##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:pgxRpi.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings pgxRpi_1.6.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/pgxRpi.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* 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 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
pgxLoader   56.276  1.403  77.451
pgxMetaplot 17.754  0.644  23.754
pgxFreqplot  4.230  0.096   6.401
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘Introduction_1_load_metadata.Rmd’ using rmarkdown
The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/pgxRpi.Rcheck/vign_test/pgxRpi/vignettes/Introduction_1_load_metadata_files/figure-html/unnamed-chunk-13-1.png" but not available.
--- finished re-building ‘Introduction_1_load_metadata.Rmd’

--- re-building ‘Introduction_2_query_variants.Rmd’ using rmarkdown

Quitting from Introduction_2_query_variants.Rmd:92-95 [unnamed-chunk-5]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `file()`:
! cannot open the connection to 'https://progenetix.org/services/pgxsegvariants/?biosampleIds=pgxbs-kftvkvw8&limit=0'
---
Backtrace:
    ▆
 1. └─pgxRpi::pgxLoader(...)
 2.   └─pgxRpi:::pgxVariantLoader(...)
 3.     └─future.apply::future_lapply(...)
 4.       └─future.apply:::future_xapply(...)
 5.         └─base::tryCatch(...)
 6.           └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 7.             └─base (local) tryCatchOne(...)
 8.               └─value[[3L]](cond)
 9.                 └─future.apply:::onError(e, futures = fs, debug = debug)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'Introduction_2_query_variants.Rmd' failed with diagnostics:
cannot open the connection to 'https://progenetix.org/services/pgxsegvariants/?biosampleIds=pgxbs-kftvkvw8&limit=0'
--- failed re-building ‘Introduction_2_query_variants.Rmd’

--- re-building ‘Introduction_3_access_cnv_frequency.Rmd’ using rmarkdown
The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/pgxRpi.Rcheck/vign_test/pgxRpi/vignettes/Introduction_3_access_cnv_frequency_files/figure-html/unnamed-chunk-13-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/pgxRpi.Rcheck/vign_test/pgxRpi/vignettes/Introduction_3_access_cnv_frequency_files/figure-html/unnamed-chunk-14-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/pgxRpi.Rcheck/vign_test/pgxRpi/vignettes/Introduction_3_access_cnv_frequency_files/figure-html/unnamed-chunk-15-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/pgxRpi.Rcheck/vign_test/pgxRpi/vignettes/Introduction_3_access_cnv_frequency_files/figure-html/unnamed-chunk-16-1.png" but not available.
--- finished re-building ‘Introduction_3_access_cnv_frequency.Rmd’

--- re-building ‘Introduction_4_process_pgxseg.Rmd’ using rmarkdown
The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/pgxRpi.Rcheck/vign_test/pgxRpi/vignettes/Introduction_4_process_pgxseg_files/figure-html/unnamed-chunk-6-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/pgxRpi.Rcheck/vign_test/pgxRpi/vignettes/Introduction_4_process_pgxseg_files/figure-html/unnamed-chunk-7-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/pgxRpi.Rcheck/vign_test/pgxRpi/vignettes/Introduction_4_process_pgxseg_files/figure-html/unnamed-chunk-8-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/pgxRpi.Rcheck/vign_test/pgxRpi/vignettes/Introduction_4_process_pgxseg_files/figure-html/unnamed-chunk-13-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/pgxRpi.Rcheck/vign_test/pgxRpi/vignettes/Introduction_4_process_pgxseg_files/figure-html/unnamed-chunk-14-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/pgxRpi.Rcheck/vign_test/pgxRpi/vignettes/Introduction_4_process_pgxseg_files/figure-html/unnamed-chunk-15-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/pgxRpi.Rcheck/vign_test/pgxRpi/vignettes/Introduction_4_process_pgxseg_files/figure-html/unnamed-chunk-16-1.png" but not available.
--- finished re-building ‘Introduction_4_process_pgxseg.Rmd’

SUMMARY: processing the following file failed:
  ‘Introduction_2_query_variants.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/pgxRpi.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL pgxRpi
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-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 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 

 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 

 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 0 | WARN 0 | SKIP 0 | PASS 42 ]
> 
> proc.time()
   user  system elapsed 
  5.482   0.327 393.085