Installation failed.
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/harmony.Rcheck/00install.out' for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/harmony.Rcheck/00install.out’ for details.
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/harmony.Rcheck/00install.out’ for details.
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-devel/harmony.Rcheck/00install.out’ for details.
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:
See 'd:/Rcompile/CRANpkg/local/4.3/harmony.Rcheck/00install.out' for details.
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
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
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
Installation failed.
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/harmony.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/harmony.Rcheck/00install.out’ for details.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   4.9Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   5.1Mb
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:
See 'd:/Rcompile/CRANpkg/local/4.2/harmony.Rcheck/00install.out' for details.
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
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
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
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   5.9Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   5.1Mb
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:
See 'd:/Rcompile/CRANpkg/local/4.1/harmony.Rcheck/00install.out' for details.
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
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
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
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
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