdf' 'RF_BIO_TCandNLCD_OOB_error.jpg'
     'RF_BIO_TCandNLCD_OOB_error.pdf'
     'RF_BIO_TCandNLCD_OOB_importance.jpg'
     'RF_BIO_TCandNLCD_OOB_importance.pdf'
     'RF_BIO_TCandNLCD_OOB_scatterplot.jpg'
     'RF_BIO_TCandNLCD_OOB_scatterplot.pdf'
     'RF_BIO_TCandNLCD_model_building_arguments.txt'
     'RF_Bio_TC_model_building_arguments.txt' 'example.test.csv'
     'example.train.csv'
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64

Version: 3.4.0.1
Check: for non-standard things in the check directory
Result: NOTE
    Found the following files/directories:
     ‘BIO_TCandNLCD_NLCD.jpg’ ‘BIO_TCandNLCD_TCB.jpg’
     ‘BIO_TCandNLCD_TCG.jpg’ ‘BIO_TCandNLCD_TCW.jpg’
     ‘BIO_TCandNLCD_corrplot.jpg’ ‘BIO_TCandNLCD_mask_all_predictors.jpg’
     ‘BIO_TCandNLCD_projections.txt’ ‘RF_BIO_TCandNLCD_01.img’
     ‘RF_BIO_TCandNLCD_01.img.aux.xml’
     ‘RF_BIO_TCandNLCD_01_mapmake_arguments.txt’
     ‘RF_BIO_TCandNLCD_01_projections.txt’ ‘RF_BIO_TCandNLCD_OOB.csv’
     ‘RF_BIO_TCandNLCD_OOB_corrplot.jpg’
     ‘RF_BIO_TCandNLCD_OOB_corrplot.pdf’ ‘RF_BIO_TCandNLCD_OOB_error.jpg’
     ‘RF_BIO_TCandNLCD_OOB_error.pdf’
     ‘RF_BIO_TCandNLCD_OOB_importance.jpg’
     ‘RF_BIO_TCandNLCD_OOB_importance.pdf’
     ‘RF_BIO_TCandNLCD_OOB_scatterplot.jpg’
     ‘RF_BIO_TCandNLCD_OOB_scatterplot.pdf’
     ‘RF_BIO_TCandNLCD_model_building_arguments.txt’
     ‘RF_Bio_TC_model_building_arguments.txt’ ‘example.test.csv’
     ‘example.train.csv’
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-solaris-x86

Version: 3.4.0.1
Check: re-building of vignette outputs
Result: NOTE
    Error(s) in re-building vignettes:
    --- re-building ‘ExploreModelMap.Rnw’ using Sweave
    Loading required package: randomForest
    randomForest 4.6-14
    Type rfNews() to see new features/changes/bug fixes.
    Loading required package: raster
    Loading required package: sp
    Loading required package: rgdal
    rgdal: version: 1.4-3, (SVN revision 828)
     Geospatial Data Abstraction Library extensions to R successfully loaded
     Loaded GDAL runtime: GDAL 2.1.3, released 2017/20/01
     Path to GDAL shared files: /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/rgdal/gdal
     GDAL binary built with GEOS: FALSE
     Loaded PROJ.4 runtime: Rel. 4.9.3, 15 August 2016, [PJ_VERSION: 493]
     Path to PROJ.4 shared files: /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/rgdal/proj
     Linking to sp version: 1.3-1
    --- finished re-building ‘ExploreModelMap.Rnw’
    
    --- re-building ‘VModelMap.Rnw’ using Sweave
    Loading required package: randomForest
    randomForest 4.6-14
    Type rfNews() to see new features/changes/bug fixes.
    Loading required package: raster
    Loading required package: sp
    Loading required package: rgdal
    rgdal: version: 1.4-3, (SVN revision 828)
     Geospatial Data Abstraction Library extensions to R successfully loaded
     Loaded GDAL runtime: GDAL 2.1.3, released 2017/20/01
     Path to GDAL shared files: /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/rgdal/gdal
     GDAL binary built with GEOS: FALSE
     Loaded PROJ.4 runtime: Rel. 4.9.3, 15 August 2016, [PJ_VERSION: 493]
     Path to PROJ.4 shared files: /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/rgdal/proj
     Linking to sp version: 1.3-1
    Warning in FNcheck(OUTPUTfn = OUTPUTfn, folder = folder, ERROR.NAME = "OUTPUTfn") :
     OUTPUTfn VModelMapEx1a_map does not include an extension, using default extension of '.img'. New OUTPUTfn is VModelMapEx1a_map.img
    Warning in FNcheck(OUTPUTfn = OUTPUTfn, folder = folder, ERROR.NAME = "OUTPUTfn") :
     OUTPUTfn VModelMapEx1b_map does not include an extension, using default extension of '.img'. New OUTPUTfn is VModelMapEx1b_map.img
    Warning in FNcheck(OUTPUTfn = OUTPUTfn, folder = folder, ERROR.NAME = "OUTPUTfn") :
     OUTPUTfn VModelMapEx2a_map does not include an extension, using default extension of '.img'. New OUTPUTfn is VModelMapEx2a_map.img
    Warning in FNcheck(OUTPUTfn = OUTPUTfn, folder = folder, ERROR.NAME = "OUTPUTfn") :
     OUTPUTfn VModelMapEx2b_map does not include an extension, using default extension of '.img'. New OUTPUTfn is VModelMapEx2b_map.img
    Warning in FNcheck(OUTPUTfn = OUTPUTfn, folder = folder, ERROR.NAME = "OUTPUTfn") :
     OUTPUTfn VModelMapEx3_map does not include an extension, using default extension of '.img'. New OUTPUTfn is VModelMapEx3_map.img
    Warning in file.remove("Rplots.pdf") :
     cannot remove file 'Rplots.pdf', reason 'No such file or directory'
    --- finished re-building ‘VModelMap.Rnw’
    
    --- re-building ‘Vquantile.Rnw’ using Sweave
    Loading required package: randomForest
    randomForest 4.6-14
    Type rfNews() to see new features/changes/bug fixes.
    Loading required package: raster
    Loading required package: sp
    Loading required package: rgdal
    rgdal: version: 1.4-3, (SVN revision 828)
     Geospatial Data Abstraction Library extensions to R successfully loaded
     Loaded GDAL runtime: GDAL 2.1.3, released 2017/20/01
     Path to GDAL shared files: /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/rgdal/gdal
     GDAL binary built with GEOS: FALSE
     Loaded PROJ.4 runtime: Rel. 4.9.3, 15 August 2016, [PJ_VERSION: 493]
     Path to PROJ.4 shared files: /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/rgdal/proj
     Linking to sp version: 1.3-1
    Warning in FNcheck(OUTPUTfn = OUTPUTfn, folder = folder, ERROR.NAME = "OUTPUTfn") :
     OUTPUTfn VQuantile_QRF_Pinyon_map does not include an extension, using default extension of '.img'. New OUTPUTfn is VQuantile_QRF_Pinyon_map.img
    Warning in FNcheck(OUTPUTfn = OUTPUTfn, folder = folder, ERROR.NAME = "OUTPUTfn") :
     OUTPUTfn VQuantile_QRF_Sage_map does not include an extension, using default extension of '.img'. New OUTPUTfn is VQuantile_QRF_Sage_map.img
    Warning in FNcheck(OUTPUTfn = OUTPUTfn, folder = folder, ERROR.NAME = "OUTPUTfn") :
     OUTPUTfn VQuantile_CF_Pinyon_map does not include an extension, using default extension of '.img'. New OUTPUTfn is VQuantile_CF_Pinyon_map.img
    Warning in FNcheck(OUTPUTfn = OUTPUTfn, folder = folder, ERROR.NAME = "OUTPUTfn") :
     OUTPUTfn VQuantile_CF_Sage_map does not include an extension, using default extension of '.img'. New OUTPUTfn is VQuantile_CF_Sage_map.img
    
    Execution halted
    SUMMARY: processing the following file failed:
     ‘Vquantile.Rnw’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-oldrel-macos-x86_64

Version: 3.4.0.1
Check: PDF version of manual
Result: FAIL
Flavor: r-oldrel-macos-x86_64

Package PresenceAbsence

Current CRAN status: NOTE: 12

Version: 1.1.9
Check: DESCRIPTION meta-information
Result: NOTE
    Malformed Title field: should not end in a period.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-macos-x86_64, r-release-windows-ix86+x86_64, r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64

Version: 1.1.9
Check: top-level files
Result: NOTE
    Non-standard file/directory found at top level:
     'COPYRIGHTS'
    Copyright information should be in file inst/COPYRIGHTS
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-linux-x86_64, r-release-linux-x86_64

Version: 1.1.9
Check: R code for possible problems
Result: NOTE
    auc: no visible global function definition for 'var'
    auc.roc.plot: no visible global function definition for 'par'
    auc.roc.plot: no visible global function definition for 'lines'
    auc.roc.plot: no visible global function definition for 'abline'
    auc.roc.plot: no visible global function definition for 'points'
    auc.roc.plot: no visible global function definition for 'text'
    auc.roc.plot: no visible global function definition for 'legend'
    calibration.plot: no visible global function definition for 'qf'
    calibration.plot: no visible global function definition for 'par'
    calibration.plot: no visible global function definition for 'abline'
    calibration.plot: no visible global function definition for 'lines'
    calibration.plot: no visible global function definition for 'points'
    calibration.plot: no visible global function definition for 'text'
    error.threshold.plot: no visible global function definition for 'par'
    error.threshold.plot: no visible global function definition for 'lines'
    error.threshold.plot: no visible global function definition for
     'abline'
    error.threshold.plot: no visible global function definition for
     'points'
    error.threshold.plot: no visible global function definition for
     'legend'
    presence.absence.hist: no visible global function definition for 'hist'
    presence.absence.hist: no visible global function definition for
     'barplot'
    presence.absence.hist: no visible global function definition for 'par'
    presence.absence.hist: no visible global function definition for 'text'
    presence.absence.hist: no visible global function definition for
     'legend'
    presence.absence.hist: no visible global function definition for
     'abline'
    presence.absence.hist: no visible global function definition for
     'points'
    presence.absence.simulation: no visible global function definition for
     'rbinom'
    presence.absence.simulation: no visible global function definition for
     'rbeta'
    presence.absence.summary: no visible global function definition for
     'par'
    presence.absence.summary: no visible global function definition for
     'mtext'
    Undefined global functions or variables:
     abline barplot hist legend lines mtext par points qf rbeta rbinom
     text var
    Consider adding
     importFrom("graphics", "abline", "barplot", "hist", "legend", "lines",
     "mtext", "par", "points", "text")
     importFrom("stats", "qf", "rbeta", "rbinom", "var")
    to your NAMESPACE file.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-macos-x86_64, r-release-windows-ix86+x86_64

Version: 1.1.9
Check: Rd line widths
Result: NOTE
    Rd file 'auc.roc.plot.Rd':
     \usage lines wider than 90 characters:
     auc.roc.plot(DATA, threshold = 101, find.auc = TRUE, which.model = (1:(ncol(DATA) - 2)), na.rm = FALSE, xlab = "1-Specificity (false po ... [TRUNCATED]
    
    Rd file 'calibration.plot.Rd':
     \usage lines wider than 90 characters:
     calibration.plot(DATA, which.model = 1, na.rm = FALSE, alpha = 0.05, N.bins = 5, xlab = "Predicted Probability of Occurrence", ylab = " ... [TRUNCATED]
    
    Rd file 'cmx.Rd':
     \examples lines wider than 100 characters:
     SIMDATA$Predicted[SIMDATA$Observed==1]<-rnorm(n=length(SIMDATA$Observed[SIMDATA$Observed==1]),mean=.8,sd=.15)
     SIMDATA$Predicted[SIMDATA$Observed==0]<-rnorm(n=length(SIMDATA$Observed[SIMDATA$Observed==0]),mean=.2,sd=.15)
     SIMDATA$Predicted<-(SIMDATA$Predicted-min(SIMDATA$Predicted))/(max(SIMDATA$Predicted)-min(SIMDATA$Predicted))
    
    Rd file 'error.threshold.plot.Rd':
     \usage lines wider than 90 characters:
     error.threshold.plot(DATA, threshold = 101, which.model = 1, na.rm = FALSE, xlab = "Threshold", ylab = "Accuracy Measures", main = NULL ... [TRUNCATED]
     \examples lines wider than 100 characters:
     opt.methods=c("Default", "Sens=Spec", "MinROCdist"), vert.lines=TRUE ... [TRUNCATED]
    
    Rd file 'optimal.thresholds.Rd':
     \usage lines wider than 90 characters:
     optimal.thresholds(DATA = NULL, threshold = 101, which.model = 1:(ncol(DATA)-2), model.names = NULL, na.rm = FALSE, opt.methods = NULL, ... [TRUNCATED]
    
    Rd file 'presence.absence.accuracy.Rd':
     \usage lines wider than 90 characters:
     presence.absence.accuracy(DATA, threshold = 0.5, find.auc = TRUE, st.dev = TRUE, which.model = (1:(ncol(DATA) - 2)), na.rm = FALSE)
    
    Rd file 'presence.absence.hist.Rd':
     \usage lines wider than 90 characters:
     presence.absence.hist(DATA, which.model = 1, na.rm = FALSE, xlab = "predicted probability", ylab = "number of plots", main = NULL, mode ... [TRUNCATED]
    
    Rd file 'presence.absence.simulation.Rd':
     \usage lines wider than 90 characters:
     presence.absence.simulation(n, prevalence, N.models = 1, shape1.absent, shape2.absent, shape1.present, shape2.present)
    
    Rd file 'presence.absence.summary.Rd':
     \usage lines wider than 90 characters:
     presence.absence.summary(DATA, threshold = 101, find.auc = TRUE, which.model = 1, na.rm = FALSE, main = NULL, model.names = NULL, alpha ... [TRUNCATED]
    
    These lines will be truncated in the PDF manual.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-linux-x86_64, r-release-linux-x86_64

Version: 1.1.9
Check: R code for possible problems
Result: NOTE
    auc: no visible global function definition for ‘var’
    auc.roc.plot: no visible global function definition for ‘par’
    auc.roc.plot: no visible global function definition for ‘plot’
    auc.roc.plot: no visible global function definition for ‘lines’
    auc.roc.plot: no visible global function definition for ‘abline’
    auc.roc.plot: no visible global function definition for ‘points’
    auc.roc.plot: no visible global function definition for ‘text’
    auc.roc.plot: no visible global function definition for ‘legend’
    calibration.plot: no visible global function definition for ‘qf’
    calibration.plot: no visible global function definition for ‘par’
    calibration.plot: no visible global function definition for ‘plot’
    calibration.plot: no visible global function definition for ‘abline’
    calibration.plot: no visible global function definition for ‘lines’
    calibration.plot: no visible global function definition for ‘points’
    calibration.plot: no visible global function definition for ‘text’
    error.threshold.plot: no visible global function definition for ‘par’
    error.threshold.plot: no visible global function definition for ‘plot’
    error.threshold.plot: no visible global function definition for ‘lines’
    error.threshold.plot: no visible global function definition for
     ‘abline’
    error.threshold.plot: no visible global function definition for
     ‘points’
    error.threshold.plot: no visible global function definition for
     ‘legend’
    presence.absence.hist: no visible global function definition for ‘hist’
    presence.absence.hist: no visible global function definition for
     ‘barplot’
    presence.absence.hist: no visible global function definition for ‘par’
    presence.absence.hist: no visible global function definition for ‘text’
    presence.absence.hist: no visible global function definition for ‘plot’
    presence.absence.hist: no visible global function definition for
     ‘legend’
    presence.absence.hist: no visible global function definition for
     ‘abline’
    presence.absence.hist: no visible global function definition for
     ‘points’
    presence.absence.simulation: no visible global function definition for
     ‘rbinom’
    presence.absence.simulation: no visible global function definition for
     ‘rbeta’
    presence.absence.summary: no visible global function definition for
     ‘par’
    presence.absence.summary: no visible global function definition for
     ‘mtext’
    Undefined global functions or variables:
     abline barplot hist legend lines mtext par plot points qf rbeta
     rbinom text var
    Consider adding
     importFrom("graphics", "abline", "barplot", "hist", "legend", "lines",
     "mtext", "par", "plot", "points", "text")
     importFrom("stats", "qf", "rbeta", "rbinom", "var")
    to your NAMESPACE file.
Flavors: r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64