Last updated on 2025-10-31 13:51:30 CET.
| Package | ERROR | OK |
|---|---|---|
| BIGr | 3 | 10 |
Current CRAN status: ERROR: 3, OK: 10
Version: 0.6.2
Check: tests
Result: ERROR
Running ‘testthat.R’ [10s/27s]
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 2 | WARN 0 | SKIP 0 | PASS 88 ]
══ 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)
── Error ('test-madc2vcf_targets.R:75:3'): bottom strand markers have correct REF/ALT ──
Error in `checkForRemoteErrors(val)`: one node produced an error: 'recursive' must be a length-1 vector
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-madc2vcf_targets.R:75:3
2. │ └─base::withCallingHandlers(...)
3. └─BIGr::madc2vcf_all(...)
4. └─BIGr:::loop_though_dartag_report(...)
5. └─parallel::parLapply(...)
6. ├─base::do.call(...)
7. └─parallel::clusterApply(...)
8. └─parallel:::staticClusterApply(cl, fun, length(x), argfun)
9. └─parallel:::checkForRemoteErrors(val)
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 88 ]
Error: Test failures
In addition: Warning messages:
1: In for (i in seq_along(col)) col[i] <- length(scan(file, what = "", :
closing unused connection 7 (<-localhost:11775)
2: In for (i in seq_along(col)) col[i] <- length(scan(file, what = "", :
closing unused connection 6 (<-localhost:11775)
3: In for (i in seq_along(col)) col[i] <- length(scan(file, what = "", :
closing unused connection 5 (<-localhost:11775)
Execution halted
Flavor: r-release-macos-arm64
Version: 0.6.2
Check: tests
Result: ERROR
Running ‘testthat.R’ [17s/69s]
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 2 | WARN 0 | SKIP 0 | PASS 88 ]
══ 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)
── Error ('test-madc2vcf_targets.R:75:3'): bottom strand markers have correct REF/ALT ──
Error in `checkForRemoteErrors(val)`: one node produced an error: 'recursive' must be a length-1 vector
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-madc2vcf_targets.R:75:3
2. │ └─base::withCallingHandlers(...)
3. └─BIGr::madc2vcf_all(...)
4. └─BIGr:::loop_though_dartag_report(...)
5. └─parallel::parLapply(...)
6. ├─base::do.call(...)
7. └─parallel::clusterApply(...)
8. └─parallel:::staticClusterApply(cl, fun, length(x), argfun)
9. └─parallel:::checkForRemoteErrors(val)
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 88 ]
Error: Test failures
In addition: Warning messages:
1: In for (i in seq_len(n)) { :
closing unused connection 6 (<-localhost:11357)
2: In for (i in seq_len(n)) { :
closing unused connection 5 (<-localhost:11357)
3: In several.ok : closing unused connection 7 (<-localhost:11357)
Execution halted
Flavor: r-release-macos-x86_64
Version: 0.6.2
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