CRAN Package Check Results for Package Seurat

Last updated on 2019-03-20 23:52:31 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 2.3.4 74.58 356.30 430.88 ERROR
r-devel-linux-x86_64-debian-gcc 2.3.4 64.13 281.82 345.95 ERROR
r-devel-linux-x86_64-fedora-clang 2.3.4 550.81 ERROR
r-devel-linux-x86_64-fedora-gcc 2.3.4 503.04 ERROR
r-devel-windows-ix86+x86_64 2.3.4 223.00 729.00 952.00 ERROR
r-patched-linux-x86_64 2.3.4 69.37 335.98 405.35 NOTE
r-patched-solaris-x86 2.3.4 756.50 NOTE
r-release-linux-x86_64 2.3.4 71.15 340.81 411.96 NOTE
r-release-windows-ix86+x86_64 2.3.4 141.00 519.00 660.00 NOTE
r-release-osx-x86_64 2.3.4 NOTE
r-oldrel-windows-ix86+x86_64 2.3.4 176.00 849.00 1025.00 NOTE
r-oldrel-osx-x86_64 2.3.4 NOTE

Check Details

Version: 2.3.4
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: 'loomR'
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 2.3.4
Check: tests
Result: ERROR
     Running 'testthat.R' [63s/102s]
    Running the tests in 'tests/testthat.R' failed.
    Complete output:
     > library(testthat)
     > library(Seurat)
     Loading required package: ggplot2
     Loading required package: cowplot
    
     Attaching package: 'cowplot'
    
     The following object is masked from 'package:ggplot2':
    
     ggsave
    
     Loading required package: Matrix
     >
     > test_check("Seurat")
     Running CCA
     Merging objects
     Performing log-normalization
     0% 10 20 30 40 50 60 70 80 90 100%
     [----|----|----|----|----|----|----|----|----|----|
     **************************************************|
    
     |
     | | 0%
     |
     |======================================================================| 100%
     Rescaling group 1
    
     |
     | | 0%
     |
     |======================================================================| 100%
     Rescaling group 2
    
     |
     | | 0%
     |
     |======================================================================| 100%
     Aligning dimension 1
     Aligning dimension 2
     Aligning dimension 3
     Aligning dimension 4
     Aligning dimension 5
     Calculating for group1
     Separating group1 cells
     Running Dimensional Reduction
     Calculating for group2
     Separating group2 cells
     Running Dimensional Reduction
     [1] "Computing CC 1"
     Performing log-normalization
     0% 10 20 30 40 50 60 70 80 90 100%
     [----|----|----|----|----|----|----|----|----|----|
     **************************************************|
    
     |
     | | 0%
     |
     |======================================================================| 100%
     Computing nearest neighbor graph
     Computing SNN
     -- 1. Failure: Row merging done correctly (@test_data_manipulation.R#22) ------
     m3[1, 14] not equal to -0.17.
     1/1 mismatches
     [1] 0 - -0.17 == 0.17
    
     -- 2. Failure: Row merging done correctly (@test_data_manipulation.R#23) ------
     m3[3, 2] not equal to -1.4.
     1/1 mismatches
     [1] 0 - -1.4 == 1.4
    
     -- 3. Error: Row merging done correctly (@test_data_manipulation.R#24) --------
     index larger than maximal 13
     1: expect_equal(m3[14, 18], -0.43) at testthat/test_data_manipulation.R:24
     2: quasi_label(enquo(object), label)
     3: eval_bare(get_expr(quo), get_env(quo))
     4: m3[14, 18]
     5: m3[14, 18]
     6: callGeneric(x, i = i, j = j, drop = TRUE)
     7: eval(call, parent.frame())
     8: eval(call, parent.frame())
     9: x[i = i, j = j, drop = TRUE]
     10: x[i = i, j = j, drop = TRUE]
     11: subCsp_ij(x, i, j, drop = drop)
     12: intI(i, n = d[1], dn[[1]], give.dn = FALSE)
     13: stop(gettextf("index larger than maximal %d", n), domain = NA)
    
     -- 4. Failure: max.cells.per.ident downsamples properly (@test_interaction.R#70)
     x[1] not equal to "GCAGCTCTGTTTCT".
     1/1 mismatches
     x[1]: "GGCCGATGTACTCT"
     y[1]: "GCAGCTCTGTTTCT"
    
     Performing log-normalization
     0% 10 20 30 40 50 60 70 80 90 100%
     [----|----|----|----|----|----|----|----|----|----|
     **************************************************|
    
     |
     | | 0%
     |
     |======================================================================| 100%
    
     |
     | | 0%
     |
     |======================================================================| 100%
    
     |
     | | 0%
     |
     |======================================================================| 100%
    
     |
     | | 0%
     |
     |======================================================================| 100%
     Calculating gene means
     0% 10 20 30 40 50 60 70 80 90 100%
     [----|----|----|----|----|----|----|----|----|----|
     **************************************************|
     Calculating gene variance to mean ratios
     0% 10 20 30 40 50 60 70 80 90 100%
     [----|----|----|----|----|----|----|----|----|----|
     **************************************************|
     Performing log-normalization
     0% 10 20 30 40 50 60 70 80 90 100%
     [----|----|----|----|----|----|----|----|----|----|
     **************************************************|
     NormalizeData has not been run, therefore ScaleData is running on non-normalized values. Recommended workflow is to run NormalizeData first.
     ScaleData is running on non-normalized values. Recommended workflow is to run NormalizeData first.
    
     |
     | | 0%
     |
     |======================================================================| 100%
     Calculating gene means
     0% 10 20 30 40 50 60 70 80 90 100%
     [----|----|----|----|----|----|----|----|----|----|
     **************************************************|
     Calculating gene variance to mean ratios
     0% 10 20 30 40 50 60 70 80 90 100%
     [----|----|----|----|----|----|----|----|----|----|
     **************************************************|
     Running CCA
     Merging objects
     Performing log-normalization
     0% 10 20 30 40 50 60 70 80 90 100%
     [----|----|----|----|----|----|----|----|----|----|
     **************************************************|
    
     |
     | | 0%
     |
     |======================================================================| 100%
     Running CCA
     -- 5. Failure: CCA returns the expected cell.embeddings matrix values when run o
     abs(unname(c3@dr$cca@cell.embeddings[1, 1])) not equal to 0.3108733.
     1/1 mismatches
     [1] 0.534 - 0.311 == 0.224
    
     -- 6. Failure: CCA returns the expected cell.embeddings matrix values when run o
     abs(unname(c3@dr$cca@cell.embeddings[14, 3])) not equal to 0.6064297.
     1/1 mismatches
     [1] 0.404 - 0.606 == -0.202
    
     -- 7. Failure: CCA returns the expected cell.embeddings matrix values when run o
     abs(unname(c4@dr$cca@cell.embeddings[1, 1])) not equal to 0.3108733.
     1/1 mismatches
     [1] 0.534 - 0.311 == 0.224
    
     -- 8. Failure: CCA returns the expected cell.embeddings matrix values when run o
     abs(unname(c4@dr$cca@cell.embeddings[14, 3])) not equal to 0.6064297.
     1/1 mismatches
     [1] 0.404 - 0.606 == -0.202
    
     Computing nearest neighbor graph
     Computing SNN
     == testthat results ===========================================================
     OK: 347 SKIPPED: 0 FAILED: 8
     1. Failure: Row merging done correctly (@test_data_manipulation.R#22)
     2. Failure: Row merging done correctly (@test_data_manipulation.R#23)
     3. Error: Row merging done correctly (@test_data_manipulation.R#24)
     4. Failure: max.cells.per.ident downsamples properly (@test_interaction.R#70)
     5. Failure: CCA returns the expected cell.embeddings matrix values when run on two objects (@test_seurat_object.R#228)
     6. Failure: CCA returns the expected cell.embeddings matrix values when run on two objects (@test_seurat_object.R#229)
     7. Failure: CCA returns the expected cell.embeddings matrix values when run on single object (@test_seurat_object.R#234)
     8. Failure: CCA returns the expected cell.embeddings matrix values when run on single object (@test_seurat_object.R#235)
    
     Error: testthat unit tests failed
     Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 2.3.4
Check: tests
Result: ERROR
     Running ‘testthat.R’ [54s/113s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > library(testthat)
     > library(Seurat)
     Loading required package: ggplot2
     Loading required package: cowplot
    
     Attaching package: 'cowplot'
    
     The following object is masked from 'package:ggplot2':
    
     ggsave
    
     Loading required package: Matrix
     >
     > test_check("Seurat")
     Running CCA
     Merging objects
     Performing log-normalization
     0% 10 20 30 40 50 60 70 80 90 100%
     [----|----|----|----|----|----|----|----|----|----|
     **************************************************|
    
     |
     | | 0%
     |
     |======================================================================| 100%
     Rescaling group 1
    
     |
     | | 0%
     |
     |======================================================================| 100%
     Rescaling group 2
    
     |
     | | 0%
     |
     |======================================================================| 100%
     Aligning dimension 1
     Aligning dimension 2
     Aligning dimension 3
     Aligning dimension 4
     Aligning dimension 5
     Calculating for group1
     Separating group1 cells
     Running Dimensional Reduction
     Calculating for group2
     Separating group2 cells
     Running Dimensional Reduction
     [1] "Computing CC 1"
     Performing log-normalization
     0% 10 20 30 40 50 60 70 80 90 100%
     [----|----|----|----|----|----|----|----|----|----|
     **************************************************|
    
     |
     | | 0%
     |
     |======================================================================| 100%
     Computing nearest neighbor graph
     Computing SNN
     ── 1. Failure: Row merging done correctly (@test_data_manipulation.R#22) ──────
     m3[1, 14] not equal to -0.17.
     1/1 mismatches
     [1] 0 - -0.17 == 0.17
    
     ── 2. Failure: Row merging done correctly (@test_data_manipulation.R#23) ──────
     m3[3, 2] not equal to -1.4.
     1/1 mismatches
     [1] 0 - -1.4 == 1.4
    
     ── 3. Error: Row merging done correctly (@test_data_manipulation.R#24) ────────
     index larger than maximal 13
     1: expect_equal(m3[14, 18], -0.43) at testthat/test_data_manipulation.R:24
     2: quasi_label(enquo(object), label)
     3: eval_bare(get_expr(quo), get_env(quo))
     4: m3[14, 18]
     5: m3[14, 18]
     6: callGeneric(x, i = i, j = j, drop = TRUE)
     7: eval(call, parent.frame())
     8: eval(call, parent.frame())
     9: x[i = i, j = j, drop = TRUE]
     10: x[i = i, j = j, drop = TRUE]
     11: subCsp_ij(x, i, j, drop = drop)
     12: intI(i, n = d[1], dn[[1]], give.dn = FALSE)
     13: stop(gettextf("index larger than maximal %d", n), domain = NA)
    
     ── 4. Failure: max.cells.per.ident downsamples properly (@test_interaction.R#70)
     x[1] not equal to "GCAGCTCTGTTTCT".
     1/1 mismatches
     x[1]: "GGCCGATGTACTCT"
     y[1]: "GCAGCTCTGTTTCT"
    
     Performing log-normalization
     0% 10 20 30 40 50 60 70 80 90 100%
     [----|----|----|----|----|----|----|----|----|----|
     **************************************************|
    
     |
     | | 0%
     |
     |======================================================================| 100%
    
     |
     | | 0%
     |
     |======================================================================| 100%
    
     |
     | | 0%
     |
     |======================================================================| 100%
    
     |
     | | 0%
     |
     |======================================================================| 100%
     Calculating gene means
     0% 10 20 30 40 50 60 70 80 90 100%
     [----|----|----|----|----|----|----|----|----|----|
     **************************************************|
     Calculating gene variance to mean ratios
     0% 10 20 30 40 50 60 70 80 90 100%
     [----|----|----|----|----|----|----|----|----|----|
     **************************************************|
     Performing log-normalization
     0% 10 20 30 40 50 60 70 80 90 100%
     [----|----|----|----|----|----|----|----|----|----|
     **************************************************|
     NormalizeData has not been run, therefore ScaleData is running on non-normalized values. Recommended workflow is to run NormalizeData first.
     ScaleData is running on non-normalized values. Recommended workflow is to run NormalizeData first.
    
     |
     | | 0%
     |
     |======================================================================| 100%
     Calculating gene means
     0% 10 20 30 40 50 60 70 80 90 100%
     [----|----|----|----|----|----|----|----|----|----|
     **************************************************|
     Calculating gene variance to mean ratios
     0% 10 20 30 40 50 60 70 80 90 100%
     [----|----|----|----|----|----|----|----|----|----|
     **************************************************|
     Running CCA
     Merging objects
     Performing log-normalization
     0% 10 20 30 40 50 60 70 80 90 100%
     [----|----|----|----|----|----|----|----|----|----|
     **************************************************|
    
     |
     | | 0%
     |
     |======================================================================| 100%
     Running CCA
     ── 5. Failure: CCA returns the expected cell.embeddings matrix values when run o
     abs(unname(c3@dr$cca@cell.embeddings[1, 1])) not equal to 0.3108733.
     1/1 mismatches
     [1] 0.534 - 0.311 == 0.224
    
     ── 6. Failure: CCA returns the expected cell.embeddings matrix values when run o
     abs(unname(c3@dr$cca@cell.embeddings[14, 3])) not equal to 0.6064297.
     1/1 mismatches
     [1] 0.404 - 0.606 == -0.202
    
     ── 7. Failure: CCA returns the expected cell.embeddings matrix values when run o
     abs(unname(c4@dr$cca@cell.embeddings[1, 1])) not equal to 0.3108733.
     1/1 mismatches
     [1] 0.534 - 0.311 == 0.224
    
     ── 8. Failure: CCA returns the expected cell.embeddings matrix values when run o
     abs(unname(c4@dr$cca@cell.embeddings[14, 3])) not equal to 0.6064297.
     1/1 mismatches
     [1] 0.404 - 0.606 == -0.202
    
     Computing nearest neighbor graph
     Computing SNN
     ══ testthat results ═══════════════════════════════════════════════════════════
     OK: 347 SKIPPED: 0 FAILED: 8
     1. Failure: Row merging done correctly (@test_data_manipulation.R#22)
     2. Failure: Row merging done correctly (@test_data_manipulation.R#23)
     3. Error: Row merging done correctly (@test_data_manipulation.R#24)
     4. Failure: max.cells.per.ident downsamples properly (@test_interaction.R#70)
     5. Failure: CCA returns the expected cell.embeddings matrix values when run on two objects (@test_seurat_object.R#228)
     6. Failure: CCA returns the expected cell.embeddings matrix values when run on two objects (@test_seurat_object.R#229)
     7. Failure: CCA returns the expected cell.embeddings matrix values when run on single object (@test_seurat_object.R#234)
     8. Failure: CCA returns the expected cell.embeddings matrix values when run on single object (@test_seurat_object.R#235)
    
     Error: testthat unit tests failed
     Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 2.3.4
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking: 'loomR', 'MAST'
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 2.3.4
Check: installed package size
Result: NOTE
     installed size is 8.1Mb
     sub-directories of 1Mb or more:
     libs 6.6Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 2.3.4
Check: tests
Result: ERROR
     Running ‘testthat.R’ [77s/291s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > library(testthat)
     > library(Seurat)
     Loading required package: ggplot2
     Loading required package: cowplot
    
     Attaching package: 'cowplot'
    
     The following object is masked from 'package:ggplot2':
    
     ggsave
    
     Loading required package: Matrix
     >
     > test_check("Seurat")
     Running CCA
     Merging objects
     Performing log-normalization
     0% 10 20 30 40 50 60 70 80 90 100%
     [----|----|----|----|----|----|----|----|----|----|
     **************************************************|
    
     |
     | | 0%
     |
     |======================================================================| 100%
     Rescaling group 1
    
     |
     | | 0%
     |
     |======================================================================| 100%
     Rescaling group 2
    
     |
     | | 0%
     |
     |======================================================================| 100%
     Aligning dimension 1
     Aligning dimension 2
     Aligning dimension 3
     Aligning dimension 4
     Aligning dimension 5
     Calculating for group1
     Separating group1 cells
     Running Dimensional Reduction
     Calculating for group2
     Separating group2 cells
     Running Dimensional Reduction
     [1] "Computing CC 1"
     Performing log-normalization
     0% 10 20 30 40 50 60 70 80 90 100%
     [----|----|----|----|----|----|----|----|----|----|
     **************************************************|
    
     |
     | | 0%
     |
     |======================================================================| 100%
     Computing nearest neighbor graph
     Computing SNN
     ── 1. Failure: Row merging done correctly (@test_data_manipulation.R#22) ──────
     m3[1, 14] not equal to -0.17.
     1/1 mismatches
     [1] 0 - -0.17 == 0.17
    
     ── 2. Failure: Row merging done correctly (@test_data_manipulation.R#23) ──────
     m3[3, 2] not equal to -1.4.
     1/1 mismatches
     [1] 0 - -1.4 == 1.4
    
     ── 3. Error: Row merging done correctly (@test_data_manipulation.R#24) ────────
     index larger than maximal 13
     1: expect_equal(m3[14, 18], -0.43) at testthat/test_data_manipulation.R:24
     2: quasi_label(enquo(object), label)
     3: eval_bare(get_expr(quo), get_env(quo))
     4: m3[14, 18]
     5: m3[14, 18]
     6: callGeneric(x, i = i, j = j, drop = TRUE)
     7: eval(call, parent.frame())
     8: eval(call, parent.frame())
     9: x[i = i, j = j, drop = TRUE]
     10: x[i = i, j = j, drop = TRUE]
     11: subCsp_ij(x, i, j, drop = drop)
     12: intI(i, n = d[1], dn[[1]], give.dn = FALSE)
     13: stop(gettextf("index larger than maximal %d", n), domain = NA)
    
     ── 4. Failure: max.cells.per.ident downsamples properly (@test_interaction.R#70)
     x[1] not equal to "GCAGCTCTGTTTCT".
     1/1 mismatches
     x[1]: "GGCCGATGTACTCT"
     y[1]: "GCAGCTCTGTTTCT"
    
     Performing log-normalization
     0% 10 20 30 40 50 60 70 80 90 100%
     [----|----|----|----|----|----|----|----|----|----|
     **************************************************|
    
     |
     | | 0%
     |
     |======================================================================| 100%
    
     |
     | | 0%
     |
     |======================================================================| 100%
    
     |
     | | 0%
     |
     |======================================================================| 100%
    
     |
     | | 0%
     |
     |======================================================================| 100%
     Calculating gene means
     0% 10 20 30 40 50 60 70 80 90 100%
     [----|----|----|----|----|----|----|----|----|----|
     **************************************************|
     Calculating gene variance to mean ratios
     0% 10 20 30 40 50 60 70 80 90 100%
     [----|----|----|----|----|----|----|----|----|----|
     **************************************************|
     Performing log-normalization
     0% 10 20 30 40 50 60 70 80 90 100%
     [----|----|----|----|----|----|----|----|----|----|
     **************************************************|
     NormalizeData has not been run, therefore ScaleData is running on non-normalized values. Recommended workflow is to run NormalizeData first.
     ScaleData is running on non-normalized values. Recommended workflow is to run NormalizeData first.
    
     |
     | | 0%
     |
     |======================================================================| 100%
     Calculating gene means
     0% 10 20 30 40 50 60 70 80 90 100%
     [----|----|----|----|----|----|----|----|----|----|
     **************************************************|
     Calculating gene variance to mean ratios
     0% 10 20 30 40 50 60 70 80 90 100%
     [----|----|----|----|----|----|----|----|----|----|
     **************************************************|
     Running CCA
     Merging objects
     Performing log-normalization
     0% 10 20 30 40 50 60 70 80 90 100%
     [----|----|----|----|----|----|----|----|----|----|
     **************************************************|
    
     |
     | | 0%
     |
     |======================================================================| 100%
     Running CCA
     ── 5. Failure: CCA returns the expected cell.embeddings matrix values when run o
     abs(unname(c3@dr$cca@cell.embeddings[1, 1])) not equal to 0.3108733.
     1/1 mismatches
     [1] 0.534 - 0.311 == 0.224
    
     ── 6. Failure: CCA returns the expected cell.embeddings matrix values when run o
     abs(unname(c3@dr$cca@cell.embeddings[14, 3])) not equal to 0.6064297.
     1/1 mismatches
     [1] 0.404 - 0.606 == -0.202
    
     ── 7. Failure: CCA returns the expected cell.embeddings matrix values when run o
     abs(unname(c4@dr$cca@cell.embeddings[1, 1])) not equal to 0.3108733.
     1/1 mismatches
     [1] 0.534 - 0.311 == 0.224
    
     ── 8. Failure: CCA returns the expected cell.embeddings matrix values when run o
     abs(unname(c4@dr$cca@cell.embeddings[14, 3])) not equal to 0.6064297.
     1/1 mismatches
     [1] 0.404 - 0.606 == -0.202
    
     Computing nearest neighbor graph
     Computing SNN
     ══ testthat results ═══════════════════════════════════════════════════════════
     OK: 347 SKIPPED: 0 FAILED: 8
     1. Failure: Row merging done correctly (@test_data_manipulation.R#22)
     2. Failure: Row merging done correctly (@test_data_manipulation.R#23)
     3. Error: Row merging done correctly (@test_data_manipulation.R#24)
     4. Failure: max.cells.per.ident downsamples properly (@test_interaction.R#70)
     5. Failure: CCA returns the expected cell.embeddings matrix values when run on two objects (@test_seurat_object.R#228)
     6. Failure: CCA returns the expected cell.embeddings matrix values when run on two objects (@test_seurat_object.R#229)
     7. Failure: CCA returns the expected cell.embeddings matrix values when run on single object (@test_seurat_object.R#234)
     8. Failure: CCA returns the expected cell.embeddings matrix values when run on single object (@test_seurat_object.R#235)
    
     Error: testthat unit tests failed
     Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 2.3.4
Check: tests
Result: ERROR
     Running ‘testthat.R’ [75s/117s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > library(testthat)
     > library(Seurat)
     Loading required package: ggplot2
     Loading required package: cowplot
    
     Attaching package: 'cowplot'
    
     The following object is masked from 'package:ggplot2':
    
     ggsave
    
     Loading required package: Matrix
     >
     > test_check("Seurat")
     Running CCA
     Merging objects
     Performing log-normalization
     0% 10 20 30 40 50 60 70 80 90 100%
     [----|----|----|----|----|----|----|----|----|----|
     **************************************************|
    
     |
     | | 0%
     |
     |======================================================================| 100%
     Rescaling group 1
    
     |
     | | 0%
     |
     |======================================================================| 100%
     Rescaling group 2
    
     |
     | | 0%
     |
     |======================================================================| 100%
     Aligning dimension 1
     Aligning dimension 2
     Aligning dimension 3
     Aligning dimension 4
     Aligning dimension 5
     Calculating for group1
     Separating group1 cells
     Running Dimensional Reduction
     Calculating for group2
     Separating group2 cells
     Running Dimensional Reduction
     [1] "Computing CC 1"
     Performing log-normalization
     0% 10 20 30 40 50 60 70 80 90 100%
     [----|----|----|----|----|----|----|----|----|----|
     **************************************************|
    
     |
     | | 0%
     |
     |======================================================================| 100%
     Computing nearest neighbor graph
     Computing SNN
     ── 1. Failure: Row merging done correctly (@test_data_manipulation.R#22) ──────
     m3[1, 14] not equal to -0.17.
     1/1 mismatches
     [1] 0 - -0.17 == 0.17
    
     ── 2. Failure: Row merging done correctly (@test_data_manipulation.R#23) ──────
     m3[3, 2] not equal to -1.4.
     1/1 mismatches
     [1] 0 - -1.4 == 1.4
    
     ── 3. Error: Row merging done correctly (@test_data_manipulation.R#24) ────────
     index larger than maximal 13
     1: expect_equal(m3[14, 18], -0.43) at testthat/test_data_manipulation.R:24
     2: quasi_label(enquo(object), label)
     3: eval_bare(get_expr(quo), get_env(quo))
     4: m3[14, 18]
     5: m3[14, 18]
     6: callGeneric(x, i = i, j = j, drop = TRUE)
     7: eval(call, parent.frame())
     8: eval(call, parent.frame())
     9: x[i = i, j = j, drop = TRUE]
     10: x[i = i, j = j, drop = TRUE]
     11: subCsp_ij(x, i, j, drop = drop)
     12: intI(i, n = d[1], dn[[1]], give.dn = FALSE)
     13: stop(gettextf("index larger than maximal %d", n), domain = NA)
    
     ── 4. Failure: max.cells.per.ident downsamples properly (@test_interaction.R#70)
     x[1] not equal to "GCAGCTCTGTTTCT".
     1/1 mismatches
     x[1]: "GGCCGATGTACTCT"
     y[1]: "GCAGCTCTGTTTCT"
    
     Performing log-normalization
     0% 10 20 30 40 50 60 70 80 90 100%
     [----|----|----|----|----|----|----|----|----|----|
     **************************************************|
    
     |
     | | 0%
     |
     |======================================================================| 100%
    
     |
     | | 0%
     |
     |======================================================================| 100%
    
     |
     | | 0%
     |
     |======================================================================| 100%
    
     |
     | | 0%
     |
     |======================================================================| 100%
     Calculating gene means
     0% 10 20 30 40 50 60 70 80 90 100%
     [----|----|----|----|----|----|----|----|----|----|
     **************************************************|
     Calculating gene variance to mean ratios
     0% 10 20 30 40 50 60 70 80 90 100%
     [----|----|----|----|----|----|----|----|----|----|
     **************************************************|
     Performing log-normalization
     0% 10 20 30 40 50 60 70 80 90 100%
     [----|----|----|----|----|----|----|----|----|----|
     **************************************************|
     NormalizeData has not been run, therefore ScaleData is running on non-normalized values. Recommended workflow is to run NormalizeData first.
     ScaleData is running on non-normalized values. Recommended workflow is to run NormalizeData first.
    
     |
     | | 0%
     |
     |======================================================================| 100%
     Calculating gene means
     0% 10 20 30 40 50 60 70 80 90 100%
     [----|----|----|----|----|----|----|----|----|----|
     **************************************************|
     Calculating gene variance to mean ratios
     0% 10 20 30 40 50 60 70 80 90 100%
     [----|----|----|----|----|----|----|----|----|----|
     **************************************************|
     Running CCA
     Merging objects
     Performing log-normalization
     0% 10 20 30 40 50 60 70 80 90 100%
     [----|----|----|----|----|----|----|----|----|----|
     **************************************************|
    
     |
     | | 0%
     |
     |======================================================================| 100%
     Running CCA
     ── 5. Failure: CCA returns the expected cell.embeddings matrix values when run o
     abs(unname(c3@dr$cca@cell.embeddings[1, 1])) not equal to 0.3108733.
     1/1 mismatches
     [1] 0.534 - 0.311 == 0.224
    
     ── 6. Failure: CCA returns the expected cell.embeddings matrix values when run o
     abs(unname(c3@dr$cca@cell.embeddings[14, 3])) not equal to 0.6064297.
     1/1 mismatches
     [1] 0.404 - 0.606 == -0.202
    
     ── 7. Failure: CCA returns the expected cell.embeddings matrix values when run o
     abs(unname(c4@dr$cca@cell.embeddings[1, 1])) not equal to 0.3108733.
     1/1 mismatches
     [1] 0.534 - 0.311 == 0.224
    
     ── 8. Failure: CCA returns the expected cell.embeddings matrix values when run o
     abs(unname(c4@dr$cca@cell.embeddings[14, 3])) not equal to 0.6064297.
     1/1 mismatches
     [1] 0.404 - 0.606 == -0.202
    
     Computing nearest neighbor graph
     Computing SNN
     ══ testthat results ═══════════════════════════════════════════════════════════
     OK: 347 SKIPPED: 0 FAILED: 8
     1. Failure: Row merging done correctly (@test_data_manipulation.R#22)
     2. Failure: Row merging done correctly (@test_data_manipulation.R#23)
     3. Error: Row merging done correctly (@test_data_manipulation.R#24)
     4. Failure: max.cells.per.ident downsamples properly (@test_interaction.R#70)
     5. Failure: CCA returns the expected cell.embeddings matrix values when run on two objects (@test_seurat_object.R#228)
     6. Failure: CCA returns the expected cell.embeddings matrix values when run on two objects (@test_seurat_object.R#229)
     7. Failure: CCA returns the expected cell.embeddings matrix values when run on single object (@test_seurat_object.R#234)
     8. Failure: CCA returns the expected cell.embeddings matrix values when run on single object (@test_seurat_object.R#235)
    
     Error: testthat unit tests failed
     Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 2.3.4
Check: running tests for arch ‘i386’
Result: ERROR
     Running 'testthat.R' [98s]
    Running the tests in 'tests/testthat.R' failed.
    Complete output:
     > library(testthat)
     > library(Seurat)
     Loading required package: ggplot2
     Loading required package: cowplot
    
     Attaching package: 'cowplot'
    
     The following object is masked from 'package:ggplot2':
    
     ggsave
    
     Loading required package: Matrix
     >
     > test_check("Seurat")
     Running CCA
     Merging objects
     Performing log-normalization
     0% 10 20 30 40 50 60 70 80 90 100%
     [----|----|----|----|----|----|----|----|----|----|
     **************************************************|
    
     |
     | | 0%
     |
     |======================================================================| 100%
     Rescaling group 1
    
     |
     | | 0%
     |
     |======================================================================| 100%
     Rescaling group 2
    
     |
     | | 0%
     |
     |======================================================================| 100%
     Aligning dimension 1
     Aligning dimension 2
     Aligning dimension 3
     Aligning dimension 4
     Aligning dimension 5
     Calculating for group1
     Separating group1 cells
     Running Dimensional Reduction
     Calculating for group2
     Separating group2 cells
     Running Dimensional Reduction
     [1] "Computing CC 1"
     Performing log-normalization
     0% 10 20 30 40 50 60 70 80 90 100%
     [----|----|----|----|----|----|----|----|----|----|
     **************************************************|
    
     |
     | | 0%
     |
     |======================================================================| 100%
     Computing nearest neighbor graph
     Computing SNN
     -- 1. Failure: Row merging done correctly (@test_data_manipulation.R#22) ------
     m3[1, 14] not equal to -0.17.
     1/1 mismatches
     [1] 0 - -0.17 == 0.17
    
     -- 2. Failure: Row merging done correctly (@test_data_manipulation.R#23) ------
     m3[3, 2] not equal to -1.4.
     1/1 mismatches
     [1] 0 - -1.4 == 1.4
    
     -- 3. Error: Row merging done correctly (@test_data_manipulation.R#24) --------
     index larger than maximal 13
     1: expect_equal(m3[14, 18], -0.43) at testthat/test_data_manipulation.R:24
     2: quasi_label(enquo(object), label)
     3: eval_bare(get_expr(quo), get_env(quo))
     4: m3[14, 18]
     5: m3[14, 18]
     6: callGeneric(x, i = i, j = j, drop = TRUE)
     7: eval(call, parent.frame())
     8: eval(call, parent.frame())
     9: x[i = i, j = j, drop = TRUE]
     10: x[i = i, j = j, drop = TRUE]
     11: subCsp_ij(x, i, j, drop = drop)
     12: intI(i, n = d[1], dn[[1]], give.dn = FALSE)
     13: stop(gettextf("index larger than maximal %d", n), domain = NA)
    
     -- 4. Failure: max.cells.per.ident downsamples properly (@test_interaction.R#70)
     x[1] not equal to "GCAGCTCTGTTTCT".
     1/1 mismatches
     x[1]: "GGCCGATGTACTCT"
     y[1]: "GCAGCTCTGTTTCT"
    
     Performing log-normalization
     0% 10 20 30 40 50 60 70 80 90 100%
     [----|----|----|----|----|----|----|----|----|----|
     **************************************************|
    
     |
     | | 0%
     |
     |======================================================================| 100%
    
     |
     | | 0%
     |
     |======================================================================| 100%
    
     |
     | | 0%
     |
     |======================================================================| 100%
    
     |
     | | 0%
     |
     |======================================================================| 100%
     Calculating gene means
     0% 10 20 30 40 50 60 70 80 90 100%
     [----|----|----|----|----|----|----|----|----|----|
     **************************************************|
     Calculating gene variance to mean ratios
     0% 10 20 30 40 50 60 70 80 90 100%
     [----|----|----|----|----|----|----|----|----|----|
     **************************************************|
     Performing log-normalization
     0% 10 20 30 40 50 60 70 80 90 100%
     [----|----|----|----|----|----|----|----|----|----|
     **************************************************|
     NormalizeData has not been run, therefore ScaleData is running on non-normalized values. Recommended workflow is to run NormalizeData first.
     ScaleData is running on non-normalized values. Recommended workflow is to run NormalizeData first.
    
     |
     | | 0%
     |
     |======================================================================| 100%
     Calculating gene means
     0% 10 20 30 40 50 60 70 80 90 100%
     [----|----|----|----|----|----|----|----|----|----|
     **************************************************|
     Calculating gene variance to mean ratios
     0% 10 20 30 40 50 60 70 80 90 100%
     [----|----|----|----|----|----|----|----|----|----|
     **************************************************|
     Running CCA
     Merging objects
     Performing log-normalization
     0% 10 20 30 40 50 60 70 80 90 100%
     [----|----|----|----|----|----|----|----|----|----|
     **************************************************|
    
     |
     | | 0%
     |
     |======================================================================| 100%
     Running CCA
     -- 5. Failure: CCA returns the expected cell.embeddings matrix values when run o
     abs(unname(c3@dr$cca@cell.embeddings[1, 1])) not equal to 0.3108733.
     1/1 mismatches
     [1] 0.534 - 0.311 == 0.224
    
     -- 6. Failure: CCA returns the expected cell.embeddings matrix values when run o
     abs(unname(c3@dr$cca@cell.embeddings[14, 3])) not equal to 0.6064297.
     1/1 mismatches
     [1] 0.404 - 0.606 == -0.202
    
     -- 7. Failure: CCA returns the expected cell.embeddings matrix values when run o
     abs(unname(c4@dr$cca@cell.embeddings[1, 1])) not equal to 0.3108733.
     1/1 mismatches
     [1] 0.534 - 0.311 == 0.224
    
     -- 8. Failure: CCA returns the expected cell.embeddings matrix values when run o
     abs(unname(c4@dr$cca@cell.embeddings[14, 3])) not equal to 0.6064297.
     1/1 mismatches
     [1] 0.404 - 0.606 == -0.202
    
     Computing nearest neighbor graph
     Computing SNN
     == testthat results ===========================================================
     OK: 347 SKIPPED: 0 FAILED: 8
     1. Failure: Row merging done correctly (@test_data_manipulation.R#22)
     2. Failure: Row merging done correctly (@test_data_manipulation.R#23)
     3. Error: Row merging done correctly (@test_data_manipulation.R#24)
     4. Failure: max.cells.per.ident downsamples properly (@test_interaction.R#70)
     5. Failure: CCA returns the expected cell.embeddings matrix values when run on two objects (@test_seurat_object.R#228)
     6. Failure: CCA returns the expected cell.embeddings matrix values when run on two objects (@test_seurat_object.R#229)
     7. Failure: CCA returns the expected cell.embeddings matrix values when run on single object (@test_seurat_object.R#234)
     8. Failure: CCA returns the expected cell.embeddings matrix values when run on single object (@test_seurat_object.R#235)
    
     Error: testthat unit tests failed
     Execution halted
Flavor: r-devel-windows-ix86+x86_64

Version: 2.3.4
Check: running tests for arch ‘x64’
Result: ERROR
     Running 'testthat.R' [109s]
    Running the tests in 'tests/testthat.R' failed.
    Complete output:
     > library(testthat)
     > library(Seurat)
     Loading required package: ggplot2
     Loading required package: cowplot
    
     Attaching package: 'cowplot'
    
     The following object is masked from 'package:ggplot2':
    
     ggsave
    
     Loading required package: Matrix
     >
     > test_check("Seurat")
     Running CCA
     Merging objects
     Performing log-normalization
     0% 10 20 30 40 50 60 70 80 90 100%
     [----|----|----|----|----|----|----|----|----|----|
     **************************************************|
    
     |
     | | 0%
     |
     |======================================================================| 100%
     Rescaling group 1
    
     |
     | | 0%
     |
     |======================================================================| 100%
     Rescaling group 2
    
     |
     | | 0%
     |
     |======================================================================| 100%
     Aligning dimension 1
     Aligning dimension 2
     Aligning dimension 3
     Aligning dimension 4
     Aligning dimension 5
     Calculating for group1
     Separating group1 cells
     Running Dimensional Reduction
     Calculating for group2
     Separating group2 cells
     Running Dimensional Reduction
     [1] "Computing CC 1"
     Performing log-normalization
     0% 10 20 30 40 50 60 70 80 90 100%
     [----|----|----|----|----|----|----|----|----|----|
     **************************************************|
    
     |
     | | 0%
     |
     |======================================================================| 100%
     Computing nearest neighbor graph
     Computing SNN
     -- 1. Failure: Row merging done correctly (@test_data_manipulation.R#22) ------
     m3[1, 14] not equal to -0.17.
     1/1 mismatches
     [1] 0 - -0.17 == 0.17
    
     -- 2. Failure: Row merging done correctly (@test_data_manipulation.R#23) ------
     m3[3, 2] not equal to -1.4.
     1/1 mismatches
     [1] 0 - -1.4 == 1.4
    
     -- 3. Error: Row merging done correctly (@test_data_manipulation.R#24) --------
     index larger than maximal 13
     1: expect_equal(m3[14, 18], -0.43) at testthat/test_data_manipulation.R:24
     2: quasi_label(enquo(object), label)
     3: eval_bare(get_expr(quo), get_env(quo))
     4: m3[14, 18]
     5: m3[14, 18]
     6: callGeneric(x, i = i, j = j, drop = TRUE)
     7: eval(call, parent.frame())
     8: eval(call, parent.frame())
     9: x[i = i, j = j, drop = TRUE]
     10: x[i = i, j = j, drop = TRUE]
     11: subCsp_ij(x, i, j, drop = drop)
     12: intI(i, n = d[1], dn[[1]], give.dn = FALSE)
     13: stop(gettextf("index larger than maximal %d", n), domain = NA)
    
     -- 4. Failure: max.cells.per.ident downsamples properly (@test_interaction.R#70)
     x[1] not equal to "GCAGCTCTGTTTCT".
     1/1 mismatches
     x[1]: "GGCCGATGTACTCT"
     y[1]: "GCAGCTCTGTTTCT"
    
     Performing log-normalization
     0% 10 20 30 40 50 60 70 80 90 100%
     [----|----|----|----|----|----|----|----|----|----|
     **************************************************|
    
     |
     | | 0%
     |
     |======================================================================| 100%
    
     |
     | | 0%
     |
     |======================================================================| 100%
    
     |
     | | 0%
     |
     |======================================================================| 100%
    
     |
     | | 0%
     |
     |======================================================================| 100%
     Calculating gene means
     0% 10 20 30 40 50 60 70 80 90 100%
     [----|----|----|----|----|----|----|----|----|----|
     **************************************************|
     Calculating gene variance to mean ratios
     0% 10 20 30 40 50 60 70 80 90 100%
     [----|----|----|----|----|----|----|----|----|----|
     **************************************************|
     Performing log-normalization
     0% 10 20 30 40 50 60 70 80 90 100%
     [----|----|----|----|----|----|----|----|----|----|
     **************************************************|
     NormalizeData has not been run, therefore ScaleData is running on non-normalized values. Recommended workflow is to run NormalizeData first.
     ScaleData is running on non-normalized values. Recommended workflow is to run NormalizeData first.
    
     |
     | | 0%
     |
     |======================================================================| 100%
     Calculating gene means
     0% 10 20 30 40 50 60 70 80 90 100%
     [----|----|----|----|----|----|----|----|----|----|
     **************************************************|
     Calculating gene variance to mean ratios
     0% 10 20 30 40 50 60 70 80 90 100%
     [----|----|----|----|----|----|----|----|----|----|
     **************************************************|
     Running CCA
     Merging objects
     Performing log-normalization
     0% 10 20 30 40 50 60 70 80 90 100%
     [----|----|----|----|----|----|----|----|----|----|
     **************************************************|
    
     |
     | | 0%
     |
     |======================================================================| 100%
     Running CCA
     -- 5. Failure: CCA returns the expected cell.embeddings matrix values when run o
     abs(unname(c3@dr$cca@cell.embeddings[1, 1])) not equal to 0.3108733.
     1/1 mismatches
     [1] 0.534 - 0.311 == 0.224
    
     -- 6. Failure: CCA returns the expected cell.embeddings matrix values when run o
     abs(unname(c3@dr$cca@cell.embeddings[14, 3])) not equal to 0.6064297.
     1/1 mismatches
     [1] 0.404 - 0.606 == -0.202
    
     -- 7. Failure: CCA returns the expected cell.embeddings matrix values when run o
     abs(unname(c4@dr$cca@cell.embeddings[1, 1])) not equal to 0.3108733.
     1/1 mismatches
     [1] 0.534 - 0.311 == 0.224
    
     -- 8. Failure: CCA returns the expected cell.embeddings matrix values when run o
     abs(unname(c4@dr$cca@cell.embeddings[14, 3])) not equal to 0.6064297.
     1/1 mismatches
     [1] 0.404 - 0.606 == -0.202
    
     Computing nearest neighbor graph
     Computing SNN
     == testthat results ===========================================================
     OK: 347 SKIPPED: 0 FAILED: 8
     1. Failure: Row merging done correctly (@test_data_manipulation.R#22)
     2. Failure: Row merging done correctly (@test_data_manipulation.R#23)
     3. Error: Row merging done correctly (@test_data_manipulation.R#24)
     4. Failure: max.cells.per.ident downsamples properly (@test_interaction.R#70)
     5. Failure: CCA returns the expected cell.embeddings matrix values when run on two objects (@test_seurat_object.R#228)
     6. Failure: CCA returns the expected cell.embeddings matrix values when run on two objects (@test_seurat_object.R#229)
     7. Failure: CCA returns the expected cell.embeddings matrix values when run on single object (@test_seurat_object.R#234)
     8. Failure: CCA returns the expected cell.embeddings matrix values when run on single object (@test_seurat_object.R#235)
    
     Error: testthat unit tests failed
     Execution halted
Flavor: r-devel-windows-ix86+x86_64

Version: 2.3.4
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking:
     ‘loomR’ ‘made4’ ‘SingleCellExperiment’ ‘MAST’
Flavors: r-release-osx-x86_64, r-oldrel-osx-x86_64