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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_1.3.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/pgxRpi.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.1
* 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 ... 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
pgxLoader   8.706  0.092  21.546
pgxMetaplot 3.346  0.060   8.620
* 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 18 | WARN 4 | SKIP 0 | PASS 18 ]
  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: 1 ERROR, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/pgxRpi.Rcheck/00check.log’
for details.

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### Running command:
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###   /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 ‘1.3.2’
** 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 Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"
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&output=pgxfreq 

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

 trying: http://progenetix.org/beacon/biosamples?filters=NCIT:C3697 

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

 trying: http://progenetix.org/beacon/individuals?biosampleIds=pgxbs-kftvh94d,pgxbs-kftvjji1 

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

 trying: http://progenetix.org/beacon/individuals?filters=NCIT:C3512&limit=5 

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

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

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

 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 
[ FAIL 18 | WARN 4 | SKIP 0 | PASS 18 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_variants.R:28:5'): retrieve variants with pgxseg ─────────────
http_type(r) not equal to "text/plain".
1/1 mismatches
x[1]: "text/html"
y[1]: "text/plain"
── Failure ('test_variants.R:29:5'): retrieve variants with pgxseg ─────────────
Expected `... <- NULL` to run without any errors.
ℹ Actually got a <simpleError> with text:
  cannot open the connection to 'https://progenetix.org/services/pgxsegvariants/?biosampleIds=pgxbs-kftvh94d,pgxbs-kftvh94g,pgxbs-kftvh972'
── Error ('test_variants.R:30:5'): retrieve variants with pgxseg ───────────────
Error in `eval(code, test_env)`: object 'result' not found
Backtrace:
    ▆
 1. ├─testthat::expect_gt(nrow(result), 0) at test_variants.R:30:5
 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
 3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
 4. └─base::nrow(result)
── Failure ('test_variants.R:37:5'): retrieve pgxmatrix variant with biosample id ──
http_type(r) not equal to "text/plain".
1/1 mismatches
x[1]: "text/html"
y[1]: "text/plain"
── Failure ('test_variants.R:38:5'): retrieve pgxmatrix variant with biosample id ──
Expected `... <- NULL` to run without any errors.
ℹ Actually got a <simpleError> with text:
  cannot open the connection to 'https://progenetix.org/services/samplematrix/?biosampleIds=pgxbs-kftvh94d,pgxbs-kftvh94g,pgxbs-kftvh972'
── Error ('test_variants.R:39:5'): retrieve pgxmatrix variant with biosample id ──
Error in `eval(code, test_env)`: object 'result' not found
Backtrace:
    ▆
 1. ├─testthat::expect_gt(nrow(result), 0) at test_variants.R:39:5
 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
 3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
 4. └─base::nrow(result)
── Failure ('test_variants.R:46:5'): retrieve pgxmatrix variant with individual id ──
http_type(r) not equal to "text/plain".
1/1 mismatches
x[1]: "text/html"
y[1]: "text/plain"
── Failure ('test_variants.R:47:5'): retrieve pgxmatrix variant with individual id ──
Expected `... <- NULL` to run without any errors.
ℹ Actually got a <simpleError> with text:
  cannot open the connection to 'https://progenetix.org/services/samplematrix/?individualIds=pgxind-kftx3565,pgxind-kftx5g4v'
── Error ('test_variants.R:48:5'): retrieve pgxmatrix variant with individual id ──
Error in `eval(code, test_env)`: object 'result' not found
Backtrace:
    ▆
 1. ├─testthat::expect_gt(nrow(result), 0) at test_variants.R:48:5
 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
 3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
 4. └─base::nrow(result)
── Failure ('test_variants.R:55:5'): retrieve pgxmatrix variant with filters ───
http_type(r) not equal to "text/plain".
1/1 mismatches
x[1]: "text/html"
y[1]: "text/plain"
── Failure ('test_variants.R:56:5'): retrieve pgxmatrix variant with filters ───
Expected `... <- NULL` to run without any errors.
ℹ Actually got a <simpleError> with text:
  cannot open the connection to 'https://progenetix.org/services/samplematrix/?filters=pgx:icdom-88503'
── Error ('test_variants.R:57:5'): retrieve pgxmatrix variant with filters ─────
Error in `eval(code, test_env)`: object 'result' not found
Backtrace:
    ▆
 1. ├─testthat::expect_gt(nrow(result), 0) at test_variants.R:57:5
 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
 3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
 4. └─base::nrow(result)
── Failure ('test_variants.R:64:5'): retrieve fraction variant with biosample id ──
result$responseSummary$exists not equal to TRUE.
target is NULL, current is logical
── Failure ('test_variants.R:67:5'): retrieve fraction variant with biosample id ──
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 18 | WARN 4 | SKIP 0 | PASS 18 ]
Error: Test failures
Execution halted