CRAN Package Check Results for Package harmony

Last updated on 2022-10-30 07:55:14 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.1.0 ERROR
r-devel-linux-x86_64-debian-gcc 0.1.0 20.84 2.53 23.37 ERROR
r-devel-linux-x86_64-fedora-clang 0.1.0 57.86 ERROR
r-devel-linux-x86_64-fedora-gcc 0.1.0 49.67 ERROR
r-devel-windows-x86_64 0.1.0 45.00 138.00 183.00 ERROR
r-patched-linux-x86_64 0.1.0 23.45 3.44 26.89 ERROR
r-release-linux-x86_64 0.1.0 22.05 3.45 25.50 ERROR
r-release-macos-arm64 0.1.0 50.00 NOTE
r-release-macos-x86_64 0.1.0 100.00 NOTE
r-release-windows-x86_64 0.1.0 48.00 140.00 188.00 ERROR
r-oldrel-macos-arm64 0.1.0 76.00 NOTE
r-oldrel-macos-x86_64 0.1.0 69.00 NOTE
r-oldrel-windows-ix86+x86_64 0.1.0 118.00 158.00 276.00 ERROR

Check Details

Version: 0.1.0
Check: whether package can be installed
Result: ERROR
    Installation failed.
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: 0.1.0
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     harmony.cpp:211:80: warning: ISO C++ says that these are ambiguous, even though the worst conversion for the first is better than the worst conversion for the second:
Flavors: r-devel-windows-x86_64, r-release-windows-x86_64, r-oldrel-windows-ix86+x86_64

Version: 0.1.0
Check: examples
Result: ERROR
    Running examples in 'harmony-Ex.R' failed
    The error most likely occurred in:
    
    > ### Name: HarmonyMatrix
    > ### Title: Main Harmony interface
    > ### Aliases: HarmonyMatrix
    >
    > ### ** Examples
    >
    >
    >
    > ## By default, Harmony inputs a normalized gene expression matrix
    > ## Not run:
    > ##D harmony_embeddings <- HarmonyMatrix(exprs_matrix, meta_data, 'dataset')
    > ## End(Not run)
    >
    > ## Harmony can also take a PCA embeddings matrix
    > data(cell_lines_small)
    > pca_matrix <- cell_lines_small$scaled_pcs
    > meta_data <- cell_lines_small$meta_data
    > harmony_embeddings <- HarmonyMatrix(pca_matrix, meta_data, 'dataset',
    + do_pca=FALSE)
    Harmony 1/10
    0% 10 20 30 40 50 60 70 80 90 100%
    [----|----|----|----|----|----|----|----|----|----|
    **************************************************|
    Error in harmonyObj$cluster_cpp() :
     element-wise pow(): incompatible matrix dimensions: 10x3 and 3x1
    Calls: HarmonyMatrix -> harmonize -> cluster -> <Anonymous> -> .External
    Execution halted
Flavors: r-devel-windows-x86_64, r-release-windows-x86_64

Version: 0.1.0
Check: tests
Result: ERROR
     Running 'testthat.R' [9s]
    Running the tests in 'tests/testthat.R' failed.
    Complete output:
     > library(testthat)
     > library(harmony)
     Loading required package: Rcpp
     >
     > test_check("harmony")
     [ FAIL 1 | WARN 0 | SKIP 1 | PASS 0 ]
    
     ══ Skipped tests ═══════════════════════════════════════════════════════════════
     • Seurat V3 not available (1)
    
     ══ Failed tests ════════════════════════════════════════════════════════════════
     ── Error (test_integration.R:5:1): (code run outside of `test_that()`) ─────────
     <std::logic_error/C++Error/error/condition>
     Error in `harmonyObj$cluster_cpp()`: element-wise pow(): incompatible matrix dimensions: 50x3 and 3x1
     Backtrace:
     ▆
     1. └─harmony::HarmonyMatrix(...) at test_integration.R:5:0
     2. └─harmony:::harmonize(harmonyObj, max.iter.harmony, verbose)
     3. └─harmony:::cluster(harmonyObj)
     4. └─harmonyObj$cluster_cpp()
    
     [ FAIL 1 | WARN 0 | SKIP 1 | PASS 0 ]
     Error: Test failures
     Execution halted
Flavor: r-devel-windows-x86_64

Version: 0.1.0
Check: re-building of vignette outputs
Result: ERROR
    Error(s) in re-building vignettes:
    --- re-building 'quickstart.Rmd' using rmarkdown
    Quitting from lines 148-152 (quickstart.Rmd)
    Error: processing vignette 'quickstart.Rmd' failed with diagnostics:
    element-wise pow(): incompatible matrix dimensions: 79x3 and 3x1
    --- failed re-building 'quickstart.Rmd'
    
    SUMMARY: processing the following file failed:
     'quickstart.Rmd'
    
    Error: Vignette re-building failed.
    Execution halted
Flavors: r-devel-windows-x86_64, r-release-windows-x86_64

Version: 0.1.0
Check: installed package size
Result: NOTE
     installed size is 6.9Mb
     sub-directories of 1Mb or more:
     doc 1.4Mb
     libs 4.9Mb
Flavors: r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64

Version: 0.1.0
Check: tests
Result: ERROR
     Running 'testthat.R' [9s]
    Running the tests in 'tests/testthat.R' failed.
    Complete output:
     > library(testthat)
     > library(harmony)
     Loading required package: Rcpp
     >
     > test_check("harmony")
     [ FAIL 1 | WARN 0 | SKIP 1 | PASS 0 ]
    
     ══ Skipped tests ═══════════════════════════════════════════════════════════════
     • Seurat V3 not available (1)
    
     ══ Failed tests ════════════════════════════════════════════════════════════════
     ── Error ('test_integration.R:5'): (code run outside of `test_that()`) ─────────
     <std::logic_error/C++Error/error/condition>
     Error in `harmonyObj$cluster_cpp()`: element-wise pow(): incompatible matrix dimensions: 50x3 and 3x1
     Backtrace:
     ▆
     1. └─harmony::HarmonyMatrix(...) at test_integration.R:5:0
     2. └─harmony:::harmonize(harmonyObj, max.iter.harmony, verbose)
     3. └─harmony:::cluster(harmonyObj)
     4. └─harmonyObj$cluster_cpp()
    
     [ FAIL 1 | WARN 0 | SKIP 1 | PASS 0 ]
     Error: Test failures
     Execution halted
Flavor: r-release-windows-x86_64

Version: 0.1.0
Check: running examples for arch ‘i386’
Result: ERROR
    Running examples in 'harmony-Ex.R' failed
    The error most likely occurred in:
    
    > ### Name: HarmonyMatrix
    > ### Title: Main Harmony interface
    > ### Aliases: HarmonyMatrix
    >
    > ### ** Examples
    >
    >
    >
    > ## By default, Harmony inputs a normalized gene expression matrix
    > ## Not run:
    > ##D harmony_embeddings <- HarmonyMatrix(exprs_matrix, meta_data, 'dataset')
    > ## End(Not run)
    >
    > ## Harmony can also take a PCA embeddings matrix
    > data(cell_lines_small)
    > pca_matrix <- cell_lines_small$scaled_pcs
    > meta_data <- cell_lines_small$meta_data
    > harmony_embeddings <- HarmonyMatrix(pca_matrix, meta_data, 'dataset',
    + do_pca=FALSE)
    Harmony 1/10
    0% 10 20 30 40 50 60 70 80 90 100%
    [----|----|----|----|----|----|----|----|----|----|
    **************************************************|
    Error in harmonyObj$cluster_cpp() :
     element-wise pow(): incompatible matrix dimensions: 10x3 and 3x1
    Calls: HarmonyMatrix -> harmonize -> cluster -> <Anonymous> -> .External
    Execution halted
Flavor: r-oldrel-windows-ix86+x86_64

Version: 0.1.0
Check: running examples for arch ‘x64’
Result: ERROR
    Running examples in 'harmony-Ex.R' failed
    The error most likely occurred in:
    
    > ### Name: HarmonyMatrix
    > ### Title: Main Harmony interface
    > ### Aliases: HarmonyMatrix
    >
    > ### ** Examples
    >
    >
    >
    > ## By default, Harmony inputs a normalized gene expression matrix
    > ## Not run:
    > ##D harmony_embeddings <- HarmonyMatrix(exprs_matrix, meta_data, 'dataset')
    > ## End(Not run)
    >
    > ## Harmony can also take a PCA embeddings matrix
    > data(cell_lines_small)
    > pca_matrix <- cell_lines_small$scaled_pcs
    > meta_data <- cell_lines_small$meta_data
    > harmony_embeddings <- HarmonyMatrix(pca_matrix, meta_data, 'dataset',
    + do_pca=FALSE)
    Harmony 1/10
    0% 10 20 30 40 50 60 70 80 90 100%
    [----|----|----|----|----|----|----|----|----|----|
    **************************************************|
    Error in harmonyObj$cluster_cpp() :
     element-wise pow(): incompatible matrix dimensions: 10x3 and 3x1
    Calls: HarmonyMatrix -> harmonize -> cluster -> <Anonymous> -> .External
    Execution halted
Flavor: r-oldrel-windows-ix86+x86_64

Version: 0.1.0
Check: running tests for arch ‘i386’
Result: ERROR
     Running 'testthat.R' [9s]
    Running the tests in 'tests/testthat.R' failed.
    Complete output:
     > library(testthat)
     > library(harmony)
     Loading required package: Rcpp
     >
     > test_check("harmony")
     [ FAIL 1 | WARN 0 | SKIP 1 | PASS 0 ]
    
     == Skipped tests ===============================================================
     * Seurat V3 not available (1)
    
     == Failed tests ================================================================
     -- Error (test_integration.R:5:1): (code run outside of `test_that()`) ---------
     <std::logic_error/C++Error/error/condition>
     Error in `harmonyObj$cluster_cpp()`: element-wise pow(): incompatible matrix dimensions: 50x3 and 3x1
     Backtrace:
     x
     1. \-harmony::HarmonyMatrix(...) at test_integration.R:5:0
     2. \-harmony:::harmonize(harmonyObj, max.iter.harmony, verbose)
     3. \-harmony:::cluster(harmonyObj)
     4. \-harmonyObj$cluster_cpp()
    
     [ FAIL 1 | WARN 0 | SKIP 1 | PASS 0 ]
     Error: Test failures
     Execution halted
Flavor: r-oldrel-windows-ix86+x86_64

Version: 0.1.0
Check: running tests for arch ‘x64’
Result: ERROR
     Running 'testthat.R' [10s]
    Running the tests in 'tests/testthat.R' failed.
    Complete output:
     > library(testthat)
     > library(harmony)
     Loading required package: Rcpp
     >
     > test_check("harmony")
     [ FAIL 1 | WARN 0 | SKIP 1 | PASS 0 ]
    
     == Skipped tests ===============================================================
     * Seurat V3 not available (1)
    
     == Failed tests ================================================================
     -- Error (test_integration.R:5:1): (code run outside of `test_that()`) ---------
     <std::logic_error/C++Error/error/condition>
     Error in `harmonyObj$cluster_cpp()`: element-wise pow(): incompatible matrix dimensions: 50x3 and 3x1
     Backtrace:
     x
     1. \-harmony::HarmonyMatrix(...) at test_integration.R:5:0
     2. \-harmony:::harmonize(harmonyObj, max.iter.harmony, verbose)
     3. \-harmony:::cluster(harmonyObj)
     4. \-harmonyObj$cluster_cpp()
    
     [ FAIL 1 | WARN 0 | SKIP 1 | PASS 0 ]
     Error: Test failures
     Execution halted
Flavor: r-oldrel-windows-ix86+x86_64

Version: 0.1.0
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building 'quickstart.Rmd' using rmarkdown
    Quitting from lines 148-152 (quickstart.Rmd)
    Error: processing vignette 'quickstart.Rmd' failed with diagnostics:
    element-wise pow(): incompatible matrix dimensions: 79x3 and 3x1
    --- failed re-building 'quickstart.Rmd'
    
    SUMMARY: processing the following file failed:
     'quickstart.Rmd'
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-oldrel-windows-ix86+x86_64