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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD check --install=check:pgxRpi.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings pgxRpi_1.3.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/pgxRpi.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pgxRpi/DESCRIPTION’ ... OK
* this is package ‘pgxRpi’ version ‘1.3.2’
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘pgxRpi’ can be installed ... OK
* checking installed package size ... 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 ...Warning: program compiled against libxml 212 using older 211
 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 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 ... NOTE
pgxSegprocess: no visible binding for global variable
  ‘followup_state_id’
Undefined global functions or variables:
  followup_state_id
* checking Rd files ... OK
* checking Rd metadata ... 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 ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘pgxRpi-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: pgxFreqplot
> ### Title: Plot CNV frequency data
> ### Aliases: pgxFreqplot
> 
> ### ** Examples
> 
> ## load necessary data (this step can be skipped in real implementation)
> data("hg38_cytoband")
> ## get frequency data
> freq <- pgxLoader(type="cnv_frequency", output ='pgxfreq', filters="NCIT:C3512")
No encoding supplied: defaulting to UTF-8.
Error in pg_data$responseSummary : 
  $ operator is invalid for atomic vectors
Calls: pgxLoader -> pgxFreqLoader
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  nrow(table) is not strictly more than 0. Difference: 0
  ── Failure ('test_variants.R:73:5'): retrieve fraction variant with individual id ──
  result$responseSummary$exists not equal to TRUE.
  target is NULL, current is logical
  ── Failure ('test_variants.R:76:5'): retrieve fraction variant with individual id ──
  nrow(table) is not strictly more than 0. Difference: 0
  ── Failure ('test_variants.R:82:5'): retrieve fraction variant with filters ────
  result$responseSummary$exists not equal to TRUE.
  target is NULL, current is logical
  ── Failure ('test_variants.R:85:5'): retrieve fraction variant with filters ────
  nrow(table) is not strictly more than 0. Difference: 0
  
  [ FAIL 36 | WARN 6 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/pgxRpi.Rcheck/00check.log’
for details.