* using log directory ‘/home/hornik/tmp/CRAN_special_noSuggests/SomaDataIO.Rcheck’
* using R Under development (unstable) (2025-02-05 r87692)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc-14 (Debian 14.2.0-12) 14.2.0
    GNU Fortran (Debian 14.2.0-12) 14.2.0
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘SomaDataIO/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SomaDataIO’ version ‘6.2.0’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [6s/7s] NOTE
Maintainer: ‘Caleb Scheidel <calebjscheidel@gmail.com>’

New maintainer:
  Caleb Scheidel <calebjscheidel@gmail.com>
Old maintainer(s):
  Stu Field <stu.g.field@gmail.com>
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘SomaDataIO’ can be installed ... [8s/8s] OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [1s/1s] OK
* checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the package can be unloaded cleanly ... [0s/0s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
* checking loading without being on the library search path ... [1s/1s] OK
* checking whether startup messages can be suppressed ... [1s/1s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [7s/7s] OK
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [0s/0s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [2s/2s] 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
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [18s/18s] 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()`) ─────────
  <packageNotFoundError/error/condition>
  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
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [0s/0s] OK
* checking PDF version of manual ... [3s/3s] OK
* checking HTML version of manual ... [1s/1s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 2 ERRORs, 1 NOTE