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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:pgxRpi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings pgxRpi_1.6.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/pgxRpi.Rcheck’
* using R version 4.5.2 Patched (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pgxRpi/DESCRIPTION’ ... OK
* this is package ‘pgxRpi’ version ‘1.6.0’
* 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 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 ... 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 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: pgxMetaplot
> ### Title: Plot survival data of individuals
> ### Aliases: pgxMetaplot
> 
> ### ** Examples
> 
> individuals <- pgxLoader(type="individuals",filters="NCIT:C3512")
Warning in value[[3L]](cond) : 
 No matching data for filter NCIT:C3512 in progenetix.org

Warning in pgxmetaLoader(type = type, biosample_id = biosample_id, individual_id = individual_id,  :
  No data retrieved
> pgxMetaplot(individuals, group_id="age_iso", condition="P65Y")
Error in if (nrow(meta.sel.df) == 0) stop("\n No available survival data \n") : 
  argument is of length zero
Calls: pgxMetaplot
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
pgxFreqplot 5.130  0.142  10.097
pgxLoader   2.961  0.121   8.661
* 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:
  Differences:
  1 element mismatch
  ── Error ('test_samples.R:47:5'): retrieve limited individuals with group id ───
  <subscriptOutOfBoundsError/error/condition>
  Error in `result$response$resultSets[[1]]`: subscript out of bounds
  Backtrace:
      ▆
   1. └─testthat::expect_equal(...) at test_samples.R:47:5
   2.   └─testthat::quasi_label(enquo(object), label)
   3.     └─rlang::eval_bare(expr, quo_get_env(quo))
  
  [ FAIL 4 | WARN 0 | SKIP 0 | PASS 38 ]
  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
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/pgxRpi.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL pgxRpi
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘pgxRpi’ ...
** this is package ‘pgxRpi’ version ‘1.6.0’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (pgxRpi)

R version 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(pgxRpi)
> 
> test_check("pgxRpi")

 trying: http://www.progenetix.org/services/intervalFrequencies/?filters=NCIT:C4323,pgx:icdom-85003 

 trying: http://progenetix.org/beacon/biosamples?filters=NCIT:C3697 
Saving _problems/test_samples-14.R
Saving _problems/test_samples-15.R

 trying: http://progenetix.org/beacon/biosamples/pgxbs-kftvh94d,pgxbs-kftvh94g 

 trying: http://progenetix.org/beacon/biosamples/pgxbs-kftvh94d,pgxbs-kftvjji1/individuals 

 trying: http://progenetix.org/beacon/individuals/pgxind-kftx3565,pgxind-kftx5g4v 

 trying: http://progenetix.org/beacon/individuals?filters=NCIT:C3512&limit=5 
Saving _problems/test_samples-46.R
Saving _problems/test_samples-47.R

 trying: http://progenetix.org/beacon/biosamples/pgxbs-kftvh94d/g_variants 

 trying: https://progenetix.org/services/pgxsegvariants/?biosampleIds=pgxbs-kftvlaih,pgxbs-kftvjgcc 

 trying: https://progenetix.org/services/variantsbedfile/?output=igv&biosampleIds=pgxbs-kftvlaih,pgxbs-kftvjgcc 

 trying: https://progenetix.org/services/samplematrix/?biosampleIds=pgxbs-kftvlaih,pgxbs-kftvjgcc 

 trying: https://progenetix.org/services/samplematrix/?individualIds=pgxind-kftx3565,pgxind-kftx5g4v 

 trying: https://progenetix.org/services/samplematrix/?filters=pgx:icdom-88503 

 trying: https://progenetix.org/services/cnvstats/?biosampleIds=pgxbs-kftvh94d,pgxbs-kftvh94g,pgxbs-kftvh972 

 trying: https://progenetix.org/services/cnvstats/?individualIds=pgxind-kftx3565,pgxind-kftx5g4v 

 trying: https://progenetix.org/services/cnvstats/?filters=pgx:icdom-88503 

 trying: https://cancercelllines.org/beacon/biosamples/cellzbs-kftvksak/g_variants 
[ FAIL 4 | WARN 0 | SKIP 0 | PASS 38 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_samples.R:14:5'): retrieve samples with group id ─────────────
Expected `result$responseSummary$exists` to equal TRUE.
Differences:
1 element mismatch
── Failure ('test_samples.R:15:5'): retrieve samples with group id ─────────────
Expected `result$responseSummary$numTotalResults` > 0.
Actual comparison: 0.0 <= 0.0
Difference: 0.0 <= 0
── Failure ('test_samples.R:46:5'): retrieve limited individuals with group id ──
Expected `result$responseSummary$exists` to equal TRUE.
Differences:
1 element mismatch
── Error ('test_samples.R:47:5'): retrieve limited individuals with group id ───
<subscriptOutOfBoundsError/error/condition>
Error in `result$response$resultSets[[1]]`: subscript out of bounds
Backtrace:
    ▆
 1. └─testthat::expect_equal(...) at test_samples.R:47:5
 2.   └─testthat::quasi_label(enquo(object), label)
 3.     └─rlang::eval_bare(expr, quo_get_env(quo))

[ FAIL 4 | WARN 0 | SKIP 0 | PASS 38 ]
Error:
! Test failures.
Execution halted