• using R Under development (unstable) (2026-09-11 r90523)
• 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: 2026-09-11 11:55:18 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 ... [103s/118s] OK See the install log 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/15s] OK
• checking whether the package can be loaded with stated dependencies ... [10s/12s] OK
• checking whether the package can be unloaded cleanly ... [10s/14s] OK
• checking whether the namespace can be loaded with stated dependencies ... [10s/11s] OK
• checking whether the namespace can be unloaded cleanly ... [10s/11s] OK
• checking loading without being on the library search path ... [10s/16s] OK
• checking whether startup messages can be suppressed ... [10s/11s] NOTE warning: Failed to inspect Python interpreter from search path at `/usr/sbin/pypy`   Caused by: Can't use Python at `/usr/sbin/pypy`   Caused by: 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`   Caused by: Can't use Python at `/usr/sbin/pypy`   Caused by: 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`   Caused by: Can't use Python at `/usr/sbin/pypy`   Caused by: 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`   Caused by: Can't use Python at `/usr/sbin/pypy`   Caused by: 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`   Caused by: Can't use Python at `/usr/sbin/pypy`   Caused by: 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 ... [56s/74s] NOTE warning: Failed to inspect Python interpreter from search path at `/usr/sbin/pypy`   Caused by: Can't use Python at `/usr/sbin/pypy`   Caused by: 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`   Caused by: Can't use Python at `/usr/sbin/pypy`   Caused by: 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`   Caused by: Can't use Python at `/usr/sbin/pypy`   Caused by: 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`   Caused by: Can't use Python at `/usr/sbin/pypy`   Caused by: 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`   Caused by: Can't use Python at `/usr/sbin/pypy`   Caused by: 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`   Caused by: Can't use Python at `/usr/sbin/pypy`   Caused by: 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`   Caused by: Can't use Python at `/usr/sbin/pypy`   Caused by: 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`   Caused by: Can't use Python at `/usr/sbin/pypy`   Caused by: 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 ... [18s/18s] 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/28s] OK   Running ‘testthat.R’ [19s/28s]
• checking PDF version of manual ... [9s/12s] 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