CRAN Package Check Results for Package BIGr

Last updated on 2025-10-31 01:48:52 CET.

Flavor	Version	Tinstall	Tcheck	Ttotal	Status	Flags
r-devel-linux-x86_64-debian-clang	0.6.2	29.31	253.94	283.25	OK
r-devel-linux-x86_64-debian-gcc	0.6.2	21.24	177.13	198.37	OK
r-devel-linux-x86_64-fedora-clang	0.6.2	132.00	324.40	456.40	OK
r-devel-linux-x86_64-fedora-gcc	0.6.2	162.00	292.12	454.12	OK
r-devel-windows-x86_64	0.6.2	27.00	319.00	346.00	OK
r-patched-linux-x86_64	0.6.2	25.48	236.45	261.93	OK
r-release-linux-x86_64	0.6.2	25.00	238.37	263.37	OK
r-release-macos-arm64	0.6.2	12.00	109.00	121.00	ERROR
r-release-macos-x86_64	0.6.2	30.00	285.00	315.00	ERROR
r-release-windows-x86_64	0.6.2	31.00	315.00	346.00	OK
r-oldrel-macos-arm64	0.6.2	13.00	169.00	182.00	OK
r-oldrel-macos-x86_64	0.6.2			12.00	ERROR
r-oldrel-windows-x86_64	0.6.2	40.00	420.00	460.00	OK

Check Details

Version: 0.6.2
Check: tests
Result: ERROR Running ‘testthat.R’ [9s/25s] 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:11269) 2: In for (i in seq_along(col)) col[i] <- length(scan(file, what = "", : closing unused connection 6 (<-localhost:11269) 3: In for (i in seq_along(col)) col[i] <- length(scan(file, what = "", : closing unused connection 5 (<-localhost:11269) Execution halted Flavor: r-release-macos-arm64

Version: 0.6.2
Check: tests
Result: ERROR Running ‘testthat.R’ [17s/77s] 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:11873) 2: In for (i in seq_len(n)) { : closing unused connection 5 (<-localhost:11873) 3: In if (!is.logical(decreasing) || length(decreasing) != 1L) stop("'decreasing' must be a length-1 logical vector.\nDid you intend to set 'partial'?") : closing unused connection 7 (<-localhost:11873) 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