Last updated on 2025-05-31 20:50:30 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.5.5 | 25.58 | 246.38 | 271.96 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.5.5 | 19.25 | 178.17 | 197.42 | OK | |
| r-devel-linux-x86_64-fedora-clang | 0.5.5 | 430.00 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 0.5.5 | 408.42 | OK | |||
| r-devel-windows-x86_64 | 0.5.5 | 29.00 | 289.00 | 318.00 | OK | |
| r-patched-linux-x86_64 | 0.5.5 | 26.22 | 234.30 | 260.52 | OK | |
| r-release-linux-x86_64 | 0.5.5 | 26.22 | 233.28 | 259.50 | OK | |
| r-release-macos-arm64 | 0.5.5 | 101.00 | ERROR | |||
| r-release-macos-x86_64 | 0.5.5 | 199.00 | ERROR | |||
| r-release-windows-x86_64 | 0.5.5 | 31.00 | 290.00 | 321.00 | 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 | 41.00 | 385.00 | 426.00 | OK |
Version: 0.5.5
Check: tests
Result: ERROR
Running ‘testthat.R’ [7s/13s]
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 if (index.return && !is.na(na.last)) stop("'index.return' only for 'na.last = NA'") :
closing unused connection 6 (<-localhost:11920)
2: In if (index.return && !is.na(na.last)) stop("'index.return' only for 'na.last = NA'") :
closing unused connection 5 (<-localhost:11920)
Execution halted
Flavor: r-release-macos-arm64
Version: 0.5.5
Check: tests
Result: ERROR
Running ‘testthat.R’ [13s/21s]
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:11067)
2: In sort.list(x, decreasing = decreasing) :
closing unused connection 5 (<-localhost:11067)
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