CRAN Package Check Results for Package dimRed

Last updated on 2022-07-05 10:48:52 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.2.5 19.57 282.64 302.21 ERROR
r-devel-linux-x86_64-debian-gcc 0.2.5 16.33 206.06 222.39 ERROR
r-devel-linux-x86_64-fedora-clang 0.2.5 350.53 ERROR
r-devel-linux-x86_64-fedora-gcc 0.2.5 376.46 ERROR
r-devel-windows-x86_64 0.2.5 60.00 324.00 384.00 OK
r-patched-linux-x86_64 0.2.5 23.90 259.28 283.18 ERROR
r-release-linux-x86_64 0.2.5 17.62 260.20 277.82 ERROR
r-release-macos-arm64 0.2.5 114.00 OK
r-release-macos-x86_64 0.2.5 146.00 OK
r-release-windows-x86_64 0.2.5 61.00 327.00 388.00 OK
r-oldrel-macos-arm64 0.2.5 108.00 NOTE
r-oldrel-macos-x86_64 0.2.5 133.00 OK
r-oldrel-windows-ix86+x86_64 0.2.5 42.00 335.00 377.00 OK

Additional issues

noSuggests

Check Details

Version: 0.2.5
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: 'lle'
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: 0.2.5
Check: Rd cross-references
Result: NOTE
    Unknown package 'lle' in Rd xrefs
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-gcc, r-patched-linux-x86_64, r-release-linux-x86_64

Version: 0.2.5
Check: examples
Result: ERROR
    Running examples in 'dimRed-Ex.R' failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: LLE-class
    > ### Title: Locally Linear Embedding
    > ### Aliases: LLE-class LLE
    >
    > ### ** Examples
    >
    > dat <- loadDataSet("3D S Curve", n = 500)
    > emb <- embed(dat, "LLE", knn = 45)
    Error in chckpkg("lle") :
     require 'lle' package, install it using install.packages('lle')
    Calls: embed ... embed -> .local -> do.call -> <Anonymous> -> chckpkg
    Execution halted
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: 0.2.5
Check: tests
Result: ERROR
     Running 'testthat.R' [158s/190s]
    Running the tests in 'tests/testthat.R' failed.
    Complete output:
     > library(testthat)
     > library(dimRed)
     Loading required package: DRR
     Loading required package: kernlab
     Loading required package: CVST
     Loading required package: Matrix
    
     Attaching package: 'dimRed'
    
     The following object is masked from 'package:stats':
    
     embed
    
     The following object is masked from 'package:base':
    
     as.data.frame
    
     >
     > test_check("dimRed")
     embedding: AutoEncoder
     embedding: DiffusionMaps
     quality: Q_local
     quality: Q_global
     quality: mean_R_NX
     quality: AUC_lnK_R_NX
     quality: total_correlation
     quality: cophenetic_correlation
     quality: distance_correlation
     quality: reconstruction_rmse
     embedding: DRR
     quality: Q_local
     quality: Q_global
     quality: mean_R_NX
     quality: AUC_lnK_R_NX
     quality: total_correlation
     quality: cophenetic_correlation
     quality: distance_correlation
     quality: reconstruction_rmse
     embedding: FastICA
     quality: Q_local
     quality: Q_global
     quality: mean_R_NX
     quality: AUC_lnK_R_NX
     quality: total_correlation
     quality: cophenetic_correlation
     quality: distance_correlation
     quality: reconstruction_rmse
     embedding: KamadaKawai
     quality: Q_local
     quality: Q_global
     quality: mean_R_NX
     quality: AUC_lnK_R_NX
     quality: total_correlation
     quality: cophenetic_correlation
     quality: distance_correlation
     quality: reconstruction_rmse
     embedding: DrL
     quality: Q_local
     quality: Q_global
     quality: mean_R_NX
     quality: AUC_lnK_R_NX
     quality: total_correlation
     quality: cophenetic_correlation
     quality: distance_correlation
     quality: reconstruction_rmse
     embedding: FruchtermanReingold
     quality: Q_local
     quality: Q_global
     quality: mean_R_NX
     quality: AUC_lnK_R_NX
     quality: total_correlation
     quality: cophenetic_correlation
     quality: distance_correlation
     quality: reconstruction_rmse
     embedding: HLLE
     quality: Q_local
     quality: Q_global
     quality: mean_R_NX
     quality: AUC_lnK_R_NX
     quality: total_correlation
     quality: cophenetic_correlation
     quality: distance_correlation
     quality: reconstruction_rmse
     embedding: Isomap
     quality: Q_local
     quality: Q_global
     quality: mean_R_NX
     quality: AUC_lnK_R_NX
     quality: total_correlation
     quality: cophenetic_correlation
     quality: distance_correlation
     quality: reconstruction_rmse
     embedding: kPCA
     quality: Q_local
     quality: Q_global
     quality: mean_R_NX
     quality: AUC_lnK_R_NX
     quality: total_correlation
     quality: cophenetic_correlation
     quality: distance_correlation
     quality: reconstruction_rmse
     embedding: PCA_L1
     quality: Q_local
     quality: Q_global
     quality: mean_R_NX
     quality: AUC_lnK_R_NX
     quality: total_correlation
     quality: cophenetic_correlation
     quality: distance_correlation
     quality: reconstruction_rmse
     embedding: LaplacianEigenmaps
     quality: Q_local
     quality: Q_global
     quality: mean_R_NX
     quality: AUC_lnK_R_NX
     quality: total_correlation
     quality: cophenetic_correlation
     quality: distance_correlation
     quality: reconstruction_rmse
     embedding: LLE
     2022-07-04 23:02:09: Isomap START
     2022-07-04 23:02:09: constructing knn graph
     2022-07-04 23:02:09: calculating geodesic distances
     2022-07-04 23:02:09: Classical Scaling
     2022-07-04 23:02:09: Isomap START
     2022-07-04 23:02:09: constructing knn graph
     2022-07-04 23:02:09: calculating geodesic distances
     2022-07-04 23:02:09: Classical Scaling
     2022-07-04 23:02:09: Calculating kernel PCA
     2022-07-04 23:02:09: Trying to calculate reverse
     2022-07-04 23:02:09: DONE
     2022-07-04 23:02:09: Calculating kernel PCA
     2022-07-04 23:02:09: Trying to calculate reverse
     2022-07-04 23:02:09: DONE
     2022-07-04 23:02:09: Calculating kernel PCA
     2022-07-04 23:02:09: Trying to calculate reverse
     No inverse function.
     2022-07-04 23:02:09: DONE
     2022-07-04 23:02:09: Calculating kernel PCA
     2022-07-04 23:02:09: Trying to calculate reverse
     2022-07-04 23:02:09: DONE
     2022-07-04 23:02:09: Calculating kernel PCA
     2022-07-04 23:02:09: Trying to calculate reverse
     2022-07-04 23:02:09: DONE
     2022-07-04 23:02:09: Calculating kernel PCA
     2022-07-04 23:02:10: Trying to calculate reverse
     2022-07-04 23:02:10: DONE
     2022-07-04 23:02:10: Calculating kernel PCA
     2022-07-04 23:02:10: Trying to calculate reverse
     2022-07-04 23:02:10: DONE
     2022-07-04 23:02:10: Calculating kernel PCA
     2022-07-04 23:02:10: Trying to calculate reverse
     2022-07-04 23:02:10: DONE
     2022-07-04 23:02:10: Calculating kernel PCA
     2022-07-04 23:02:10: Trying to calculate reverse
     No inverse function.
     2022-07-04 23:02:11: DONE
     2022-07-04 23:02:11: Calculating kernel PCA
     2022-07-04 23:02:11: Trying to calculate reverse
     No inverse function.
     2022-07-04 23:02:12: DONE
     [ FAIL 1 | WARN 0 | SKIP 6 | PASS 175 ]
    
     == Skipped tests ===============================================================
     * TensorFlow not available for testing (5)
     * umap-learn not available, install with `pip install umap-learn==0.4` (1)
    
     == Failed tests ================================================================
     -- Error (test_high_level_functions.R:21:11): high level functions working? ----
     Error in `chckpkg("lle")`: require 'lle' package, install it using install.packages('lle')
     Backtrace:
     x
     1. +-base::suppressWarnings(...) at test_high_level_functions.R:21:10
     2. | \-base::withCallingHandlers(...)
     3. +-dimRed::embed(scurve, e, .mute = c("message", "output"))
     4. \-dimRed::embed(scurve, e, .mute = c("message", "output"))
     5. \-dimRed (local) .local(.data, ...)
     6. +-base::do.call(methodObject@fun, args)
     7. \-dimRed (local) `<fn>`(data = `<dimRedDt>`, keep.org.data = TRUE, pars = `<named list>`)
     8. \-dimRed:::chckpkg("lle")
    
     [ FAIL 1 | WARN 0 | SKIP 6 | PASS 175 ]
     Error: Test failures
     Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 0.2.5
Check: tests
Result: ERROR
     Running ‘testthat.R’ [113s/180s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > library(testthat)
     > library(dimRed)
     Loading required package: DRR
     Loading required package: kernlab
     Loading required package: CVST
     Loading required package: Matrix
    
     Attaching package: 'dimRed'
    
     The following object is masked from 'package:stats':
    
     embed
    
     The following object is masked from 'package:base':
    
     as.data.frame
    
     >
     > test_check("dimRed")
     embedding: AutoEncoder
     embedding: DiffusionMaps
     quality: Q_local
     quality: Q_global
     quality: mean_R_NX
     quality: AUC_lnK_R_NX
     quality: total_correlation
     quality: cophenetic_correlation
     quality: distance_correlation
     quality: reconstruction_rmse
     embedding: DRR
     quality: Q_local
     quality: Q_global
     quality: mean_R_NX
     quality: AUC_lnK_R_NX
     quality: total_correlation
     quality: cophenetic_correlation
     quality: distance_correlation
     quality: reconstruction_rmse
     embedding: FastICA
     quality: Q_local
     quality: Q_global
     quality: mean_R_NX
     quality: AUC_lnK_R_NX
     quality: total_correlation
     quality: cophenetic_correlation
     quality: distance_correlation
     quality: reconstruction_rmse
     embedding: KamadaKawai
     quality: Q_local
     quality: Q_global
     quality: mean_R_NX
     quality: AUC_lnK_R_NX
     quality: total_correlation
     quality: cophenetic_correlation
     quality: distance_correlation
     quality: reconstruction_rmse
     embedding: DrL
     quality: Q_local
     quality: Q_global
     quality: mean_R_NX
     quality: AUC_lnK_R_NX
     quality: total_correlation
     quality: cophenetic_correlation
     quality: distance_correlation
     quality: reconstruction_rmse
     embedding: FruchtermanReingold
     quality: Q_local
     quality: Q_global
     quality: mean_R_NX
     quality: AUC_lnK_R_NX
     quality: total_correlation
     quality: cophenetic_correlation
     quality: distance_correlation
     quality: reconstruction_rmse
     embedding: HLLE
     quality: Q_local
     quality: Q_global
     quality: mean_R_NX
     quality: AUC_lnK_R_NX
     quality: total_correlation
     quality: cophenetic_correlation
     quality: distance_correlation
     quality: reconstruction_rmse
     embedding: Isomap
     quality: Q_local
     quality: Q_global
     quality: mean_R_NX
     quality: AUC_lnK_R_NX
     quality: total_correlation
     quality: cophenetic_correlation
     quality: distance_correlation
     quality: reconstruction_rmse
     embedding: kPCA
     quality: Q_local
     quality: Q_global
     quality: mean_R_NX
     quality: AUC_lnK_R_NX
     quality: total_correlation
     quality: cophenetic_correlation
     quality: distance_correlation
     quality: reconstruction_rmse
     embedding: PCA_L1
     quality: Q_local
     quality: Q_global
     quality: mean_R_NX
     quality: AUC_lnK_R_NX
     quality: total_correlation
     quality: cophenetic_correlation
     quality: distance_correlation
     quality: reconstruction_rmse
     embedding: LaplacianEigenmaps
     quality: Q_local
     quality: Q_global
     quality: mean_R_NX
     quality: AUC_lnK_R_NX
     quality: total_correlation
     quality: cophenetic_correlation
     quality: distance_correlation
     quality: reconstruction_rmse
     embedding: LLE
     2022-07-04 19:35:23: Isomap START
     2022-07-04 19:35:23: constructing knn graph
     2022-07-04 19:35:23: calculating geodesic distances
     2022-07-04 19:35:23: Classical Scaling
     2022-07-04 19:35:23: Isomap START
     2022-07-04 19:35:23: constructing knn graph
     2022-07-04 19:35:23: calculating geodesic distances
     2022-07-04 19:35:23: Classical Scaling
     2022-07-04 19:35:23: Calculating kernel PCA
     2022-07-04 19:35:23: Trying to calculate reverse
     2022-07-04 19:35:23: DONE
     2022-07-04 19:35:23: Calculating kernel PCA
     2022-07-04 19:35:23: Trying to calculate reverse
     2022-07-04 19:35:23: DONE
     2022-07-04 19:35:23: Calculating kernel PCA
     2022-07-04 19:35:23: Trying to calculate reverse
     No inverse function.
     2022-07-04 19:35:23: DONE
     2022-07-04 19:35:23: Calculating kernel PCA
     2022-07-04 19:35:24: Trying to calculate reverse
     2022-07-04 19:35:24: DONE
     2022-07-04 19:35:24: Calculating kernel PCA
     2022-07-04 19:35:24: Trying to calculate reverse
     2022-07-04 19:35:24: DONE
     2022-07-04 19:35:24: Calculating kernel PCA
     2022-07-04 19:35:24: Trying to calculate reverse
     2022-07-04 19:35:24: DONE
     2022-07-04 19:35:24: Calculating kernel PCA
     2022-07-04 19:35:24: Trying to calculate reverse
     2022-07-04 19:35:24: DONE
     2022-07-04 19:35:24: Calculating kernel PCA
     2022-07-04 19:35:24: Trying to calculate reverse
     2022-07-04 19:35:24: DONE
     2022-07-04 19:35:24: Calculating kernel PCA
     2022-07-04 19:35:24: Trying to calculate reverse
     No inverse function.
     2022-07-04 19:35:25: DONE
     2022-07-04 19:35:25: Calculating kernel PCA
     2022-07-04 19:35:25: Trying to calculate reverse
     No inverse function.
     2022-07-04 19:35:26: DONE
     [ FAIL 1 | WARN 0 | SKIP 6 | PASS 175 ]
    
     ══ Skipped tests ═══════════════════════════════════════════════════════════════
     • TensorFlow not available for testing (5)
     • umap-learn not available, install with `pip install umap-learn==0.4` (1)
    
     ══ Failed tests ════════════════════════════════════════════════════════════════
     ── Error (test_high_level_functions.R:21:11): high level functions working? ────
     Error in `chckpkg("lle")`: require 'lle' package, install it using install.packages('lle')
     Backtrace:
     ▆
     1. ├─base::suppressWarnings(...) at test_high_level_functions.R:21:10
     2. │ └─base::withCallingHandlers(...)
     3. ├─dimRed::embed(scurve, e, .mute = c("message", "output"))
     4. └─dimRed::embed(scurve, e, .mute = c("message", "output"))
     5. └─dimRed (local) .local(.data, ...)
     6. ├─base::do.call(methodObject@fun, args)
     7. └─dimRed (local) `<fn>`(data = `<dimRedDt>`, keep.org.data = TRUE, pars = `<named list>`)
     8. └─dimRed:::chckpkg("lle")
    
     [ FAIL 1 | WARN 0 | SKIP 6 | PASS 175 ]
     Error: Test failures
     Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 0.2.5
Check: Rd cross-references
Result: NOTE
    Undeclared package ‘CVST’ in Rd xrefs
    Unknown package ‘lle’ in Rd xrefs
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 0.2.5
Check: examples
Result: ERROR
    Running examples in ‘dimRed-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: LLE-class
    > ### Title: Locally Linear Embedding
    > ### Aliases: LLE-class LLE
    >
    > ### ** Examples
    >
    > dat <- loadDataSet("3D S Curve", n = 500)
    > emb <- embed(dat, "LLE", knn = 45)
    Error in chckpkg("lle") :
     require 'lle' package, install it using install.packages('lle')
    Calls: embed ... embed -> .local -> do.call -> <Anonymous> -> chckpkg
    Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 0.2.5
Check: tests
Result: ERROR
     Running ‘testthat.R’ [165s/199s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > library(testthat)
     > library(dimRed)
     Loading required package: DRR
     Loading required package: kernlab
     Loading required package: CVST
     Loading required package: Matrix
    
     Attaching package: 'dimRed'
    
     The following object is masked from 'package:stats':
    
     embed
    
     The following object is masked from 'package:base':
    
     as.data.frame
    
     >
     > test_check("dimRed")
     embedding: AutoEncoder
     embedding: DiffusionMaps
     quality: Q_local
     quality: Q_global
     quality: mean_R_NX
     quality: AUC_lnK_R_NX
     quality: total_correlation
     quality: cophenetic_correlation
     quality: distance_correlation
     quality: reconstruction_rmse
     embedding: DRR
     quality: Q_local
     quality: Q_global
     quality: mean_R_NX
     quality: AUC_lnK_R_NX
     quality: total_correlation
     quality: cophenetic_correlation
     quality: distance_correlation
     quality: reconstruction_rmse
     embedding: FastICA
     quality: Q_local
     quality: Q_global
     quality: mean_R_NX
     quality: AUC_lnK_R_NX
     quality: total_correlation
     quality: cophenetic_correlation
     quality: distance_correlation
     quality: reconstruction_rmse
     embedding: KamadaKawai
     quality: Q_local
     quality: Q_global
     quality: mean_R_NX
     quality: AUC_lnK_R_NX
     quality: total_correlation
     quality: cophenetic_correlation
     quality: distance_correlation
     quality: reconstruction_rmse
     embedding: DrL
     quality: Q_local
     quality: Q_global
     quality: mean_R_NX
     quality: AUC_lnK_R_NX
     quality: total_correlation
     quality: cophenetic_correlation
     quality: distance_correlation
     quality: reconstruction_rmse
     embedding: FruchtermanReingold
     quality: Q_local
     quality: Q_global
     quality: mean_R_NX
     quality: AUC_lnK_R_NX
     quality: total_correlation
     quality: cophenetic_correlation
     quality: distance_correlation
     quality: reconstruction_rmse
     embedding: HLLE
     quality: Q_local
     quality: Q_global
     quality: mean_R_NX
     quality: AUC_lnK_R_NX
     quality: total_correlation
     quality: cophenetic_correlation
     quality: distance_correlation
     quality: reconstruction_rmse
     embedding: Isomap
     quality: Q_local
     quality: Q_global
     quality: mean_R_NX
     quality: AUC_lnK_R_NX
     quality: total_correlation
     quality: cophenetic_correlation
     quality: distance_correlation
     quality: reconstruction_rmse
     embedding: kPCA
     quality: Q_local
     quality: Q_global
     quality: mean_R_NX
     quality: AUC_lnK_R_NX
     quality: total_correlation
     quality: cophenetic_correlation
     quality: distance_correlation
     quality: reconstruction_rmse
     embedding: PCA_L1
     quality: Q_local
     quality: Q_global
     quality: mean_R_NX
     quality: AUC_lnK_R_NX
     quality: total_correlation
     quality: cophenetic_correlation
     quality: distance_correlation
     quality: reconstruction_rmse
     embedding: LaplacianEigenmaps
     quality: Q_local
     quality: Q_global
     quality: mean_R_NX
     quality: AUC_lnK_R_NX
     quality: total_correlation
     quality: cophenetic_correlation
     quality: distance_correlation
     quality: reconstruction_rmse
     embedding: LLE
     2022-06-26 00:55:34: Isomap START
     2022-06-26 00:55:34: constructing knn graph
     2022-06-26 00:55:34: calculating geodesic distances
     2022-06-26 00:55:34: Classical Scaling
     2022-06-26 00:55:34: Isomap START
     2022-06-26 00:55:34: constructing knn graph
     2022-06-26 00:55:34: calculating geodesic distances
     2022-06-26 00:55:34: Classical Scaling
     2022-06-26 00:55:34: Calculating kernel PCA
     2022-06-26 00:55:34: Trying to calculate reverse
     2022-06-26 00:55:34: DONE
     2022-06-26 00:55:34: Calculating kernel PCA
     2022-06-26 00:55:34: Trying to calculate reverse
     2022-06-26 00:55:34: DONE
     2022-06-26 00:55:34: Calculating kernel PCA
     2022-06-26 00:55:34: Trying to calculate reverse
     No inverse function.
     2022-06-26 00:55:34: DONE
     2022-06-26 00:55:34: Calculating kernel PCA
     2022-06-26 00:55:34: Trying to calculate reverse
     2022-06-26 00:55:34: DONE
     2022-06-26 00:55:34: Calculating kernel PCA
     2022-06-26 00:55:34: Trying to calculate reverse
     2022-06-26 00:55:34: DONE
     2022-06-26 00:55:34: Calculating kernel PCA
     2022-06-26 00:55:34: Trying to calculate reverse
     2022-06-26 00:55:34: DONE
     2022-06-26 00:55:34: Calculating kernel PCA
     2022-06-26 00:55:34: Trying to calculate reverse
     2022-06-26 00:55:34: DONE
     2022-06-26 00:55:34: Calculating kernel PCA
     2022-06-26 00:55:34: Trying to calculate reverse
     2022-06-26 00:55:34: DONE
     2022-06-26 00:55:34: Calculating kernel PCA
     2022-06-26 00:55:35: Trying to calculate reverse
     No inverse function.
     2022-06-26 00:55:36: DONE
     2022-06-26 00:55:36: Calculating kernel PCA
     2022-06-26 00:55:36: Trying to calculate reverse
     No inverse function.
     2022-06-26 00:55:37: DONE
     [ FAIL 1 | WARN 0 | SKIP 6 | PASS 175 ]
    
     ══ Skipped tests ═══════════════════════════════════════════════════════════════
     • TensorFlow not available for testing (5)
     • umap-learn not available, install with `pip install umap-learn==0.4` (1)
    
     ══ Failed tests ════════════════════════════════════════════════════════════════
     ── Error (test_high_level_functions.R:21:11): high level functions working? ────
     Error in `chckpkg("lle")`: require 'lle' package, install it using install.packages('lle')
     Backtrace:
     ▆
     1. ├─base::suppressWarnings(...) at test_high_level_functions.R:21:10
     2. │ └─base::withCallingHandlers(...)
     3. ├─dimRed::embed(scurve, e, .mute = c("message", "output"))
     4. └─dimRed::embed(scurve, e, .mute = c("message", "output"))
     5. └─dimRed .local(.data, ...)
     6. ├─base::do.call(methodObject@fun, args)
     7. └─dimRed `<fn>`(data = `<dimRedDt>`, keep.org.data = TRUE, pars = `<named list>`)
     8. └─dimRed:::chckpkg("lle")
    
     [ FAIL 1 | WARN 0 | SKIP 6 | PASS 175 ]
     Error: Test failures
     Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 0.2.5
Check: tests
Result: ERROR
     Running ‘testthat.R’ [189s/242s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > library(testthat)
     > library(dimRed)
     Loading required package: DRR
     Loading required package: kernlab
     Loading required package: CVST
     Loading required package: Matrix
    
     Attaching package: 'dimRed'
    
     The following object is masked from 'package:stats':
    
     embed
    
     The following object is masked from 'package:base':
    
     as.data.frame
    
     >
     > test_check("dimRed")
     embedding: AutoEncoder
     embedding: DiffusionMaps
     quality: Q_local
     quality: Q_global
     quality: mean_R_NX
     quality: AUC_lnK_R_NX
     quality: total_correlation
     quality: cophenetic_correlation
     quality: distance_correlation
     quality: reconstruction_rmse
     embedding: DRR
     quality: Q_local
     quality: Q_global
     quality: mean_R_NX
     quality: AUC_lnK_R_NX
     quality: total_correlation
     quality: cophenetic_correlation
     quality: distance_correlation
     quality: reconstruction_rmse
     embedding: FastICA
     quality: Q_local
     quality: Q_global
     quality: mean_R_NX
     quality: AUC_lnK_R_NX
     quality: total_correlation
     quality: cophenetic_correlation
     quality: distance_correlation
     quality: reconstruction_rmse
     embedding: KamadaKawai
     quality: Q_local
     quality: Q_global
     quality: mean_R_NX
     quality: AUC_lnK_R_NX
     quality: total_correlation
     quality: cophenetic_correlation
     quality: distance_correlation
     quality: reconstruction_rmse
     embedding: DrL
     quality: Q_local
     quality: Q_global
     quality: mean_R_NX
     quality: AUC_lnK_R_NX
     quality: total_correlation
     quality: cophenetic_correlation
     quality: distance_correlation
     quality: reconstruction_rmse
     embedding: FruchtermanReingold
     quality: Q_local
     quality: Q_global
     quality: mean_R_NX
     quality: AUC_lnK_R_NX
     quality: total_correlation
     quality: cophenetic_correlation
     quality: distance_correlation
     quality: reconstruction_rmse
     embedding: HLLE
     quality: Q_local
     quality: Q_global
     quality: mean_R_NX
     quality: AUC_lnK_R_NX
     quality: total_correlation
     quality: cophenetic_correlation
     quality: distance_correlation
     quality: reconstruction_rmse
     embedding: Isomap
     quality: Q_local
     quality: Q_global
     quality: mean_R_NX
     quality: AUC_lnK_R_NX
     quality: total_correlation
     quality: cophenetic_correlation
     quality: distance_correlation
     quality: reconstruction_rmse
     embedding: kPCA
     quality: Q_local
     quality: Q_global
     quality: mean_R_NX
     quality: AUC_lnK_R_NX
     quality: total_correlation
     quality: cophenetic_correlation
     quality: distance_correlation
     quality: reconstruction_rmse
     embedding: PCA_L1
     quality: Q_local
     quality: Q_global
     quality: mean_R_NX
     quality: AUC_lnK_R_NX
     quality: total_correlation
     quality: cophenetic_correlation
     quality: distance_correlation
     quality: reconstruction_rmse
     embedding: LaplacianEigenmaps
     quality: Q_local
     quality: Q_global
     quality: mean_R_NX
     quality: AUC_lnK_R_NX
     quality: total_correlation
     quality: cophenetic_correlation
     quality: distance_correlation
     quality: reconstruction_rmse
     embedding: LLE
     2022-07-02 23:03:06: Isomap START
     2022-07-02 23:03:06: constructing knn graph
     2022-07-02 23:03:06: calculating geodesic distances
     2022-07-02 23:03:06: Classical Scaling
     2022-07-02 23:03:06: Isomap START
     2022-07-02 23:03:06: constructing knn graph
     2022-07-02 23:03:06: calculating geodesic distances
     2022-07-02 23:03:06: Classical Scaling
     2022-07-02 23:03:06: Calculating kernel PCA
     2022-07-02 23:03:07: Trying to calculate reverse
     2022-07-02 23:03:07: DONE
     2022-07-02 23:03:07: Calculating kernel PCA
     2022-07-02 23:03:07: Trying to calculate reverse
     2022-07-02 23:03:07: DONE
     2022-07-02 23:03:07: Calculating kernel PCA
     2022-07-02 23:03:07: Trying to calculate reverse
     No inverse function.
     2022-07-02 23:03:07: DONE
     2022-07-02 23:03:07: Calculating kernel PCA
     2022-07-02 23:03:07: Trying to calculate reverse
     2022-07-02 23:03:07: DONE
     2022-07-02 23:03:07: Calculating kernel PCA
     2022-07-02 23:03:07: Trying to calculate reverse
     2022-07-02 23:03:07: DONE
     2022-07-02 23:03:07: Calculating kernel PCA
     2022-07-02 23:03:07: Trying to calculate reverse
     2022-07-02 23:03:07: DONE
     2022-07-02 23:03:07: Calculating kernel PCA
     2022-07-02 23:03:07: Trying to calculate reverse
     2022-07-02 23:03:07: DONE
     2022-07-02 23:03:07: Calculating kernel PCA
     2022-07-02 23:03:08: Trying to calculate reverse
     2022-07-02 23:03:08: DONE
     2022-07-02 23:03:08: Calculating kernel PCA
     2022-07-02 23:03:08: Trying to calculate reverse
     No inverse function.
     2022-07-02 23:03:09: DONE
     2022-07-02 23:03:09: Calculating kernel PCA
     2022-07-02 23:03:09: Trying to calculate reverse
     No inverse function.
     2022-07-02 23:03:10: DONE
     [ FAIL 1 | WARN 0 | SKIP 6 | PASS 175 ]
    
     ══ Skipped tests ═══════════════════════════════════════════════════════════════
     • TensorFlow not available for testing (5)
     • umap-learn not available, install with `pip install umap-learn==0.4` (1)
    
     ══ Failed tests ════════════════════════════════════════════════════════════════
     ── Error (test_high_level_functions.R:21:11): high level functions working? ────
     Error in `chckpkg("lle")`: require 'lle' package, install it using install.packages('lle')
     Backtrace:
     ▆
     1. ├─base::suppressWarnings(...) at test_high_level_functions.R:21:10
     2. │ └─base::withCallingHandlers(...)
     3. ├─dimRed::embed(scurve, e, .mute = c("message", "output"))
     4. └─dimRed::embed(scurve, e, .mute = c("message", "output"))
     5. └─dimRed (local) .local(.data, ...)
     6. ├─base::do.call(methodObject@fun, args)
     7. └─dimRed (local) `<fn>`(data = `<dimRedDt>`, keep.org.data = TRUE, pars = `<named list>`)
     8. └─dimRed:::chckpkg("lle")
    
     [ FAIL 1 | WARN 0 | SKIP 6 | PASS 175 ]
     Error: Test failures
     Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 0.2.5
Check: tests
Result: ERROR
     Running ‘testthat.R’ [142s/169s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > library(testthat)
     > library(dimRed)
     Loading required package: DRR
     Loading required package: kernlab
     Loading required package: CVST
     Loading required package: Matrix
    
     Attaching package: 'dimRed'
    
     The following object is masked from 'package:stats':
    
     embed
    
     The following object is masked from 'package:base':
    
     as.data.frame
    
     >
     > test_check("dimRed")
     embedding: AutoEncoder
     embedding: DiffusionMaps
     quality: Q_local
     quality: Q_global
     quality: mean_R_NX
     quality: AUC_lnK_R_NX
     quality: total_correlation
     quality: cophenetic_correlation
     quality: distance_correlation
     quality: reconstruction_rmse
     embedding: DRR
     quality: Q_local
     quality: Q_global
     quality: mean_R_NX
     quality: AUC_lnK_R_NX
     quality: total_correlation
     quality: cophenetic_correlation
     quality: distance_correlation
     quality: reconstruction_rmse
     embedding: FastICA
     quality: Q_local
     quality: Q_global
     quality: mean_R_NX
     quality: AUC_lnK_R_NX
     quality: total_correlation
     quality: cophenetic_correlation
     quality: distance_correlation
     quality: reconstruction_rmse
     embedding: KamadaKawai
     quality: Q_local
     quality: Q_global
     quality: mean_R_NX
     quality: AUC_lnK_R_NX
     quality: total_correlation
     quality: cophenetic_correlation
     quality: distance_correlation
     quality: reconstruction_rmse
     embedding: DrL
     quality: Q_local
     quality: Q_global
     quality: mean_R_NX
     quality: AUC_lnK_R_NX
     quality: total_correlation
     quality: cophenetic_correlation
     quality: distance_correlation
     quality: reconstruction_rmse
     embedding: FruchtermanReingold
     quality: Q_local
     quality: Q_global
     quality: mean_R_NX
     quality: AUC_lnK_R_NX
     quality: total_correlation
     quality: cophenetic_correlation
     quality: distance_correlation
     quality: reconstruction_rmse
     embedding: HLLE
     quality: Q_local
     quality: Q_global
     quality: mean_R_NX
     quality: AUC_lnK_R_NX
     quality: total_correlation
     quality: cophenetic_correlation
     quality: distance_correlation
     quality: reconstruction_rmse
     embedding: Isomap
     quality: Q_local
     quality: Q_global
     quality: mean_R_NX
     quality: AUC_lnK_R_NX
     quality: total_correlation
     quality: cophenetic_correlation
     quality: distance_correlation
     quality: reconstruction_rmse
     embedding: kPCA
     quality: Q_local
     quality: Q_global
     quality: mean_R_NX
     quality: AUC_lnK_R_NX
     quality: total_correlation
     quality: cophenetic_correlation
     quality: distance_correlation
     quality: reconstruction_rmse
     embedding: PCA_L1
     quality: Q_local
     quality: Q_global
     quality: mean_R_NX
     quality: AUC_lnK_R_NX
     quality: total_correlation
     quality: cophenetic_correlation
     quality: distance_correlation
     quality: reconstruction_rmse
     embedding: LaplacianEigenmaps
     quality: Q_local
     quality: Q_global
     quality: mean_R_NX
     quality: AUC_lnK_R_NX
     quality: total_correlation
     quality: cophenetic_correlation
     quality: distance_correlation
     quality: reconstruction_rmse
     embedding: LLE
     2022-07-02 14:58:32: Isomap START
     2022-07-02 14:58:32: constructing knn graph
     2022-07-02 14:58:32: calculating geodesic distances
     2022-07-02 14:58:32: Classical Scaling
     2022-07-02 14:58:32: Isomap START
     2022-07-02 14:58:32: constructing knn graph
     2022-07-02 14:58:32: calculating geodesic distances
     2022-07-02 14:58:32: Classical Scaling
     2022-07-02 14:58:32: Calculating kernel PCA
     2022-07-02 14:58:32: Trying to calculate reverse
     2022-07-02 14:58:32: DONE
     2022-07-02 14:58:32: Calculating kernel PCA
     2022-07-02 14:58:32: Trying to calculate reverse
     2022-07-02 14:58:32: DONE
     2022-07-02 14:58:32: Calculating kernel PCA
     2022-07-02 14:58:32: Trying to calculate reverse
     No inverse function.
     2022-07-02 14:58:32: DONE
     2022-07-02 14:58:32: Calculating kernel PCA
     2022-07-02 14:58:32: Trying to calculate reverse
     2022-07-02 14:58:32: DONE
     2022-07-02 14:58:32: Calculating kernel PCA
     2022-07-02 14:58:32: Trying to calculate reverse
     2022-07-02 14:58:32: DONE
     2022-07-02 14:58:32: Calculating kernel PCA
     2022-07-02 14:58:32: Trying to calculate reverse
     2022-07-02 14:58:32: DONE
     2022-07-02 14:58:32: Calculating kernel PCA
     2022-07-02 14:58:32: Trying to calculate reverse
     2022-07-02 14:58:32: DONE
     2022-07-02 14:58:32: Calculating kernel PCA
     2022-07-02 14:58:32: Trying to calculate reverse
     2022-07-02 14:58:32: DONE
     2022-07-02 14:58:32: Calculating kernel PCA
     2022-07-02 14:58:33: Trying to calculate reverse
     No inverse function.
     2022-07-02 14:58:33: DONE
     2022-07-02 14:58:33: Calculating kernel PCA
     2022-07-02 14:58:33: Trying to calculate reverse
     No inverse function.
     2022-07-02 14:58:35: DONE
     [ FAIL 1 | WARN 0 | SKIP 6 | PASS 175 ]
    
     ══ Skipped tests ═══════════════════════════════════════════════════════════════
     • TensorFlow not available for testing (5)
     • umap-learn not available, install with `pip install umap-learn==0.4` (1)
    
     ══ Failed tests ════════════════════════════════════════════════════════════════
     ── Error (test_high_level_functions.R:21:11): high level functions working? ────
     Error in `chckpkg("lle")`: require 'lle' package, install it using install.packages('lle')
     Backtrace:
     ▆
     1. ├─base::suppressWarnings(...) at test_high_level_functions.R:21:10
     2. │ └─base::withCallingHandlers(...)
     3. ├─dimRed::embed(scurve, e, .mute = c("message", "output"))
     4. └─dimRed::embed(scurve, e, .mute = c("message", "output"))
     5. └─dimRed (local) .local(.data, ...)
     6. ├─base::do.call(methodObject@fun, args)
     7. └─dimRed (local) `<fn>`(data = `<dimRedDt>`, keep.org.data = TRUE, pars = `<named list>`)
     8. └─dimRed:::chckpkg("lle")
    
     [ FAIL 1 | WARN 0 | SKIP 6 | PASS 175 ]
     Error: Test failures
     Execution halted
Flavor: r-patched-linux-x86_64

Version: 0.2.5
Check: tests
Result: ERROR
     Running ‘testthat.R’ [142s/168s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > library(testthat)
     > library(dimRed)
     Loading required package: DRR
     Loading required package: kernlab
     Loading required package: CVST
     Loading required package: Matrix
    
     Attaching package: 'dimRed'
    
     The following object is masked from 'package:stats':
    
     embed
    
     The following object is masked from 'package:base':
    
     as.data.frame
    
     >
     > test_check("dimRed")
     embedding: AutoEncoder
     embedding: DiffusionMaps
     quality: Q_local
     quality: Q_global
     quality: mean_R_NX
     quality: AUC_lnK_R_NX
     quality: total_correlation
     quality: cophenetic_correlation
     quality: distance_correlation
     quality: reconstruction_rmse
     embedding: DRR
     quality: Q_local
     quality: Q_global
     quality: mean_R_NX
     quality: AUC_lnK_R_NX
     quality: total_correlation
     quality: cophenetic_correlation
     quality: distance_correlation
     quality: reconstruction_rmse
     embedding: FastICA
     quality: Q_local
     quality: Q_global
     quality: mean_R_NX
     quality: AUC_lnK_R_NX
     quality: total_correlation
     quality: cophenetic_correlation
     quality: distance_correlation
     quality: reconstruction_rmse
     embedding: KamadaKawai
     quality: Q_local
     quality: Q_global
     quality: mean_R_NX
     quality: AUC_lnK_R_NX
     quality: total_correlation
     quality: cophenetic_correlation
     quality: distance_correlation
     quality: reconstruction_rmse
     embedding: DrL
     quality: Q_local
     quality: Q_global
     quality: mean_R_NX
     quality: AUC_lnK_R_NX
     quality: total_correlation
     quality: cophenetic_correlation
     quality: distance_correlation
     quality: reconstruction_rmse
     embedding: FruchtermanReingold
     quality: Q_local
     quality: Q_global
     quality: mean_R_NX
     quality: AUC_lnK_R_NX
     quality: total_correlation
     quality: cophenetic_correlation
     quality: distance_correlation
     quality: reconstruction_rmse
     embedding: HLLE
     quality: Q_local
     quality: Q_global
     quality: mean_R_NX
     quality: AUC_lnK_R_NX
     quality: total_correlation
     quality: cophenetic_correlation
     quality: distance_correlation
     quality: reconstruction_rmse
     embedding: Isomap
     quality: Q_local
     quality: Q_global
     quality: mean_R_NX
     quality: AUC_lnK_R_NX
     quality: total_correlation
     quality: cophenetic_correlation
     quality: distance_correlation
     quality: reconstruction_rmse
     embedding: kPCA
     quality: Q_local
     quality: Q_global
     quality: mean_R_NX
     quality: AUC_lnK_R_NX
     quality: total_correlation
     quality: cophenetic_correlation
     quality: distance_correlation
     quality: reconstruction_rmse
     embedding: PCA_L1
     quality: Q_local
     quality: Q_global
     quality: mean_R_NX
     quality: AUC_lnK_R_NX
     quality: total_correlation
     quality: cophenetic_correlation
     quality: distance_correlation
     quality: reconstruction_rmse
     embedding: LaplacianEigenmaps
     quality: Q_local
     quality: Q_global
     quality: mean_R_NX
     quality: AUC_lnK_R_NX
     quality: total_correlation
     quality: cophenetic_correlation
     quality: distance_correlation
     quality: reconstruction_rmse
     embedding: LLE
     2022-07-03 18:30:24: Isomap START
     2022-07-03 18:30:24: constructing knn graph
     2022-07-03 18:30:24: calculating geodesic distances
     2022-07-03 18:30:24: Classical Scaling
     2022-07-03 18:30:24: Isomap START
     2022-07-03 18:30:24: constructing knn graph
     2022-07-03 18:30:24: calculating geodesic distances
     2022-07-03 18:30:24: Classical Scaling
     2022-07-03 18:30:24: Calculating kernel PCA
     2022-07-03 18:30:24: Trying to calculate reverse
     2022-07-03 18:30:24: DONE
     2022-07-03 18:30:24: Calculating kernel PCA
     2022-07-03 18:30:24: Trying to calculate reverse
     2022-07-03 18:30:24: DONE
     2022-07-03 18:30:24: Calculating kernel PCA
     2022-07-03 18:30:24: Trying to calculate reverse
     No inverse function.
     2022-07-03 18:30:24: DONE
     2022-07-03 18:30:24: Calculating kernel PCA
     2022-07-03 18:30:24: Trying to calculate reverse
     2022-07-03 18:30:24: DONE
     2022-07-03 18:30:24: Calculating kernel PCA
     2022-07-03 18:30:24: Trying to calculate reverse
     2022-07-03 18:30:24: DONE
     2022-07-03 18:30:24: Calculating kernel PCA
     2022-07-03 18:30:24: Trying to calculate reverse
     2022-07-03 18:30:24: DONE
     2022-07-03 18:30:24: Calculating kernel PCA
     2022-07-03 18:30:24: Trying to calculate reverse
     2022-07-03 18:30:24: DONE
     2022-07-03 18:30:24: Calculating kernel PCA
     2022-07-03 18:30:24: Trying to calculate reverse
     2022-07-03 18:30:24: DONE
     2022-07-03 18:30:24: Calculating kernel PCA
     2022-07-03 18:30:25: Trying to calculate reverse
     No inverse function.
     2022-07-03 18:30:25: DONE
     2022-07-03 18:30:25: Calculating kernel PCA
     2022-07-03 18:30:25: Trying to calculate reverse
     No inverse function.
     2022-07-03 18:30:26: DONE
     [ FAIL 1 | WARN 0 | SKIP 6 | PASS 175 ]
    
     ══ Skipped tests ═══════════════════════════════════════════════════════════════
     • TensorFlow not available for testing (5)
     • umap-learn not available, install with `pip install umap-learn==0.4` (1)
    
     ══ Failed tests ════════════════════════════════════════════════════════════════
     ── Error (test_high_level_functions.R:21:11): high level functions working? ────
     Error in `chckpkg("lle")`: require 'lle' package, install it using install.packages('lle')
     Backtrace:
     ▆
     1. ├─base::suppressWarnings(...) at test_high_level_functions.R:21:10
     2. │ └─base::withCallingHandlers(...)
     3. ├─dimRed::embed(scurve, e, .mute = c("message", "output"))
     4. └─dimRed::embed(scurve, e, .mute = c("message", "output"))
     5. └─dimRed (local) .local(.data, ...)
     6. ├─base::do.call(methodObject@fun, args)
     7. └─dimRed (local) `<fn>`(data = `<dimRedDt>`, keep.org.data = TRUE, pars = `<named list>`)
     8. └─dimRed:::chckpkg("lle")
    
     [ FAIL 1 | WARN 0 | SKIP 6 | PASS 175 ]
     Error: Test failures
     Execution halted
Flavor: r-release-linux-x86_64

Version: 0.2.5
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: ‘pcaL1’
Flavor: r-oldrel-macos-arm64