| Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-05-10 11:37:45 -0400 (Fri, 10 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4662 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4393 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4424 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 44/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| alabaster.matrix 1.5.0 (landing page) Aaron Lun
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
| merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the alabaster.matrix package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/alabaster.matrix.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: alabaster.matrix |
| Version: 1.5.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:alabaster.matrix.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings alabaster.matrix_1.5.0.tar.gz |
| StartedAt: 2024-05-08 23:59:59 -0400 (Wed, 08 May 2024) |
| EndedAt: 2024-05-09 00:08:05 -0400 (Thu, 09 May 2024) |
| EllapsedTime: 486.8 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: alabaster.matrix.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:alabaster.matrix.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings alabaster.matrix_1.5.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/alabaster.matrix.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘alabaster.matrix/DESCRIPTION’ ... OK
* this is package ‘alabaster.matrix’ version ‘1.5.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘alabaster.matrix’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
14. └─alabaster.base:::validate(path, metadata)
── Error ('test-storeDelayedObject.R:693:5'): saving of a ResidualMatrix works correctly ──
Error in `.Call2(.NAME, ..., PACKAGE = "SparseArray")`: SparseArray internal error in get_leaf_nzoffs():
invalid SVT leaf
Backtrace:
▆
1. └─methods::as(out@seed@.matrix, "dgCMatrix") at test-storeDelayedObject.R:693:5
2. └─SparseArray (local) asMethod(object)
3. └─SparseArray:::.make_CsparseMatrix_from_SVT_SparseMatrix(...)
4. └─SparseArray:::SparseArray.Call(...)
5. └─S4Vectors::.Call2(.NAME, ..., PACKAGE = "SparseArray")
[ FAIL 27 | WARN 14 | SKIP 0 | PASS 571 ]
Error: Test failures
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.20-bioc/meat/alabaster.matrix.Rcheck/00check.log’
for details.
alabaster.matrix.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL alabaster.matrix ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘alabaster.matrix’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c collect_attributes.cpp -o collect_attributes.o clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o alabaster.matrix.so RcppExports.o collect_attributes.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-alabaster.matrix/00new/alabaster.matrix/libs ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (alabaster.matrix)
alabaster.matrix.Rcheck/tests/testthat.Rout.fail
R version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(alabaster.matrix)
Loading required package: alabaster.base
> test_check("alabaster.matrix")
[ FAIL 27 | WARN 14 | SKIP 0 | PASS 571 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-SparseMatrix.R:31:5'): reading a sparse matrix works with different output types ──
<std::runtime_error/C++Error/error/condition>
Error: failed to validate 'compressed_sparse_matrix' object at '/tmp/RtmptgXDqt/file9fb02774c7dd'; failed to validate sparse matrix indices at '/compressed_sparse_matrix/indices'; indices should be strictly increasing
Backtrace:
▆
1. └─alabaster.base::saveObject(x, tmp) at test-SparseMatrix.R:31:5
2. └─alabaster.base::validateObject(path)
3. └─alabaster.base:::validate(path, metadata)
── Error ('test-SparseMatrix.R:53:13'): writing to a sparse matrix works as expected for numeric data ──
<std::runtime_error/C++Error/error/condition>
Error: failed to validate 'compressed_sparse_matrix' object at '/tmp/RtmptgXDqt/file9fb02891686e.h5'; failed to validate sparse matrix indices at '/compressed_sparse_matrix/indices'; indices should be strictly increasing
Backtrace:
▆
1. └─alabaster.base::saveObject(x, tmp) at test-SparseMatrix.R:53:13
2. └─alabaster.base::validateObject(path)
3. └─alabaster.base:::validate(path, metadata)
── Error ('test-SparseMatrix.R:77:13'): writing to a sparse matrix works as expected for logical data ──
<std::runtime_error/C++Error/error/condition>
Error: failed to validate 'compressed_sparse_matrix' object at '/tmp/RtmptgXDqt/file9fb02abb4a9.h5'; failed to validate sparse matrix indices at '/compressed_sparse_matrix/indices'; indices should be strictly increasing
Backtrace:
▆
1. └─alabaster.base::saveObject(x, tmp) at test-SparseMatrix.R:77:13
2. └─alabaster.base::validateObject(path)
3. └─alabaster.base:::validate(path, metadata)
── Error ('test-SparseMatrix.R:100:13'): writing to a sparse matrix works as expected for integer data ──
<std::runtime_error/C++Error/error/condition>
Error: failed to validate 'compressed_sparse_matrix' object at '/tmp/RtmptgXDqt/file9fb027c14bd7.h5'; failed to validate sparse matrix indices at '/compressed_sparse_matrix/indices'; indices should be strictly increasing
Backtrace:
▆
1. └─alabaster.base::saveObject(x, tmp) at test-SparseMatrix.R:100:13
2. └─alabaster.base::validateObject(path)
3. └─alabaster.base:::validate(path, metadata)
── Error ('test-SparseMatrix.R:152:9'): depositing small chunks works correctly ──
<std::runtime_error/C++Error/error/condition>
Error: failed to validate 'compressed_sparse_matrix' object at '/tmp/RtmptgXDqt/file9fb02637d12c'; failed to validate sparse matrix indices at '/compressed_sparse_matrix/indices'; indices should be strictly increasing
Backtrace:
▆
1. └─base::eval(...)
2. └─base::eval(...)
3. └─alabaster.base::saveObject(y, tmp) at test-SparseMatrix.R:152:9
4. └─alabaster.base::validateObject(path)
5. └─alabaster.base:::validate(path, metadata)
── Error ('test-SparseMatrix.R:174:9'): fallback to large integer types for indices works correctly ──
<std::runtime_error/C++Error/error/condition>
Error: failed to validate 'compressed_sparse_matrix' object at '/tmp/RtmptgXDqt/file9fb01ca72ba0.h5'; failed to validate sparse matrix indices at '/compressed_sparse_matrix/indices'; indices should be strictly increasing
Backtrace:
▆
1. └─alabaster.base::saveObject(x, tmp) at test-SparseMatrix.R:174:9
2. └─alabaster.base::validateObject(path)
3. └─alabaster.base:::validate(path, metadata)
── Failure ('test-SparseMatrix.R:261:9'): writing an SVT matrix works with empty or near-empty storage ──
as.matrix(readObject(tmp)) not identical to `core`.
4/2000 mismatches (average diff: 43.2)
[201] 36 - 0 == 36
[237] 0 - -16 == 16
[730] 92 - 0 == 92
[793] 0 - 29 == -29
── Failure ('test-SparseMatrix.R:271:9'): writing an SVT matrix works with empty or near-empty storage ──
as.matrix(readObject(tmp)) not identical to `core2`.
4/2000 mismatches (average diff: 43.2)
[201] 36 - 0 == 36
[237] 0 - -16 == 16
[730] 92 - 0 == 92
[793] 0 - 29 == -29
── Failure ('test-SparseMatrix.R:281:9'): writing an SVT matrix works with empty or near-empty storage ──
as.matrix(readObject(tmp)) not identical to `core2`.
4 element mismatches
── Error ('test-SparseMatrix.R:260:9'): writing an SVT matrix works with empty or near-empty storage ──
<std::runtime_error/C++Error/error/condition>
Error: failed to validate 'compressed_sparse_matrix' object at '/tmp/RtmptgXDqt/file9fb07f68a1f'; failed to validate sparse matrix indices at '/compressed_sparse_matrix/indices'; out-of-range index (65535)
Backtrace:
▆
1. └─alabaster.base::saveObject(y, tmp) at test-SparseMatrix.R:260:9
2. └─alabaster.base::validateObject(path)
3. └─alabaster.base:::validate(path, metadata)
── Failure ('test-optimize_storage.R:423:14'): storage optimization works for sparse objects ──
out$type not identical to "H5T_NATIVE_UINT16".
1/1 mismatches
x[1]: "H5T_NATIVE_UINT8"
y[1]: "H5T_NATIVE_UINT16"
── Failure ('test-optimize_storage.R:424:14'): storage optimization works for sparse objects ──
out$placeholder not equal to 2^16 - 1.
target is NULL, current is numeric
── Failure ('test-optimize_storage.R:436:14'): storage optimization works for sparse objects ──
out$placeholder not equal to -1L.
target is NULL, current is numeric
── Failure ('test-optimize_storage.R:447:14'): storage optimization works for sparse objects ──
out$type not identical to "H5T_NATIVE_DOUBLE".
1/1 mismatches
x[1]: "H5T_NATIVE_UINT8"
y[1]: "H5T_NATIVE_DOUBLE"
── Failure ('test-optimize_storage.R:448:14'): storage optimization works for sparse objects ──
out$placeholder not equal to NaN.
target is NULL, current is numeric
── Failure ('test-sparse.R:28:9'): writing to a sparse matrix works as expected ──
unname(as.matrix(H5SparseMatrix(tmp, "csc_matrix"))) not identical to unname(as.matrix(x)).
1025/2000 mismatches (average diff: 4.94)
[1] 98 - -0.21 == 98.2
[2] 70 - 0.00 == 70.0
[3] 8 - 0.00 == 8.0
[4] 0 - 1.60 == -1.6
[6] 0 - -0.30 == 0.3
[7] 0 - 1.20 == -1.2
[9] 0 - 2.00 == -2.0
[10] 0 - 1.70 == -1.7
[12] 0 - -0.70 == 0.7
...
── Failure ('test-sparse.R:32:9'): writing to a sparse matrix works as expected ──
unname(as.matrix(H5SparseMatrix(tmp, "tenx_matrix"))) not identical to unname(as.matrix(x)).
1025/2000 mismatches (average diff: 4.94)
[1] 98 - -0.21 == 98.2
[2] 70 - 0.00 == 70.0
[3] 8 - 0.00 == 8.0
[4] 0 - 1.60 == -1.6
[6] 0 - -0.30 == 0.3
[7] 0 - 1.20 == -1.2
[9] 0 - 2.00 == -2.0
[10] 0 - 1.70 == -1.7
[12] 0 - -0.70 == 0.7
...
── Failure ('test-sparse.R:28:9'): writing to a sparse matrix works as expected ──
unname(as.matrix(H5SparseMatrix(tmp, "csc_matrix"))) not identical to unname(as.matrix(x)).
1530/3000 mismatches (average diff: 4.75)
[1] 98 - 0.000 == 98.000
[2] 99 - 0.000 == 99.000
[4] 0 - -0.074 == 0.074
[9] 0 - -0.720 == 0.720
[12] 0 - -1.100 == 1.100
[17] 0 - 0.310 == -0.310
[18] 0 - 0.130 == -0.130
[21] 0 - 1.600 == -1.600
[22] 0 - -1.600 == 1.600
...
── Failure ('test-sparse.R:32:9'): writing to a sparse matrix works as expected ──
unname(as.matrix(H5SparseMatrix(tmp, "tenx_matrix"))) not identical to unname(as.matrix(x)).
1530/3000 mismatches (average diff: 4.75)
[1] 98 - 0.000 == 98.000
[2] 99 - 0.000 == 99.000
[4] 0 - -0.074 == 0.074
[9] 0 - -0.720 == 0.720
[12] 0 - -1.100 == 1.100
[17] 0 - 0.310 == -0.310
[18] 0 - 0.130 == -0.130
[21] 0 - 1.600 == -1.600
[22] 0 - -1.600 == 1.600
...
── Failure ('test-sparse.R:53:9'): writing to a sparse matrix works with tiny chunks ──
unname(as.matrix(H5SparseMatrix(tmp, "csc_matrix"))) not identical to unname(as.matrix(x)).
1034/2000 mismatches (average diff: 4.95)
[1] 99 - 1.00 == 98.00
[2] 91 - -0.71 == 91.71
[3] 74 - -0.59 == 74.59
[4] 0 - -1.00 == 1.00
[7] 0 - -0.50 == 0.50
[9] 0 - 0.86 == -0.86
[11] 0 - 0.29 == -0.29
[12] 0 - 0.18 == -0.18
[13] 0 - -1.40 == 1.40
...
── Failure ('test-sparse.R:88:9'): writing to a sparse matrix works with guessed type ──
get_type\(tmp, "csc_matrix/data"\) does not match "I32".
Actual value: "H5T_STD_U16LE"
Backtrace:
▆
1. └─testthat::expect_match(get_type(tmp, "csc_matrix/data"), "I32") at test-sparse.R:88:9
2. └─testthat:::expect_match_(...)
── Failure ('test-sparse.R:89:9'): writing to a sparse matrix works with guessed type ──
unname(as.matrix(H5SparseMatrix(tmp, "csc_matrix"))) not equal to unname(as.matrix(y)).
659/2000 mismatches (average diff: 9.47)
[1] 95 - 0 == 95
[2] 76 - 0 == 76
[3] 94 - 0 == 94
[4] 31 - 0 == 31
[8] 0 - 1 == -1
[9] 0 - 2 == -2
[10] 0 - -1 == 1
[12] 0 - 1 == -1
[13] 0 - 3 == -3
...
── Error ('test-sparse.R:96:9'): writing to a sparse matrix works with guessed type ──
Error in `(function (cond)
.Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = "subscript out of bounds",
call = ans[nzindex(sas)] <- sas_nzdata, object = structure(c(0L,
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0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
0L, 0L, 0L, 0L), dim = c(100L, 20L)), subscript = 1L, index = 1001), class = c("subscriptOutOfBoundsError",
"error", "condition")))`: error in evaluating the argument 'x' in selecting a method for function 'drop': subscript out of bounds
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-sparse.R:96:9
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─base::unname(as.matrix(H5SparseMatrix(tmp, "csc_matrix")))
5. ├─base::as.matrix(H5SparseMatrix(tmp, "csc_matrix"))
6. ├─S4Arrays::as.matrix(H5SparseMatrix(tmp, "csc_matrix"))
7. │ └─S4Arrays (local) .local(x, ...)
8. │ ├─base::drop(as.array(x))
9. │ ├─base::as.array(x)
10. │ └─S4Arrays::as.array.Array(x)
11. │ └─S4Arrays:::.from_Array_to_array(x, ...)
12. │ ├─S4Arrays::extract_array(x, index)
13. │ └─DelayedArray::extract_array(x, index)
14. │ ├─methods::callNextMethod()
15. │ └─DelayedArray (local) .nextMethod(x = x, index = index)
16. │ ├─S4Arrays::extract_array(x@seed, index)
17. │ └─HDF5Array::extract_array(x@seed, index)
18. │ ├─S4Arrays::extract_array(sas, index)
19. │ └─DelayedArray::extract_array(sas, index)
20. │ └─DelayedArray::sparse2dense(sas0)
21. └─base (local) `<fn>`(`<sbscOOBE>`)
── Error ('test-storeDelayedObject.R:156:5'): sparse matrices are saved correctly ──
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'x' in selecting a method for function 'drop': SparseArray internal error in get_leaf_nzoffs():
invalid SVT leaf
Backtrace:
▆
1. ├─testthat::expect_identical(unname(as.matrix(X)), as.matrix(roundtrip)) at test-storeDelayedObject.R:156:5
2. │ └─testthat::quasi_label(enquo(expected), expected.label, arg = "expected")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─base::as.matrix(roundtrip)
5. ├─S4Arrays::as.matrix(roundtrip)
6. │ └─S4Arrays (local) .local(x, ...)
7. │ ├─base::drop(as.array(x))
8. │ ├─base::as.array(x)
9. │ └─S4Arrays::as.array.Array(x)
10. │ └─S4Arrays:::.from_Array_to_array(x, ...)
11. │ ├─S4Arrays::extract_array(x, index)
12. │ └─DelayedArray::extract_array(x, index)
13. │ ├─methods::callNextMethod()
14. │ └─DelayedArray (local) .nextMethod(x = x, index = index)
15. │ ├─S4Arrays::extract_array(x@seed, index)
16. │ └─SparseArray::extract_array(x@seed, index)
17. │ ├─base::as.array(subset_SVT_SparseArray(x, index, ignore.dimnames = TRUE))
18. │ └─SparseArray::as.array.SVT_SparseArray(...)
19. │ └─SparseArray:::.from_SVT_SparseArray_to_array(x)
20. │ └─SparseArray:::SparseArray.Call(...)
21. │ └─S4Vectors::.Call2(.NAME, ..., PACKAGE = "SparseArray")
22. └─base::.handleSimpleError(...)
23. └─base (local) h(simpleError(msg, call))
── Failure ('test-storeDelayedObject.R:184:5'): sparse matrix saving handles dimnames ──
as(X, "SVT_SparseMatrix") not identical to roundtrip@seed.
Attributes: < Component "SVT": Component 1: Component 1: Mean relative difference: 12.33333 >
Attributes: < Component "SVT": Component 1: Component 2: Mean relative difference: 0.925 >
Attributes: < Component "SVT": Component 2: Component 1: Mean relative difference: 23.05234 >
Attributes: < Component "SVT": Component 2: Component 2: Mean relative difference: 1.045347 >
Attributes: < Component "SVT": Component 3: Component 1: Mean relative difference: 8.502423 >
Attributes: < Component "SVT": Component 3: Component 2: Mean relative difference: 0.9569091 >
Attributes: < Component "SVT": Component 4: Component 1: Mean relative difference: 9.059946 >
Attributes: < Component "SVT": Component 4: Component 2: Mean relative difference: 1.007576 >
Attributes: < Component "SVT": Component 5: Component 1: Mean relative difference: 27.38889 >
...
── Error ('test-storeDelayedObject.R:190:5'): sparse matrices are saved to external arrays if requested ──
<std::runtime_error/C++Error/error/condition>
Error: failed to validate 'compressed_sparse_matrix' object at '/tmp/RtmptgXDqt/file9fb0709c27f0/seeds/0'; failed to validate sparse matrix indices at '/compressed_sparse_matrix/indices'; indices should be strictly increasing
Backtrace:
▆
1. └─alabaster.matrix (local) saveDelayed(DelayedArray(X), save.external.array = TRUE) at test-storeDelayedObject.R:190:5
2. ├─alabaster.base::saveObject(...) at test-storeDelayedObject.R:9:5
3. └─alabaster.matrix::saveObject(...)
4. └─alabaster.matrix (local) .local(x, path, ...)
5. ├─base::do.call(...)
6. ├─alabaster.matrix (local) `<stndrdGn>`(...)
7. └─alabaster.matrix (local) `<stndrdGn>`(...)
8. └─alabaster.matrix (local) .local(x, handle, name, ...)
9. ├─methods::callNextMethod()
10. └─alabaster.matrix (local) .nextMethod(x = x, handle = handle, name = name, save.external.array = save.external.array)
11. └─alabaster.matrix (local) .local(x, handle, name, ...)
12. └─alabaster.base::saveObject(x, file.path(exdir, n), ...)
13. └─alabaster.base::validateObject(path)
14. └─alabaster.base:::validate(path, metadata)
── Error ('test-storeDelayedObject.R:693:5'): saving of a ResidualMatrix works correctly ──
Error in `.Call2(.NAME, ..., PACKAGE = "SparseArray")`: SparseArray internal error in get_leaf_nzoffs():
invalid SVT leaf
Backtrace:
▆
1. └─methods::as(out@seed@.matrix, "dgCMatrix") at test-storeDelayedObject.R:693:5
2. └─SparseArray (local) asMethod(object)
3. └─SparseArray:::.make_CsparseMatrix_from_SVT_SparseMatrix(...)
4. └─SparseArray:::SparseArray.Call(...)
5. └─S4Vectors::.Call2(.NAME, ..., PACKAGE = "SparseArray")
[ FAIL 27 | WARN 14 | SKIP 0 | PASS 571 ]
Error: Test failures
Execution halted
alabaster.matrix.Rcheck/alabaster.matrix-Ex.timings
| name | user | system | elapsed | |
| AmalgamatedArray | 0.251 | 0.012 | 0.283 | |
| DelayedMask | 0.101 | 0.013 | 0.123 | |
| ReloadedArraySeed | 0.866 | 0.050 | 0.983 | |
| WrapperArraySeed | 0.037 | 0.004 | 0.042 | |
| createRawArraySeed | 0.172 | 0.016 | 0.206 | |
| preserveDelayedOperations | 0.000 | 0.001 | 0.001 | |
| readArray | 0.226 | 0.017 | 0.265 | |
| readDelayedArray | 0.230 | 0.037 | 0.327 | |
| readSparseMatrix | 0.255 | 0.041 | 0.311 | |
| recycleHdf5Files | 0.001 | 0.000 | 0.001 | |
| saveArray | 0.037 | 0.008 | 0.047 | |
| saveDelayedArray | 0.139 | 0.021 | 0.172 | |
| saveSparseMatrix | 0.061 | 0.010 | 0.080 | |
| storeDelayedObject | 0.461 | 0.067 | 0.577 | |
| writeSparseMatrix | 0.785 | 0.054 | 0.903 | |