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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:pgxRpi.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings pgxRpi_1.2.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/pgxRpi.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘pgxRpi/DESCRIPTION’ ... OK
* this is package ‘pgxRpi’ version ‘1.2.2’
* 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 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 re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘Introduction_1_load_metadata.Rmd’ using rmarkdown

Quitting from lines 60-62 [unnamed-chunk-2] (Introduction_1_load_metadata.Rmd)
Error: processing vignette 'Introduction_1_load_metadata.Rmd' failed with diagnostics:
No data retrieved
--- failed re-building ‘Introduction_1_load_metadata.Rmd’

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

Quitting from lines 65-71 [unnamed-chunk-2] (Introduction_2_query_variants.Rmd)
Error: processing vignette 'Introduction_2_query_variants.Rmd' failed with diagnostics:
No data retrieved
--- failed re-building ‘Introduction_2_query_variants.Rmd’

--- re-building ‘Introduction_3_access_cnv_frequency.Rmd’ using rmarkdown

Quitting from lines 50-54 [unnamed-chunk-2] (Introduction_3_access_cnv_frequency.Rmd)
Error: processing vignette 'Introduction_3_access_cnv_frequency.Rmd' failed with diagnostics:
$ operator is invalid for atomic vectors
--- failed 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-3.20-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-3.20-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-3.20-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-3.20-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-3.20-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-3.20-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-3.20-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 files failed:
  ‘Introduction_1_load_metadata.Rmd’
  ‘Introduction_2_query_variants.Rmd’
  ‘Introduction_3_access_cnv_frequency.Rmd’

Error: Vignette re-building failed.
Execution halted

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

Status: 3 ERRORs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/pgxRpi.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL pgxRpi
###
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* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-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 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 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&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 36 | WARN 6 | SKIP 0 | PASS 0 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_frequency.R:9:5'): retrieve frequencies with pgxfreq by filter ──
http_type(r) not equal to "text/plain".
1/1 mismatches
x[1]: "text/"
y[1]: "text/plain"
── Failure ('test_frequency.R:10:5'): retrieve frequencies with pgxfreq by filter ──
Expected `result <- read.table(url, header = T, sep = "\t")` to run without any errors.
ℹ Actually got a <simpleError> with text:
  cannot open the connection to 'http://www.progenetix.org/services/intervalFrequencies/?filters=NCIT:C4323,pgx:icdom-85003&output=pgxfreq'
── Error ('test_frequency.R:11:5'): retrieve frequencies with pgxfreq by filter ──
Error in `eval(code, test_env)`: object 'result' not found
Backtrace:
    ▆
 1. └─testthat::expect_equal(dim(result), c(6212, 7)) at test_frequency.R:11:5
 2.   └─testthat::quasi_label(enquo(object), label, arg = "object")
 3.     └─rlang::eval_bare(expr, quo_get_env(quo))
── Failure ('test_frequency.R:20:5'): retrieve frequencies with pgxmatrix by filter ──
http_type(r) not equal to "text/plain".
1/1 mismatches
x[1]: "text/"
y[1]: "text/plain"
── Failure ('test_frequency.R:21:5'): retrieve frequencies with pgxmatrix by filter ──
Expected `result <- read.table(url, header = T, sep = "\t")` to run without any errors.
ℹ Actually got a <simpleError> with text:
  cannot open the connection to 'http://www.progenetix.org/services/intervalFrequencies/?output=pgxmatrix&filters=NCIT:C4323,pgx:icdom-85003'
── Error ('test_frequency.R:22:5'): retrieve frequencies with pgxmatrix by filter ──
Error in `eval(code, test_env)`: object 'result' not found
Backtrace:
    ▆
 1. └─testthat::expect_equal(dim(result), c(2, 6213)) at test_frequency.R:22:5
 2.   └─testthat::quasi_label(enquo(object), label, arg = "object")
 3.     └─rlang::eval_bare(expr, quo_get_env(quo))
── Failure ('test_samples.R:14:5'): retrieve samples with group id ─────────────
result$responseSummary$exists not equal to TRUE.
target is NULL, current is logical
── Error ('test_samples.R:15:5'): retrieve samples with group id ───────────────
Error in `expect_compare(">", act, exp)`: Result of comparison must be a single logical value
Backtrace:
    ▆
 1. └─testthat::expect_gt(result$responseSummary$numTotalResults, 0) at test_samples.R:15:5
 2.   └─testthat:::expect_compare(">", act, exp)
 3.     └─rlang::abort("Result of comparison must be a single logical value")
── Failure ('test_samples.R:22:5'): retrieve samples with biosample id ─────────
result$responseSummary$exists not equal to TRUE.
target is NULL, current is logical
── Error ('test_samples.R:23:5'): retrieve samples with biosample id ───────────
Error in `expect_compare(">", act, exp)`: Result of comparison must be a single logical value
Backtrace:
    ▆
 1. └─testthat::expect_gt(result$responseSummary$numTotalResults, 0) at test_samples.R:23:5
 2.   └─testthat:::expect_compare(">", act, exp)
 3.     └─rlang::abort("Result of comparison must be a single logical value")
── Failure ('test_samples.R:30:5'): retrieve individuals with biosample id ─────
result$responseSummary$exists not equal to TRUE.
target is NULL, current is logical
── Error ('test_samples.R:31:5'): retrieve individuals with biosample id ───────
Error in `expect_compare(">", act, exp)`: Result of comparison must be a single logical value
Backtrace:
    ▆
 1. └─testthat::expect_gt(result$responseSummary$numTotalResults, 0) at test_samples.R:31:5
 2.   └─testthat:::expect_compare(">", act, exp)
 3.     └─rlang::abort("Result of comparison must be a single logical value")
── Failure ('test_samples.R:38:5'): retrieve individuals with individual id ────
result$responseSummary$exists not equal to TRUE.
target is NULL, current is logical
── Error ('test_samples.R:39:5'): retrieve individuals with individual id ──────
Error in `expect_compare(">", act, exp)`: Result of comparison must be a single logical value
Backtrace:
    ▆
 1. └─testthat::expect_gt(result$responseSummary$numTotalResults, 0) at test_samples.R:39:5
 2.   └─testthat:::expect_compare(">", act, exp)
 3.     └─rlang::abort("Result of comparison must be a single logical value")
── Failure ('test_samples.R:46:5'): retrieve limited individuals with group id ──
result$responseSummary$exists not equal to TRUE.
target is NULL, current is logical
── Failure ('test_samples.R:47:5'): retrieve limited individuals with group id ──
length(result$response$resultSets[[1]]$results) not equal to 5.
1/1 mismatches
[1] 0 - 5 == -5
── Failure ('test_variants.R:18:9'): retrieve variants with JSON ───────────────
result$responseSummary$exists not equal to TRUE.
target is NULL, current is logical
── Failure ('test_variants.R:21:9'): retrieve variants with JSON ───────────────
nrow(table) is not strictly more than 0. Difference: 0
── 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 36 | WARN 6 | SKIP 0 | PASS 0 ]
Error: Test failures
Execution halted