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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PanViz.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PanViz_1.6.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/PanViz.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-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 Ventura 13.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PanViz/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PanViz’ 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 ‘PanViz’ 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 ... OK
* 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 R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘PanViz-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: get_grouped_IMON
> ### Title: get IMON with SNP and or all network vertices coloured by group
> ###   variables (either studies or phenotypes)
> ### Aliases: get_grouped_IMON
> 
> ### ** Examples
> 
> ##getting GWAS Catalog association tsv file and cleaning up using
> ##GWAS_catalog_tsv_to_dataframe function:
> path <- system.file("extdata",
+   "gwas-association-downloaded_2021-09-13-EFO_1000649.tsv",
+    package="PanViz")
> df <- PanViz::GWAS_data_reader(file = path,
+   snp_col = "SNPS",
+   study_col = "STUDY",
+   trait_col = "DISEASE/TRAIT")
> ##creating uncoloured IMON:
> G <- PanViz::get_grouped_IMON(dataframe = df,
+   groupby = "studies",
+   ego = 5,
+   save_file = FALSE,
+   colour_groups = FALSE)

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  |===================================                                   |  50%Error in entrez_check(response) : 
  HTTP failure: 429, too many requests. Functions that contact the NCBI should not be called in parallel. If you are using a shared IP, consider registerring for an API key as described in the rate-limiting section of rentrez tutorial. NCBI message:
 {"error":"API rate limit exceeded","api-key":"170.223.207.78","count":"4","limit":"3"}
Calls: <Anonymous> ... <Anonymous> -> do.call -> <Anonymous> -> entrez_check
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:
    6. │     └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    7. └─PanViz::get_grouped_IMON(...)
    8.   └─PanViz:::NCBI_dbSNP_query(snp_list, progress_bar)
    9.     ├─base::tryCatch(...)
   10.     │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   11.     │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   12.     │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
   13.     └─rentrez::entrez_summary(db = "snp", id = split_data[[i]])
   14.       ├─base::do.call(make_entrez_query, args)
   15.       └─rentrez (local) `<fn>`(...)
   16.         └─rentrez:::entrez_check(response)
  
  [ FAIL 1 | WARN 36 | 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: 2 ERRORs
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/PanViz.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL PanViz
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘PanViz’ ...
** 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 (PanViz)

R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 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(PanViz)
> Sys.setenv(R_TESTS="")
> test_check("PanViz")
This graph was created by an old(er) igraph version.
  Call upgrade_graph() on it to use with the current igraph version
  For now we convert it on the fly...

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  |                                                                      |   0%[ FAIL 1 | WARN 36 | SKIP 0 | PASS 18 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_get_grouped_IMON.R:12:3'): tests that get_grouped_IMON produces an igraph object and throws correct errors on bad inputs ──
Error in `entrez_check(response)`: HTTP failure: 429, too many requests. Functions that contact the NCBI should not be called in parallel. If you are using a shared IP, consider registerring for an API key as described in the rate-limiting section of rentrez tutorial. NCBI message:
 {"error":"API rate limit exceeded","api-key":"170.223.207.78","count":"4","limit":"3"}

Backtrace:
     ▆
  1. ├─testthat::expect_error(...) at test_get_grouped_IMON.R:12:3
  2. │ └─testthat:::expect_condition_matching(...)
  3. │   └─testthat:::quasi_capture(...)
  4. │     ├─testthat (local) .capture(...)
  5. │     │ └─base::withCallingHandlers(...)
  6. │     └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
  7. └─PanViz::get_grouped_IMON(...)
  8.   └─PanViz:::NCBI_dbSNP_query(snp_list, progress_bar)
  9.     ├─base::tryCatch(...)
 10.     │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 11.     │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 12.     │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
 13.     └─rentrez::entrez_summary(db = "snp", id = split_data[[i]])
 14.       ├─base::do.call(make_entrez_query, args)
 15.       └─rentrez (local) `<fn>`(...)
 16.         └─rentrez:::entrez_check(response)

[ FAIL 1 | WARN 36 | SKIP 0 | PASS 18 ]
Error: Test failures
Execution halted