Package check result: ERROR Check: CRAN incoming feasibility, Result: NOTE Maintainer: ‘Caleb Scheidel ’ New maintainer: Caleb Scheidel Old maintainer(s): Stu Field Check: examples, Result: ERROR Running examples in ‘SomaDataIO-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: adat2eSet > ### Title: Convert ADAT to ExpressionSet Object > ### Aliases: adat2eSet > > ### ** Examples > > eSet <- adat2eSet(example_data) Error: The `Biobase` package is required to use this function. See ?adat2eSet for installation instructions. Execution halted Check: tests, Result: ERROR Running ‘spelling.R’ [0s/0s] Running ‘testthat.R’ [17s/17s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(SomaDataIO) ═══════════════════════════════════════════════════════════════════════ Legal ══ SomaDataIO™ Copyright © 2025 Standard BioTools, Inc. The `SomaDataIO` package is licensed under the MIT license (`LICENSE.md`) and is intended solely for research use only ("RUO") purposes. The code contained herein may *not* be used for diagnostic, clinical, therapeutic, or other commercial purposes. Further, "SomaDataIO" and "SomaLogic" are trademarks owned by Standard BioTools, Inc. No license is hereby granted to these trademarks other than for purposes of identifying the origin or source of the Software. The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDER(S) BE LIABLE FOR ANY CLAIM, DAMAGES, WHETHER DIRECT OR INDIRECT, OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. ════════════════════════════════════════════════════════════════════════════════ Attaching package: 'SomaDataIO' The following object is masked from 'package:stats': filter > > test_check("SomaDataIO") v ADAT passed all checks and traps. v ADAT passed all checks and traps. v ADAT passed all checks and traps. v ADAT passed all checks and traps. x The object is not a `soma_adat` class object: "data.frame" x Header.Meta and/or Col.Meta missing from attributes. x Header.Meta and/or Col.Meta missing from attributes. x Header.Meta is missing: "HEADER", "COL_DATA", and "ROW_DATA" x Col.Meta is missing: "SeqId", "Dilution", "Target", and "Units" x Col.Meta is not a tibble! -> "list" v ADAT passed all checks and traps. v ADAT written to: "/home/hornik/tmp/scratch/RtmpcEdtb1/working_dir/Rtmphuh84a/write-1cea1d3fbfff3b.adat" v ADAT passed all checks and traps. v ADAT written to: "/home/hornik/tmp/scratch/RtmpcEdtb1/working_dir/Rtmphuh84a/write-1cea1d48d117a.adat" v ADAT passed all checks and traps. v ADAT written to: "/home/hornik/tmp/scratch/RtmpcEdtb1/working_dir/Rtmphuh84a/write-1cea1d71e4407.txt" v ADAT passed all checks and traps. v ADAT written to: "/home/hornik/tmp/scratch/RtmpcEdtb1/working_dir/Rtmphuh84a/write-1cea1d47b6fa96.adat" v ADAT passed all checks and traps. v ADAT written to: "/home/hornik/tmp/scratch/RtmpcEdtb1/working_dir/Rtmphuh84a/write-1cea1d6ebbf5b.adat" [ FAIL 2 | WARN 0 | SKIP 32 | PASS 916 ] ══ Skipped tests (32) ══════════════════════════════════════════════════════════ • On CRAN (32): 'test-S3-median.R:5:3', 'test-S3-merge.R:9:3', 'test-S3-print.R:13:3', 'test-S3-print.R:18:3', 'test-S3-print.R:23:3', 'test-S3-print.R:29:3', 'test-S3-print.R:36:3', 'test-S3-summary.R:50:3', 'test-diffAdats.R:7:3', 'test-diffAdats.R:12:3', 'test-diffAdats.R:17:3', 'test-diffAdats.R:24:3', 'test-diffAdats.R:29:3', 'test-diffAdats.R:37:3', 'test-getAnalytes.R:23:3', 'test-getTargetNames.R:13:3', 'test-groupGenerics.R:154:3', 'test-groupGenerics.R:194:3', 'test-is-intact-attr.R:46:3', 'test-loadAdatsAsList.R:23:3', 'test-loadAdatsAsList.R:28:3', 'test-loadAdatsAsList.R:62:3', 'test-parseCheck.R:10:3', 'test-parseHeader.R:29:3', 'test-read-adat.R:30:3', 'test-read-adat.R:40:3', 'test-scaleAnalytes.R:67:3', 'test-scaleAnalytes.R:73:3', 'test-utils-read-adat.R:11:3', 'test-utils-read-adat.R:152:3', 'test-utils-release.R:4:3', 'test-utils-release.R:17:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-adat2eSet.R:2:1'): (code run outside of `test_that()`) ───────── Error in `library(Biobase)`: there is no package called 'Biobase' Backtrace: ▆ 1. ├─base::suppressPackageStartupMessages(library(Biobase)) at test-adat2eSet.R:2:1 2. │ └─base::withCallingHandlers(expr, packageStartupMessage = function(c) tryInvokeRestart("muffleMessage")) 3. └─base::library(Biobase) ── Error ('test-pivotExpressionSet.R:4:1'): (code run outside of `test_that()`) ── Error: The `Biobase` package is required to use this function. See ?adat2eSet for installation instructions. Backtrace: ▆ 1. └─SomaDataIO::pivotExpressionSet(adat2eSet(sub_adat)) at test-pivotExpressionSet.R:4:1 [ FAIL 2 | WARN 0 | SKIP 32 | PASS 916 ] Error: Test failures Execution halted