* using log directory ‘/data/localhost/ripley/R/packages/tests-clang/ICESat2VegR.Rcheck’
* using R Under development (unstable) (2026-09-15 r90540)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    clang version 23.1.1
    flang version 23.1.1
* running under: Fedora Linux 44 (Server Edition)
* using session charset: UTF-8
* current time: 2026-09-16 07:12:40 UTC
* using option ‘--no-stop-on-test-error’
* checking for file ‘ICESat2VegR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ICESat2VegR’ version ‘0.0.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 ‘ICESat2VegR’ can be installed ... [118s/225s] OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-clang/ICESat2VegR-00install.html' for details.
* used C compiler: ‘clang version 23.1.1’
* used C++ compiler: ‘clang version 23.1.1’
* checking installed package size ... INFO
  installed size is 783.2Mb
  sub-directories of 1Mb or more:
    extdata    6.0Mb
    proj     774.5Mb
* checking package 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 ... [10s/23s] OK
* checking whether the package can be loaded with stated dependencies ... [10s/23s] OK
* checking whether the package can be unloaded cleanly ... [10s/20s] OK
* checking whether the namespace can be loaded with stated dependencies ... [10s/26s] OK
* checking whether the namespace can be unloaded cleanly ... [10s/23s] OK
* checking loading without being on the library search path ... [10s/23s] OK
* checking whether startup messages can be suppressed ... [11s/28s] NOTE
warning: Failed to inspect Python interpreter from search path at `/usr/sbin/pypy`
  cause: Can't use Python at `/usr/sbin/pypy`
  cause: Python executable does not support `-I` flag. Please use Python 3.6 or newer.

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
warning: Failed to inspect Python interpreter from search path at `/usr/sbin/pypy`
  cause: Can't use Python at `/usr/sbin/pypy`
  cause: Python executable does not support `-I` flag. Please use Python 3.6 or newer.
* checking S3 generic/method consistency ... WARNING
warning: Failed to inspect Python interpreter from search path at `/usr/sbin/pypy`
  cause: Can't use Python at `/usr/sbin/pypy`
  cause: Python executable does not support `-I` flag. Please use Python 3.6 or newer.
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... WARNING
warning: Failed to inspect Python interpreter from search path at `/usr/sbin/pypy`
  cause: Can't use Python at `/usr/sbin/pypy`
  cause: Python executable does not support `-I` flag. Please use Python 3.6 or newer.
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
* checking foreign function calls ... NOTE
warning: Failed to inspect Python interpreter from search path at `/usr/sbin/pypy`
  cause: Can't use Python at `/usr/sbin/pypy`
  cause: Python executable does not support `-I` flag. Please use Python 3.6 or newer.
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... [58s/152s] NOTE
warning: Failed to inspect Python interpreter from search path at `/usr/sbin/pypy`
  cause: Can't use Python at `/usr/sbin/pypy`
  cause: Python executable does not support `-I` flag. Please use Python 3.6 or newer.
warning: Failed to inspect Python interpreter from search path at `/usr/sbin/pypy`
  cause: Can't use Python at `/usr/sbin/pypy`
  cause: Python executable does not support `-I` flag. Please use Python 3.6 or newer.

warning: Failed to inspect Python interpreter from search path at `/usr/sbin/pypy`
  cause: Can't use Python at `/usr/sbin/pypy`
  cause: Python executable does not support `-I` flag. Please use Python 3.6 or newer.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
warning: Failed to inspect Python interpreter from search path at `/usr/sbin/pypy`
  cause: Can't use Python at `/usr/sbin/pypy`
  cause: Python executable does not support `-I` flag. Please use Python 3.6 or newer.
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
warning: Failed to inspect Python interpreter from search path at `/usr/sbin/pypy`
  cause: Can't use Python at `/usr/sbin/pypy`
  cause: Python executable does not support `-I` flag. Please use Python 3.6 or newer.
warning: Failed to inspect Python interpreter from search path at `/usr/sbin/pypy`
  cause: Can't use Python at `/usr/sbin/pypy`
  cause: Python executable does not support `-I` flag. Please use Python 3.6 or newer.
warning: Failed to inspect Python interpreter from search path at `/usr/sbin/pypy`
  cause: Can't use Python at `/usr/sbin/pypy`
  cause: Python executable does not support `-I` flag. Please use Python 3.6 or newer.
* checking Rd \usage sections ... NOTE
warning: Failed to inspect Python interpreter from search path at `/usr/sbin/pypy`
  cause: Can't use Python at `/usr/sbin/pypy`
  cause: Python executable does not support `-I` flag. Please use Python 3.6 or newer.
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking examples ... [19s/33s] ERROR
Running examples in ‘ICESat2VegR-Ex.R’ failed
The error most likely occurred in:

> ### Name: ATL03_ATL08_photons_attributes_dt_join
> ### Title: Join ATL03 and ATL08 photons attributes
> ### Aliases: ATL03_ATL08_photons_attributes_dt_join
> 
> ### ** Examples
> 
> if (requireNamespace("hdf5r", quietly = TRUE)) {
+ # Specifying the path to ATL03 file
+ atl03_path <- system.file("extdata",
+   "atl03_clip.h5",
+   package = "ICESat2VegR"
+ )
+ 
+ # Specifying the path to ATL08 file
+ atl08_path <- system.file("extdata",
+   "atl08_clip.h5",
+   package = "ICESat2VegR"
+ )
+ 
+ # Reading ATL03 data (h5 file)
+ atl03_h5 <- ATL03_read(atl03_path = atl03_path)
+ 
+ # Reading ATL08 data (h5 file)
+ atl08_h5 <- ATL08_read(atl08_path = atl08_path)
+ 
+ # # Extracting ATL03 and ATL08 photons and heights
+ atl03_atl08_dt <- ATL03_ATL08_photons_attributes_dt_join(atl03_h5, atl08_h5)
+ head(atl03_atl08_dt)
+ 
+ close(atl03_h5)
+ close(atl08_h5)
+ 
+ }
Error in (function ()  : id is invalid
Calls: ATL08_read ... initialize -> <Anonymous> -> <Anonymous> -> <Anonymous>
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [19s/30s] OK
  Running ‘testthat.R’ [19s/30s]
* checking PDF version of manual ... [10s/15s] 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, 4 WARNINGs, 5 NOTEs