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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_1.0.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/pgxRpi.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pgxRpi/DESCRIPTION’ ... OK
* this is package ‘pgxRpi’ version ‘1.0.1’
* 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’
pgxSegprocess: no visible binding for global variable ‘followup_time’
Undefined global functions or variables:
  followup_state_id followup_time
* 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
pgxFilter   11.251  0.099  14.020
pgxFreqplot  3.570  0.156  11.551
pgxLoader    1.591  0.124  16.565
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.19-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/4.4-x86_64/Resources/library’
* installing *source* package ‘pgxRpi’ ...
** 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 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-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&output=pgxfreq&datasetIds=progenetix 

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

 trying: http://www.progenetix.org/services/intervalFrequencies/?output=pgxmatrix&filters=NCIT:C5228,pgx:icdom-87203&datasetIds=cellz 

 trying: http://progenetix.org/services/sampletable/?filters=NCIT:C3697&datasetIds=progenetix 

 trying: http://progenetix.org/services/sampletable/?biosampleIds=pgxbs-kftvh94d,pgxbs-kftvh94g&datasetIds=progenetix 

 trying: http://progenetix.org/services/sampletable/?biosampleIds=pgxbs-kftvh94d,pgxbs-kftvjji1&requestEntityPathId=individual&datasetIds=progenetix 

 trying: http://progenetix.org/services/sampletable/?individualIds=pgxind-kftx3565,pgxind-kftx5g4v&requestEntityPathId=individual&datasetIds=progenetix 

 trying: http://progenetix.org/services/sampletable/?filters=NCIT:C3512&requestEntityPathId=individual&limit=1000&datasetIds=progenetix 

 trying: http://progenetix.org/services/sampletable/?filters=NCIT:C7707&datasetIds=cellz 

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

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

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

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

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

 trying: https://progenetix.org/beacon/analyses/?output=cnvstats&biosampleIds=pgxbs-kftvh94d,pgxbs-kftvh94g,pgxbs-kftvh972&datasetIds=progenetix 

 trying: https://progenetix.org/beacon/analyses/?output=cnvstats&individualIds=pgxind-kftx3565,pgxind-kftx5g4v&datasetIds=progenetix 

 trying: https://progenetix.org/beacon/analyses/?output=cnvstats&filters=pgx:icdom-88503&datasetIds=progenetix 

 trying: http://progenetix.org/beacon/biosamples/cellzbs-0821E6df/g_variants?datasetIds=cellz 
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 54 ]
> 
> proc.time()
   user  system elapsed 
 15.756   0.384  66.495