Last updated on 2025-06-08 03:50:47 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.5.5 | 27.53 | 246.91 | 274.44 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.5.5 | 18.86 | 177.29 | 196.15 | OK | |
| r-devel-linux-x86_64-fedora-clang | 0.5.5 | 459.10 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 0.5.5 | 430.45 | OK | |||
| r-devel-windows-x86_64 | 0.5.5 | 29.00 | 285.00 | 314.00 | OK | |
| r-patched-linux-x86_64 | 0.5.5 | 29.37 | 235.72 | 265.09 | OK | |
| r-release-linux-x86_64 | 0.5.5 | 27.13 | 233.55 | 260.68 | OK | |
| r-release-macos-arm64 | 0.5.5 | 123.00 | ERROR | |||
| r-release-macos-x86_64 | 0.5.5 | 223.00 | ERROR | |||
| r-release-windows-x86_64 | 0.5.5 | 29.00 | 288.00 | 317.00 | OK | |
| r-oldrel-macos-arm64 | 0.5.5 | 151.00 | OK | |||
| r-oldrel-macos-x86_64 | 0.5.5 | 11.00 | ERROR | |||
| r-oldrel-windows-x86_64 | 0.5.5 | 37.00 | 389.00 | 426.00 | OK |
Version: 0.5.5
Check: tests
Result: ERROR
Running ‘testthat.R’ [10s/18s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(BIGr)
>
> test_check("BIGr")
The Ref_0001 sequence had to be added for: 0 tags
The Alt_0002 sequence had to be added for: 1 tags
Tags discarded due to lack of Ref_0001 sequence: 0 tags
Tags discarded due to lack of Alt_0002 sequence: 0 tags
Scanning file to determine attributes.
File attributes:
meta lines: 14
header_line: 15
variant count: 499
column count: 159
Meta line 14 read in.
All meta lines processed.
gt matrix initialized.
Character matrix gt created.
Character matrix gt rows: 499
Character matrix gt cols: 159
skip: 0
nrows: 499
row_num: 0
Processed variant: 499
All variants processed
Scanning file to determine attributes.
File attributes:
meta lines: 14
header_line: 15
variant count: 499
column count: 159
Meta line 14 read in.
All meta lines processed.
gt matrix initialized.
Character matrix gt created.
Character matrix gt rows: 499
Character matrix gt cols: 159
skip: 0
nrows: 499
row_num: 0
Processed variant: 499
All variants processed
Scanning file to determine attributes.
File attributes:
meta lines: 14
header_line: 15
variant count: 499
column count: 159
Meta line 14 read in.
All meta lines processed.
gt matrix initialized.
Character matrix gt created.
Character matrix gt rows: 499
Character matrix gt cols: 159
skip: 0
nrows: 499
row_num: 0
Processed variant: 499
All variants processed
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 58 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-madc2vcf_all.R:16:3'): test madc offtargets ────────────────────
Error in `checkForRemoteErrors(val)`: 2 nodes produced errors; first error: 'recursive' must be a length-1 vector
Backtrace:
▆
1. └─BIGr::madc2vcf_all(...) at test-madc2vcf_all.R:16:3
2. └─BIGr:::loop_though_dartag_report(...)
3. └─parallel::parLapply(...)
4. ├─base::do.call(...)
5. └─parallel::clusterApply(...)
6. └─parallel:::staticClusterApply(cl, fun, length(x), argfun)
7. └─parallel:::checkForRemoteErrors(val)
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 58 ]
Error: Test failures
In addition: Warning messages:
1: closing unused connection 6 (<-localhost:11060)
2: closing unused connection 5 (<-localhost:11060)
Execution halted
Flavor: r-release-macos-arm64
Version: 0.5.5
Check: tests
Result: ERROR
Running ‘testthat.R’ [15s/28s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(BIGr)
>
> test_check("BIGr")
The Ref_0001 sequence had to be added for: 0 tags
The Alt_0002 sequence had to be added for: 1 tags
Tags discarded due to lack of Ref_0001 sequence: 0 tags
Tags discarded due to lack of Alt_0002 sequence: 0 tags
Scanning file to determine attributes.
File attributes:
meta lines: 14
header_line: 15
variant count: 499
column count: 159
Meta line 14 read in.
All meta lines processed.
gt matrix initialized.
Character matrix gt created.
Character matrix gt rows: 499
Character matrix gt cols: 159
skip: 0
nrows: 499
row_num: 0
Processed variant: 499
All variants processed
Scanning file to determine attributes.
File attributes:
meta lines: 14
header_line: 15
variant count: 499
column count: 159
Meta line 14 read in.
All meta lines processed.
gt matrix initialized.
Character matrix gt created.
Character matrix gt rows: 499
Character matrix gt cols: 159
skip: 0
nrows: 499
row_num: 0
Processed variant: 499
All variants processed
Scanning file to determine attributes.
File attributes:
meta lines: 14
header_line: 15
variant count: 499
column count: 159
Meta line 14 read in.
All meta lines processed.
gt matrix initialized.
Character matrix gt created.
Character matrix gt rows: 499
Character matrix gt cols: 159
skip: 0
nrows: 499
row_num: 0
Processed variant: 499
All variants processed
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 58 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-madc2vcf_all.R:16:3'): test madc offtargets ────────────────────
Error in `checkForRemoteErrors(val)`: 2 nodes produced errors; first error: 'recursive' must be a length-1 vector
Backtrace:
▆
1. └─BIGr::madc2vcf_all(...) at test-madc2vcf_all.R:16:3
2. └─BIGr:::loop_though_dartag_report(...)
3. └─parallel::parLapply(...)
4. ├─base::do.call(...)
5. └─parallel::clusterApply(...)
6. └─parallel:::staticClusterApply(cl, fun, length(x), argfun)
7. └─parallel:::checkForRemoteErrors(val)
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 58 ]
Error: Test failures
In addition: Warning messages:
1: In sort.list(x, decreasing = decreasing) :
closing unused connection 6 (<-localhost:11524)
2: In sort.list(x, decreasing = decreasing) :
closing unused connection 5 (<-localhost:11524)
Execution halted
Flavor: r-release-macos-x86_64
Version: 0.5.5
Check: package dependencies
Result: ERROR
Package required but not available: ‘pwalign’
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Flavor: r-oldrel-macos-x86_64