* using log directory ‘/data/gannet/ripley/R/packages/tests-Suggests/NEONiso.Rcheck’
* using R Under development (unstable) (2026-03-14 r89622)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)
    GNU Fortran (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)
* running under: Fedora Linux 42 (Workstation Edition)
* using session charset: UTF-8
* current time: 2026-03-14 17:14:56 UTC
* using option ‘--no-stop-on-test-error’
* checking for file ‘NEONiso/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘NEONiso’ version ‘0.8.0’
* package encoding: UTF-8
* 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 ‘NEONiso’ can be installed ... [16s/20s] OK
* checking package directory ... 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 ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... 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 ... [25s/25s] OK
* checking Rd files ... 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 R/sysdata.rda ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [11s/12s]
 [12s/12s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(NEONiso)
  > 
  > test_check("NEONiso")
  Saving _problems/test-data_extraction-9.R
  Saving _problems/test-data_ingestion-23.R
  Saving _problems/test-data_regression-12.R
  Saving _problems/test-gold_file_regression-51.R
  Saving _problems/test-gold_file_regression-64.R
  Saving _problems/test-gold_file_regression-81.R
  Saving _problems/test-gold_file_regression-92.R
  Saving _problems/test-gold_file_regression-106.R
  Saving _problems/test-gold_file_regression-115.R
  Saving _problems/test-hdf5_roundtrip-18.R
  Saving _problems/test-hdf5_roundtrip-43.R
  Saving _problems/test-hdf5_roundtrip-61.R
  Saving _problems/test-hdf5_roundtrip-75.R
  Saving _problems/test-hdf5_roundtrip-91.R
  Saving _problems/test-hdf5_roundtrip-106.R
  Saving _problems/test-hdf5_roundtrip-126.R
  Saving _problems/test-hdf5_roundtrip-140.R
  Saving _problems/test-hdf5_roundtrip-156.R
  Saving _problems/test-hdf5_roundtrip-180.R
  Saving _problems/test-hdf5_roundtrip-200.R
  Saving _problems/test-hdf5_roundtrip-217.R
  Saving _problems/test-hdf5_roundtrip-238.R
  Saving _problems/test-hdf5_utils-5.R
  Saving _problems/test-hdf5_utils-13.R
  Saving _problems/test-hdf5_utils-25.R
  Saving _problems/test-hdf5_utils-44.R
  Saving _problems/test-hdf5_utils-68.R
  Saving _problems/test-hdf5_utils-95.R
  Saving _problems/test-hdf5_utils-120.R
  Saving _problems/test-hdf5_utils-136.R
  Saving _problems/test-hdf5_utils-154.R
  Saving _problems/test-hdf5_utils-174.R
  Saving _problems/test-hdf5_utils-183.R
  Saving _problems/test-high_level_functions-35.R
  Saving _problems/test-high_level_functions-47.R
  Saving _problems/test-high_level_functions-60.R
  Saving _problems/test-high_level_functions-72.R
  Saving _problems/test-high_level_functions-81.R
  Saving _problems/test-high_level_functions-85.R
  Saving _problems/test-output_values-11.R
  Saving _problems/test-regression_snapshots-20.R
  Saving _problems/test-regression_snapshots-48.R
  Saving _problems/test-regression_snapshots-68.R
  Saving _problems/test-regression_snapshots-94.R
  Saving _problems/test-regression_snapshots-111.R
  Saving _problems/test-regression_snapshots-133.R
  [ FAIL 46 | WARN 0 | SKIP 0 | PASS 38 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-data_extraction.R:9:1'): (code run outside of `test_that()`) ───
  Error in `.hdf5_backend()`: An HDF5 package is required. Install one with:
    install.packages('hdf5r')       # recommended (CRAN)
    BiocManager::install('rhdf5')    # alternative (Bioconductor)
  Backtrace:
      ▆
   1. └─NEONiso::ingest_data(fin, analyte = "Co2", amb_avg = 9, ref_avg = 9) at test-data_extraction.R:9:1
   2.   └─NEONiso:::h5_ls(inname[1])
   3.     └─NEONiso:::.hdf5_backend()
  ── Error ('test-data_ingestion.R:23:1'): (code run outside of `test_that()`) ───
  Error in `.hdf5_backend()`: An HDF5 package is required. Install one with:
    install.packages('hdf5r')       # recommended (CRAN)
    BiocManager::install('rhdf5')    # alternative (Bioconductor)
  Backtrace:
      ▆
   1. └─NEONiso::ingest_data(fin, analyte = "Co2", amb_avg = 9, ref_avg = 9) at test-data_ingestion.R:23:1
   2.   └─NEONiso:::h5_ls(inname[1])
   3.     └─NEONiso:::.hdf5_backend()
  ── Error ('test-data_regression.R:12:1'): (code run outside of `test_that()`) ──
  Error in `.hdf5_backend()`: An HDF5 package is required. Install one with:
    install.packages('hdf5r')       # recommended (CRAN)
    BiocManager::install('rhdf5')    # alternative (Bioconductor)
  Backtrace:
      ▆
   1. └─NEONiso::ingest_data(fin, analyte = "Co2", amb_avg = 9, ref_avg = 9) at test-data_regression.R:12:1
   2.   └─NEONiso:::h5_ls(inname[1])
   3.     └─NEONiso:::.hdf5_backend()
  ── Error ('test-gold_file_regression.R:49:5'): carbon gainoffset cal_df matches baseline ──
  Error in `.hdf5_backend()`: An HDF5 package is required. Install one with:
    install.packages('hdf5r')       # recommended (CRAN)
    BiocManager::install('rhdf5')    # alternative (Bioconductor)
  Backtrace:
      ▆
   1. ├─base::suppressWarnings(...) at test-gold_file_regression.R:48:3
   2. │ └─base::withCallingHandlers(...)
   3. └─NEONiso::calibrate_carbon(...) at test-gold_file_regression.R:49:5
   4.   └─NEONiso::ingest_data(...)
   5.     └─NEONiso:::h5_ls(inname[1])
   6.       └─NEONiso:::.hdf5_backend()
  ── Error ('test-gold_file_regression.R:62:5'): carbon gainoffset ambient matches baseline ──
  Error in `.hdf5_backend()`: An HDF5 package is required. Install one with:
    install.packages('hdf5r')       # recommended (CRAN)
    BiocManager::install('rhdf5')    # alternative (Bioconductor)
  Backtrace:
      ▆
   1. ├─base::suppressWarnings(...) at test-gold_file_regression.R:61:3
   2. │ └─base::withCallingHandlers(...)
   3. └─NEONiso::calibrate_carbon(...) at test-gold_file_regression.R:62:5
   4.   └─NEONiso::ingest_data(...)
   5.     └─NEONiso:::h5_ls(inname[1])
   6.       └─NEONiso:::.hdf5_backend()
  ── Error ('test-gold_file_regression.R:79:3'): carbon linreg cal_df matches baseline ──
  Error in `.hdf5_backend()`: An HDF5 package is required. Install one with:
    install.packages('hdf5r')       # recommended (CRAN)
    BiocManager::install('rhdf5')    # alternative (Bioconductor)
  Backtrace:
      ▆
   1. └─NEONiso::calibrate_carbon(...) at test-gold_file_regression.R:79:3
   2.   └─NEONiso::ingest_data(...)
   3.     └─NEONiso:::h5_ls(inname[1])
   4.       └─NEONiso:::.hdf5_backend()
  ── Error ('test-gold_file_regression.R:90:3'): carbon linreg ambient matches baseline ──
  Error in `.hdf5_backend()`: An HDF5 package is required. Install one with:
    install.packages('hdf5r')       # recommended (CRAN)
    BiocManager::install('rhdf5')    # alternative (Bioconductor)
  Backtrace:
      ▆
   1. └─NEONiso::calibrate_carbon(...) at test-gold_file_regression.R:90:3
   2.   └─NEONiso::ingest_data(...)
   3.     └─NEONiso:::h5_ls(inname[1])
   4.       └─NEONiso:::.hdf5_backend()
  ── Error ('test-gold_file_regression.R:106:3'): water cal_df matches baseline ──
  Error in `.hdf5_backend()`: An HDF5 package is required. Install one with:
    install.packages('hdf5r')       # recommended (CRAN)
    BiocManager::install('rhdf5')    # alternative (Bioconductor)
  Backtrace:
      ▆
   1. └─NEONiso:::calibrate_water(fin, tempfile(), "ONAQ", write_to_file = FALSE) at test-gold_file_regression.R:106:3
   2.   └─NEONiso::ingest_data(inname, analyte = "H2o", amb_avg = 9, ref_avg = 3)
   3.     └─NEONiso:::h5_ls(inname[1])
   4.       └─NEONiso:::.hdf5_backend()
  ── Error ('test-gold_file_regression.R:115:3'): water ambient matches baseline ──
  Error in `.hdf5_backend()`: An HDF5 package is required. Install one with:
    install.packages('hdf5r')       # recommended (CRAN)
    BiocManager::install('rhdf5')    # alternative (Bioconductor)
  Backtrace:
      ▆
   1. └─NEONiso:::calibrate_water(fin, tempfile(), "ONAQ", write_to_file = FALSE) at test-gold_file_regression.R:115:3
   2.   └─NEONiso::ingest_data(inname, analyte = "H2o", amb_avg = 9, ref_avg = 3)
   3.     └─NEONiso:::h5_ls(inname[1])
   4.       └─NEONiso:::.hdf5_backend()
  ── Error ('test-hdf5_roundtrip.R:16:3'): carbon calibration output file has correct HDF5 structure ──
  Error in `.hdf5_backend()`: An HDF5 package is required. Install one with:
    install.packages('hdf5r')       # recommended (CRAN)
    BiocManager::install('rhdf5')    # alternative (Bioconductor)
  Backtrace:
      ▆
   1. └─NEONiso::calibrate_carbon(...) at test-hdf5_roundtrip.R:16:3
   2.   └─NEONiso::ingest_data(...)
   3.     └─NEONiso:::h5_ls(inname[1])
   4.       └─NEONiso:::.hdf5_backend()
  ── Error ('test-hdf5_roundtrip.R:41:3'): carbon output file has correct site attributes ──
  Error in `.hdf5_backend()`: An HDF5 package is required. Install one with:
    install.packages('hdf5r')       # recommended (CRAN)
    BiocManager::install('rhdf5')    # alternative (Bioconductor)
  Backtrace:
      ▆
   1. └─NEONiso::calibrate_carbon(...) at test-hdf5_roundtrip.R:41:3
   2.   └─NEONiso::ingest_data(...)
   3.     └─NEONiso:::h5_ls(inname[1])
   4.       └─NEONiso:::.hdf5_backend()
  ── Error ('test-hdf5_roundtrip.R:59:3'): carbon output file calData has correct dataset ──
  Error in `.hdf5_backend()`: An HDF5 package is required. Install one with:
    install.packages('hdf5r')       # recommended (CRAN)
    BiocManager::install('rhdf5')    # alternative (Bioconductor)
  Backtrace:
      ▆
   1. └─NEONiso::calibrate_carbon(...) at test-hdf5_roundtrip.R:59:3
   2.   └─NEONiso::ingest_data(...)
   3.     └─NEONiso:::h5_ls(inname[1])
   4.       └─NEONiso:::.hdf5_backend()
  ── Error ('test-hdf5_roundtrip.R:73:3'): carbon output file passes validate_output_file ──
  Error in `.hdf5_backend()`: An HDF5 package is required. Install one with:
    install.packages('hdf5r')       # recommended (CRAN)
    BiocManager::install('rhdf5')    # alternative (Bioconductor)
  Backtrace:
      ▆
   1. └─NEONiso::calibrate_carbon(...) at test-hdf5_roundtrip.R:73:3
   2.   └─NEONiso::ingest_data(...)
   3.     └─NEONiso:::h5_ls(inname[1])
   4.       └─NEONiso:::.hdf5_backend()
  ── Error ('test-hdf5_roundtrip.R:89:5'): carbon gainoffset output passes validate_output_file ──
  Error in `.hdf5_backend()`: An HDF5 package is required. Install one with:
    install.packages('hdf5r')       # recommended (CRAN)
    BiocManager::install('rhdf5')    # alternative (Bioconductor)
  Backtrace:
      ▆
   1. ├─base::suppressWarnings(...) at test-hdf5_roundtrip.R:88:3
   2. │ └─base::withCallingHandlers(...)
   3. └─NEONiso::calibrate_carbon(...) at test-hdf5_roundtrip.R:89:5
   4.   └─NEONiso::ingest_data(...)
   5.     └─NEONiso:::h5_ls(inname[1])
   6.       └─NEONiso:::.hdf5_backend()
  ── Error ('test-hdf5_roundtrip.R:106:3'): water calibration output file has correct HDF5 structure ──
  Error in `.hdf5_backend()`: An HDF5 package is required. Install one with:
    install.packages('hdf5r')       # recommended (CRAN)
    BiocManager::install('rhdf5')    # alternative (Bioconductor)
  Backtrace:
      ▆
   1. └─NEONiso:::calibrate_water(fin, fout, "ONAQ", write_to_file = TRUE) at test-hdf5_roundtrip.R:106:3
   2.   └─NEONiso::ingest_data(inname, analyte = "H2o", amb_avg = 9, ref_avg = 3)
   3.     └─NEONiso:::h5_ls(inname[1])
   4.       └─NEONiso:::.hdf5_backend()
  ── Error ('test-hdf5_roundtrip.R:126:3'): water output file has correct site attributes ──
  Error in `.hdf5_backend()`: An HDF5 package is required. Install one with:
    install.packages('hdf5r')       # recommended (CRAN)
    BiocManager::install('rhdf5')    # alternative (Bioconductor)
  Backtrace:
      ▆
   1. └─NEONiso:::calibrate_water(fin, fout, "ONAQ", write_to_file = TRUE) at test-hdf5_roundtrip.R:126:3
   2.   └─NEONiso::ingest_data(inname, analyte = "H2o", amb_avg = 9, ref_avg = 3)
   3.     └─NEONiso:::h5_ls(inname[1])
   4.       └─NEONiso:::.hdf5_backend()
  ── Error ('test-hdf5_roundtrip.R:140:3'): water output file passes validate_output_file ──
  Error in `.hdf5_backend()`: An HDF5 package is required. Install one with:
    install.packages('hdf5r')       # recommended (CRAN)
    BiocManager::install('rhdf5')    # alternative (Bioconductor)
  Backtrace:
      ▆
   1. └─NEONiso:::calibrate_water(fin, fout, "ONAQ", write_to_file = TRUE) at test-hdf5_roundtrip.R:140:3
   2.   └─NEONiso::ingest_data(inname, analyte = "H2o", amb_avg = 9, ref_avg = 3)
   3.     └─NEONiso:::h5_ls(inname[1])
   4.       └─NEONiso:::.hdf5_backend()
  ── Error ('test-hdf5_roundtrip.R:154:3'): write_carbon_calibration_data works standalone (fid = NULL) ──
  Error in `.hdf5_backend()`: An HDF5 package is required. Install one with:
    install.packages('hdf5r')       # recommended (CRAN)
    BiocManager::install('rhdf5')    # alternative (Bioconductor)
  Backtrace:
      ▆
   1. └─NEONiso::calibrate_carbon(...) at test-hdf5_roundtrip.R:154:3
   2.   └─NEONiso::ingest_data(...)
   3.     └─NEONiso:::h5_ls(inname[1])
   4.       └─NEONiso:::.hdf5_backend()
  ── Error ('test-hdf5_roundtrip.R:178:3'): write_carbon_ambient_data works standalone (fid = NULL) ──
  Error in `.hdf5_backend()`: An HDF5 package is required. Install one with:
    install.packages('hdf5r')       # recommended (CRAN)
    BiocManager::install('rhdf5')    # alternative (Bioconductor)
  Backtrace:
      ▆
   1. └─NEONiso::calibrate_carbon(...) at test-hdf5_roundtrip.R:178:3
   2.   └─NEONiso::ingest_data(...)
   3.     └─NEONiso:::h5_ls(inname[1])
   4.       └─NEONiso:::.hdf5_backend()
  ── Error ('test-hdf5_roundtrip.R:200:3'): write_water_calibration_data works standalone (fid = NULL) ──
  Error in `.hdf5_backend()`: An HDF5 package is required. Install one with:
    install.packages('hdf5r')       # recommended (CRAN)
    BiocManager::install('rhdf5')    # alternative (Bioconductor)
  Backtrace:
      ▆
   1. └─NEONiso:::calibrate_water(fin, fout, "ONAQ", write_to_file = FALSE) at test-hdf5_roundtrip.R:200:3
   2.   └─NEONiso::ingest_data(inname, analyte = "H2o", amb_avg = 9, ref_avg = 3)
   3.     └─NEONiso:::h5_ls(inname[1])
   4.       └─NEONiso:::.hdf5_backend()
  ── Error ('test-hdf5_roundtrip.R:217:3'): write_water_ambient_data works standalone (fid = NULL) ──
  Error in `.hdf5_backend()`: An HDF5 package is required. Install one with:
    install.packages('hdf5r')       # recommended (CRAN)
    BiocManager::install('rhdf5')    # alternative (Bioconductor)
  Backtrace:
      ▆
   1. └─NEONiso:::calibrate_water(fin, fout, "ONAQ", write_to_file = FALSE) at test-hdf5_roundtrip.R:217:3
   2.   └─NEONiso::ingest_data(inname, analyte = "H2o", amb_avg = 9, ref_avg = 3)
   3.     └─NEONiso:::h5_ls(inname[1])
   4.       └─NEONiso:::.hdf5_backend()
  ── Error ('test-hdf5_roundtrip.R:238:3'): validate_output_file errors on incomplete output file ──
  Error in `.hdf5_backend()`: An HDF5 package is required. Install one with:
    install.packages('hdf5r')       # recommended (CRAN)
    BiocManager::install('rhdf5')    # alternative (Bioconductor)
  Backtrace:
      ▆
   1. └─NEONiso:::setup_output_file(fin, fout, "ONAQ", "Co2") at test-hdf5_roundtrip.R:238:3
   2.   └─NEONiso:::h5_create_file(outname)
   3.     └─NEONiso:::.hdf5_backend()
  ── Error ('test-hdf5_utils.R:5:3'): .hdf5_backend returns a valid backend string ──
  Error in `NEONiso:::.hdf5_backend()`: An HDF5 package is required. Install one with:
    install.packages('hdf5r')       # recommended (CRAN)
    BiocManager::install('rhdf5')    # alternative (Bioconductor)
  Backtrace:
      ▆
   1. └─NEONiso:::.hdf5_backend() at test-hdf5_utils.R:5:3
  ── Error ('test-hdf5_utils.R:13:3'): h5_create_file creates a new HDF5 file and returns a handle ──
  Error in `.hdf5_backend()`: An HDF5 package is required. Install one with:
    install.packages('hdf5r')       # recommended (CRAN)
    BiocManager::install('rhdf5')    # alternative (Bioconductor)
  Backtrace:
      ▆
   1. └─NEONiso:::h5_create_file(tmp) at test-hdf5_utils.R:13:3
   2.   └─NEONiso:::.hdf5_backend()
  ── Error ('test-hdf5_utils.R:25:3'): h5_create_file overwrites an existing file ──
  Error in `.hdf5_backend()`: An HDF5 package is required. Install one with:
    install.packages('hdf5r')       # recommended (CRAN)
    BiocManager::install('rhdf5')    # alternative (Bioconductor)
  Backtrace:
      ▆
   1. └─NEONiso:::h5_create_file(tmp) at test-hdf5_utils.R:25:3
   2.   └─NEONiso:::.hdf5_backend()
  ── Error ('test-hdf5_utils.R:44:3'): h5_create_group and h5_open_group work ────
  Error in `.hdf5_backend()`: An HDF5 package is required. Install one with:
    install.packages('hdf5r')       # recommended (CRAN)
    BiocManager::install('rhdf5')    # alternative (Bioconductor)
  Backtrace:
      ▆
   1. └─NEONiso:::h5_create_file(tmp) at test-hdf5_utils.R:44:3
   2.   └─NEONiso:::.hdf5_backend()
  ── Error ('test-hdf5_utils.R:68:3'): h5_write_attr and h5_read_attrs round-trip correctly ──
  Error in `.hdf5_backend()`: An HDF5 package is required. Install one with:
    install.packages('hdf5r')       # recommended (CRAN)
    BiocManager::install('rhdf5')    # alternative (Bioconductor)
  Backtrace:
      ▆
   1. └─NEONiso:::h5_create_file(tmp) at test-hdf5_utils.R:68:3
   2.   └─NEONiso:::.hdf5_backend()
  ── Error ('test-hdf5_utils.R:95:3'): h5_write_dataset writes data.frames correctly ──
  Error in `.hdf5_backend()`: An HDF5 package is required. Install one with:
    install.packages('hdf5r')       # recommended (CRAN)
    BiocManager::install('rhdf5')    # alternative (Bioconductor)
  Backtrace:
      ▆
   1. └─NEONiso:::h5_create_file(tmp) at test-hdf5_utils.R:95:3
   2.   └─NEONiso:::.hdf5_backend()
  ── Error ('test-hdf5_utils.R:120:3'): h5_ls returns top-level groups ───────────
  Error in `.hdf5_backend()`: An HDF5 package is required. Install one with:
    install.packages('hdf5r')       # recommended (CRAN)
    BiocManager::install('rhdf5')    # alternative (Bioconductor)
  Backtrace:
      ▆
   1. └─NEONiso:::h5_create_file(tmp) at test-hdf5_utils.R:120:3
   2.   └─NEONiso:::.hdf5_backend()
  ── Error ('test-hdf5_utils.R:136:3'): h5_ls_group returns children of a specific group ──
  Error in `.hdf5_backend()`: An HDF5 package is required. Install one with:
    install.packages('hdf5r')       # recommended (CRAN)
    BiocManager::install('rhdf5')    # alternative (Bioconductor)
  Backtrace:
      ▆
   1. └─NEONiso:::h5_create_file(tmp) at test-hdf5_utils.R:136:3
   2.   └─NEONiso:::.hdf5_backend()
  ── Error ('test-hdf5_utils.R:154:3'): h5_open opens file for read-write ────────
  Error in `.hdf5_backend()`: An HDF5 package is required. Install one with:
    install.packages('hdf5r')       # recommended (CRAN)
    BiocManager::install('rhdf5')    # alternative (Bioconductor)
  Backtrace:
      ▆
   1. └─NEONiso:::h5_create_file(tmp) at test-hdf5_utils.R:154:3
   2.   └─NEONiso:::.hdf5_backend()
  ── Error ('test-hdf5_utils.R:174:3'): h5_ls on real NEON file returns site code ──
  Error in `.hdf5_backend()`: An HDF5 package is required. Install one with:
    install.packages('hdf5r')       # recommended (CRAN)
    BiocManager::install('rhdf5')    # alternative (Bioconductor)
  Backtrace:
      ▆
   1. └─NEONiso:::h5_ls(fin) at test-hdf5_utils.R:174:3
   2.   └─NEONiso:::.hdf5_backend()
  ── Error ('test-hdf5_utils.R:183:3'): h5_read_attrs on real NEON file returns site attributes ──
  Error in `.hdf5_backend()`: An HDF5 package is required. Install one with:
    install.packages('hdf5r')       # recommended (CRAN)
    BiocManager::install('rhdf5')    # alternative (Bioconductor)
  Backtrace:
      ▆
   1. └─NEONiso:::h5_read_attrs(fin, "ONAQ") at test-hdf5_utils.R:183:3
   2.   └─NEONiso:::.hdf5_backend()
  ── Failure ('test-high_level_functions.R:25:3'): calibrate_carbon returns no error ──
  Expected `calibrate_carbon(...)` not to throw any errors.
  Actually got a <simpleError> with message:
    An HDF5 package is required. Install one with:
      install.packages('hdf5r')       # recommended (CRAN)
      BiocManager::install('rhdf5')    # alternative (Bioconductor)
  ── Failure ('test-high_level_functions.R:37:3'): calibrate_carbon returns no error ──
  Expected `calibrate_carbon(...)` not to throw any errors.
  Actually got a <simpleError> with message:
    An HDF5 package is required. Install one with:
      install.packages('hdf5r')       # recommended (CRAN)
      BiocManager::install('rhdf5')    # alternative (Bioconductor)
  ── Failure ('test-high_level_functions.R:50:3'): calibrate_carbon returns no error ──
  Expected `calibrate_carbon(...)` not to throw any errors.
  Actually got a <simpleError> with message:
    An HDF5 package is required. Install one with:
      install.packages('hdf5r')       # recommended (CRAN)
      BiocManager::install('rhdf5')    # alternative (Bioconductor)
  ── Error ('test-high_level_functions.R:62:3'): calibrate_carbon returns no error ──
  Error in `.hdf5_backend()`: An HDF5 package is required. Install one with:
    install.packages('hdf5r')       # recommended (CRAN)
    BiocManager::install('rhdf5')    # alternative (Bioconductor)
  Backtrace:
       ▆
    1. ├─testthat::expect_warning(...) at test-high_level_functions.R:62:3
    2. │ └─testthat:::expect_condition_matching_(...)
    3. │   └─testthat:::quasi_capture(...)
    4. │     ├─testthat (local) .capture(...)
    5. │     │ └─base::withCallingHandlers(...)
    6. │     └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    7. └─NEONiso::calibrate_carbon(...)
    8.   └─NEONiso::ingest_data(...)
    9.     └─NEONiso:::h5_ls(inname[1])
   10.       └─NEONiso:::.hdf5_backend()
  ── Failure ('test-high_level_functions.R:79:3'): calibrate_water returns no error ──
  Expected `calibrate_water(...)` not to throw any errors.
  Actually got a <simpleError> with message:
    An HDF5 package is required. Install one with:
      install.packages('hdf5r')       # recommended (CRAN)
      BiocManager::install('rhdf5')    # alternative (Bioconductor)
  ── Failure ('test-high_level_functions.R:83:3'): calibrate_water returns no error ──
  Expected `calibrate_water(...)` not to throw any errors.
  Actually got a <simpleError> with message:
    An HDF5 package is required. Install one with:
      install.packages('hdf5r')       # recommended (CRAN)
      BiocManager::install('rhdf5')    # alternative (Bioconductor)
  ── Error ('test-output_values.R:11:1'): (code run outside of `test_that()`) ────
  Error in `.hdf5_backend()`: An HDF5 package is required. Install one with:
    install.packages('hdf5r')       # recommended (CRAN)
    BiocManager::install('rhdf5')    # alternative (Bioconductor)
  Backtrace:
      ▆
   1. └─NEONiso:::ingest_data(fin, analyte = "Co2", ref_avg = 9, amb_avg = 9) at test-output_values.R:11:1
   2.   └─NEONiso:::h5_ls(inname[1])
   3.     └─NEONiso:::.hdf5_backend()
  ── Error ('test-regression_snapshots.R:18:5'): calibrate_carbon gainoffset produces stable calibration parameters ──
  Error in `.hdf5_backend()`: An HDF5 package is required. Install one with:
    install.packages('hdf5r')       # recommended (CRAN)
    BiocManager::install('rhdf5')    # alternative (Bioconductor)
  Backtrace:
      ▆
   1. ├─base::suppressWarnings(...) at test-regression_snapshots.R:17:3
   2. │ └─base::withCallingHandlers(...)
   3. └─NEONiso::calibrate_carbon(...) at test-regression_snapshots.R:18:5
   4.   └─NEONiso::ingest_data(...)
   5.     └─NEONiso:::h5_ls(inname[1])
   6.       └─NEONiso:::.hdf5_backend()
  ── Error ('test-regression_snapshots.R:46:5'): calibrate_carbon gainoffset produces stable ambient d13C values ──
  Error in `.hdf5_backend()`: An HDF5 package is required. Install one with:
    install.packages('hdf5r')       # recommended (CRAN)
    BiocManager::install('rhdf5')    # alternative (Bioconductor)
  Backtrace:
      ▆
   1. ├─base::suppressWarnings(...) at test-regression_snapshots.R:45:3
   2. │ └─base::withCallingHandlers(...)
   3. └─NEONiso::calibrate_carbon(...) at test-regression_snapshots.R:46:5
   4.   └─NEONiso::ingest_data(...)
   5.     └─NEONiso:::h5_ls(inname[1])
   6.       └─NEONiso:::.hdf5_backend()
  ── Error ('test-regression_snapshots.R:66:3'): calibrate_carbon linreg produces stable calibration parameters ──
  Error in `.hdf5_backend()`: An HDF5 package is required. Install one with:
    install.packages('hdf5r')       # recommended (CRAN)
    BiocManager::install('rhdf5')    # alternative (Bioconductor)
  Backtrace:
      ▆
   1. └─NEONiso::calibrate_carbon(...) at test-regression_snapshots.R:66:3
   2.   └─NEONiso::ingest_data(...)
   3.     └─NEONiso:::h5_ls(inname[1])
   4.       └─NEONiso:::.hdf5_backend()
  ── Error ('test-regression_snapshots.R:92:3'): calibrate_carbon linreg produces stable ambient d13C values ──
  Error in `.hdf5_backend()`: An HDF5 package is required. Install one with:
    install.packages('hdf5r')       # recommended (CRAN)
    BiocManager::install('rhdf5')    # alternative (Bioconductor)
  Backtrace:
      ▆
   1. └─NEONiso::calibrate_carbon(...) at test-regression_snapshots.R:92:3
   2.   └─NEONiso::ingest_data(...)
   3.     └─NEONiso:::h5_ls(inname[1])
   4.       └─NEONiso:::.hdf5_backend()
  ── Error ('test-regression_snapshots.R:111:3'): calibrate_water produces stable calibration parameters ──
  Error in `.hdf5_backend()`: An HDF5 package is required. Install one with:
    install.packages('hdf5r')       # recommended (CRAN)
    BiocManager::install('rhdf5')    # alternative (Bioconductor)
  Backtrace:
      ▆
   1. └─NEONiso:::calibrate_water(fin, tempfile(), "ONAQ", write_to_file = FALSE) at test-regression_snapshots.R:111:3
   2.   └─NEONiso::ingest_data(inname, analyte = "H2o", amb_avg = 9, ref_avg = 3)
   3.     └─NEONiso:::h5_ls(inname[1])
   4.       └─NEONiso:::.hdf5_backend()
  ── Error ('test-regression_snapshots.R:133:3'): calibrate_water produces stable ambient isotope values ──
  Error in `.hdf5_backend()`: An HDF5 package is required. Install one with:
    install.packages('hdf5r')       # recommended (CRAN)
    BiocManager::install('rhdf5')    # alternative (Bioconductor)
  Backtrace:
      ▆
   1. └─NEONiso:::calibrate_water(fin, tempfile(), "ONAQ", write_to_file = FALSE) at test-regression_snapshots.R:133:3
   2.   └─NEONiso::ingest_data(inname, analyte = "H2o", amb_avg = 9, ref_avg = 3)
   3.     └─NEONiso:::h5_ls(inname[1])
   4.       └─NEONiso:::.hdf5_backend()
  
  [ FAIL 46 | WARN 0 | SKIP 0 | PASS 38 ]
  Error:
  ! Test failures.
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... [10s/11s] OK
* checking HTML version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 1 ERROR
See
  ‘/data/gannet/ripley/R/packages/tests-Suggests/NEONiso.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 2:39.56, 134.50 + 13.06