CRAN Package Check Results for Maintainer ‘Alexander M. Sandercock <ams866 at cornell.edu>’

Last updated on 2025-06-04 17:55:00 CEST.

Package	ERROR	OK
BIGr	3	10
castgen		13

Package BIGr

Current CRAN status: ERROR: 3, OK: 10

Version: 0.5.5
Check: tests
Result: ERROR Running ‘testthat.R’ [10s/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 if (index.return && !is.na(na.last)) stop("'index.return' only for 'na.last = NA'") : closing unused connection 6 (<-localhost:11924) 2: In if (index.return && !is.na(na.last)) stop("'index.return' only for 'na.last = NA'") : closing unused connection 5 (<-localhost:11924) Execution halted Flavor: r-release-macos-arm64

Version: 0.5.5
Check: tests
Result: ERROR Running ‘testthat.R’ [15s/36s] 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:11958) 2: In sort.list(x, decreasing = decreasing) : closing unused connection 5 (<-localhost:11958) 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

Package castgen

Current CRAN status: OK: 13