CRAN Package Check Results for Package statVisual

Last updated on 2021-12-03 19:50:28 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.2.1 18.60 220.92 239.52 OK
r-devel-linux-x86_64-debian-gcc 1.2.1 14.12 141.89 156.01 ERROR
r-devel-linux-x86_64-fedora-clang 1.2.1 292.38 NOTE
r-devel-linux-x86_64-fedora-gcc 1.2.1 273.83 NOTE
r-devel-windows-x86_64-new-UL 1.2.1 36.00 294.00 330.00 OK
r-devel-windows-x86_64-new-TK 1.2.1 NOTE
r-devel-windows-x86_64-old 1.2.1 20.00 180.00 200.00 OK
r-patched-linux-x86_64 1.2.1 24.23 198.78 223.01 OK
r-release-linux-x86_64 1.2.1 15.81 203.62 219.43 OK
r-release-macos-arm64 1.2.1 ERROR
r-release-macos-x86_64 1.2.1 ERROR
r-release-windows-ix86+x86_64 1.2.1 46.00 251.00 297.00 OK
r-oldrel-macos-x86_64 1.2.1 ERROR
r-oldrel-windows-ix86+x86_64 1.2.1 44.00 255.00 299.00 OK

Check Details

Version: 1.2.1
Check: examples
Result: ERROR
    Running examples in ‘statVisual-Ex.R’ failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: PCA_score
    > ### Title: Scatter Plot of 2 Specified Principal Components
    > ### Aliases: PCA_score
    > ### Keywords: method
    >
    > ### ** Examples
    >
    > library(factoextra)
    Welcome! Want to learn more? See two factoextra-related books at https://goo.gl/ve3WBa
    >
    > data(esSim)
    > print(esSim)
    ExpressionSet (storageMode: lockedEnvironment)
    assayData: 100 features, 20 samples
     element names: exprs
    protocolData: none
    phenoData
     sampleNames: subj1 subj2 ... subj20 (20 total)
     varLabels: sid grp
     varMetadata: labelDescription
    featureData
     featureNames: probe1 probe2 ... probe100 (100 total)
     fvarLabels: probeid gene chr
     fvarMetadata: labelDescription
    experimentData: use 'experimentData(object)'
    Annotation:
    >
    > # expression data
    > dat = exprs(esSim)
    > print(dim(dat))
    [1] 100 20
    > print(dat[1:2,])
     subj1 subj2 subj3 subj4 subj5 subj6 subj7 subj8
    probe1 1.462929 1.596203 2.252267 1.974616 1.842606 1.677204 2.242665 1.705923
    probe2 1.574342 2.232537 1.846260 1.980999 2.483777 2.048599 1.786081 1.934728
     subj9 subj10 subj11 subj12 subj13 subj14 subj15
    probe1 1.758028 1.919597 0.07477602 0.3054811 0.12356526 0.3221119 -0.1346480
    probe2 1.740329 1.942189 0.08308643 -0.1012774 -0.06669481 0.5413783 0.0245575
     subj16 subj17 subj18 subj19 subj20
    probe1 -0.03845011 0.3504460 0.4173905 -0.1438801 0.3335083
    probe2 -0.03849619 -0.2536194 0.1420066 -0.1072697 -0.1750033
    >
    > # phenotype data
    > pDat = pData(esSim)
    > print(dim(pDat))
    [1] 20 2
    > print(pDat[1:2,])
     sid grp
    subj1 subj1 1
    subj2 subj2 1
    >
    > # feature data
    > fDat = fData(esSim)
    > print(dim(fDat))
    [1] 100 3
    > print(fDat[1:2,])
     probeid gene chr
    probe1 probe1 fakeGene1 1
    probe2 probe2 fakeGene2 1
    >
    > # choose the first 6 probes (3 OE probes, 2 UE probes, and 1 NE probe)
    > pDat$probe1 = dat[1,]
    > pDat$probe2 = dat[2,]
    > pDat$probe3 = dat[3,]
    > pDat$probe4 = dat[4,]
    > pDat$probe5 = dat[5,]
    > pDat$probe6 = dat[6,]
    >
    > print(pDat[1:2, ])
     sid grp probe1 probe2 probe3 probe4 probe5 probe6
    subj1 subj1 1 1.462929 1.574342 2.015327 -2.137848 -1.992898 1.0472686
    subj2 subj2 1 1.596203 2.232537 2.141727 -2.639981 -1.926786 0.3904537
    >
    > # check histograms of probe 1 expression in cases and controls
    > print(table(pDat$grp, useNA = "ifany"))
    
     0 1
    10 10
    >
    > pDat$grp = factor(pDat$grp)
    >
    > ###
    >
    > pca.obj = iprcomp(pDat[, c(3:8)], scale. = TRUE)
    >
    > # scree plot
    > factoextra::fviz_eig(pca.obj, addlabels = TRUE)
    >
    > # scatter plot of PC1 vs PC2
    > statVisual(type = 'PCA_score',
    + prcomp_obj = pca.obj,
    + dims = c(1, 2),
    + data = pDat,
    + color = 'grp',
    + loadings = FALSE)
    Warning: `select_()` was deprecated in dplyr 0.7.0.
    Please use `select()` instead.
    This warning is displayed once every 8 hours.
    Call `lifecycle::last_lifecycle_warnings()` to see where this warning was generated.
    Error in FUN(x, aperm(array(STATS, dims[perm]), order(perm)), ...) :
     non-numeric argument to binary operator
    Calls: statVisual -> PCA_score -> mahalanobis -> sweep
    Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 1.2.1
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building ‘statVisual.Rmd’ using rmarkdown
    Loading required package: BiocGenerics
    
    Attaching package: 'BiocGenerics'
    
    The following objects are masked from 'package:stats':
    
     IQR, mad, sd, var, xtabs
    
    The following objects are masked from 'package:base':
    
     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
     as.data.frame, basename, cbind, colnames, dirname, do.call,
     duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
     lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
     pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
     tapply, union, unique, unsplit, which.max, which.min
    
    Welcome to Bioconductor
    
     Vignettes contain introductory material; view with
     'browseVignettes()'. To cite Bioconductor, see
     'citation("Biobase")', and for packages 'citation("pkgname")'.
    
    
    Attaching package: 'limma'
    
    The following object is masked from 'package:BiocGenerics':
    
     plotMA
    
    
    Attaching package: 'dplyr'
    
    The following object is masked from 'package:Biobase':
    
     combine
    
    The following objects are masked from 'package:BiocGenerics':
    
     combine, intersect, setdiff, union
    
    The following objects are masked from 'package:stats':
    
     filter, lag
    
    The following objects are masked from 'package:base':
    
     intersect, setdiff, setequal, union
    
    Loading required package: ggplot2
    Welcome! Want to learn more? See two factoextra-related books at https://goo.gl/ve3WBa
    Loading required package: grid
    Loading required package: magrittr
    Loading required package: checkmate
    
    Attaching package: 'checkmate'
    
    The following object is masked from 'package:Biobase':
    
     anyMissing
    
    Loaded gbm 2.1.8
    Loading required package: Matrix
    Loaded glmnet 4.1-3
    
    Attaching package: 'gridExtra'
    
    The following object is masked from 'package:dplyr':
    
     combine
    
    The following object is masked from 'package:Biobase':
    
     combine
    
    The following object is masked from 'package:BiocGenerics':
    
     combine
    
    Type 'citation("pROC")' for a citation.
    
    Attaching package: 'pROC'
    
    The following object is masked from 'package:BiocGenerics':
    
     var
    
    The following objects are masked from 'package:stats':
    
     cov, smooth, var
    
    randomForest 4.6-14
    Type rfNews() to see new features/changes/bug fixes.
    
    Attaching package: 'randomForest'
    
    The following object is masked from 'package:gridExtra':
    
     combine
    
    The following object is masked from 'package:ggplot2':
    
     margin
    
    The following object is masked from 'package:dplyr':
    
     combine
    
    The following object is masked from 'package:Biobase':
    
     combine
    
    The following object is masked from 'package:BiocGenerics':
    
     combine
    
    Loading required package: rpart
    ── Attaching packages ─────────────────────────────────────── tidyverse 1.3.1 ──
    ✔ tidyr 1.1.4 ✔ stringr 1.4.0
    ✔ readr 2.1.1 ✔ forcats 0.5.1
    ✔ purrr 0.3.4
    ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
    ✖ ggplot2::Position() masks BiocGenerics::Position(), base::Position()
    ✖ randomForest::combine() masks gridExtra::combine(), dplyr::combine(), Biobase::combine(), BiocGenerics::combine()
    ✖ tidyr::expand() masks Matrix::expand()
    ✖ tidyr::extract() masks magrittr::extract()
    ✖ dplyr::filter() masks stats::filter()
    ✖ dplyr::lag() masks stats::lag()
    ✖ randomForest::margin() masks ggplot2::margin()
    ✖ tidyr::pack() masks Matrix::pack()
    ✖ purrr::set_names() masks magrittr::set_names()
    ✖ tidyr::unpack() masks Matrix::unpack()
    Warning: `group_by_()` was deprecated in dplyr 0.7.0.
    Please use `group_by()` instead.
    See vignette('programming') for more help
    This warning is displayed once every 8 hours.
    Call `lifecycle::last_lifecycle_warnings()` to see where this warning was generated.
    Warning: `funs()` was deprecated in dplyr 0.8.0.
    Please use a list of either functions or lambdas:
    
     # Simple named list:
     list(mean = mean, median = median)
    
     # Auto named with `tibble::lst()`:
     tibble::lst(mean, median)
    
     # Using lambdas
     list(~ mean(., trim = .2), ~ median(., na.rm = TRUE))
    This warning is displayed once every 8 hours.
    Call `lifecycle::last_lifecycle_warnings()` to see where this warning was generated.
    Scale for 'linetype' is already present. Adding another scale for 'linetype',
    which will replace the existing scale.
    Warning: `fun.y` is deprecated. Use `fun` instead.
    Warning: `summarise_()` was deprecated in dplyr 0.7.0.
    Please use `summarise()` instead.
    This warning is displayed once every 8 hours.
    Call `lifecycle::last_lifecycle_warnings()` to see where this warning was generated.
    Joining, by = c("grp", "time")
    Warning: `fun.y` is deprecated. Use `fun` instead.
    Joining, by = c("grp", "time")
    Warning: `select_()` was deprecated in dplyr 0.7.0.
    Please use `select()` instead.
    This warning is displayed once every 8 hours.
    Call `lifecycle::last_lifecycle_warnings()` to see where this warning was generated.
    Quitting from lines 805-811 (statVisual.Rmd)
    Error: processing vignette ‘statVisual.Rmd’ failed with diagnostics:
    non-numeric argument to binary operator
    --- failed re-building ‘statVisual.Rmd’
    
    SUMMARY: processing the following file failed:
     ‘statVisual.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 1.2.1
Check: package dependencies
Result: NOTE
    Imports includes 23 non-default packages.
    Importing from so many packages makes the package vulnerable to any of
    them becoming unavailable. Move as many as possible to Suggests and
    use conditionally.
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 1.2.1
Check: dependencies in R code
Result: NOTE
    Namespaces in Imports field not imported from:
     ‘gbm’ ‘ggfortify’ ‘tibble’ ‘tidyverse’
     All declared Imports should be used.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64-new-TK

Version: 1.2.1
Check: package dependencies
Result: ERROR
    Package required but not available: ‘pvca’
    
    See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
    manual.
Flavors: r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-x86_64