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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:phantasusLite.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings phantasusLite_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/phantasusLite.Rcheck’
* using R version 4.4.3 (2025-02-28)
* 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 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘phantasusLite/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘phantasusLite’ version ‘1.4.0’
* 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 ‘phantasusLite’ 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 ... NOTE
Unexported object imported by a ':::' call: ‘rhdf5client:::submitRequest’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
getCountsMetaPart: no visible binding for global variable ‘file_name’
loadCountsFromH5FileHSDS: no visible binding for global variable
  ‘file_name’
loadCountsFromHSDS: no visible global function definition for ‘.’
loadCountsFromHSDS: no visible binding for global variable ‘directory’
loadCountsFromHSDS: no visible binding for global variable ‘accession’
loadCountsFromHSDS: no visible binding for global variable
  ‘collection_type’
updateARCHS4meta: no visible global function definition for ‘H5Fopen’
updateARCHS4meta: no visible global function definition for ‘H5Lexists’
updateIndexH5: no visible binding for global variable ‘list_dirs’
validateCountsCollection: no visible binding for global variable
  ‘file_name’
validateCountsCollection: no visible global function definition for
  ‘H5Lexists’
Undefined global functions or variables:
  . H5Fopen H5Lexists accession collection_type directory file_name
  list_dirs
* 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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘phantasusLite-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: loadCountsFromH5FileHSDS
> ### Title: Load count matrix from remote HDF5-file
> ### Aliases: loadCountsFromH5FileHSDS
> 
> ### ** Examples
> 
> ess <- GEOquery::getGEO("GSE53053")
Found 0 file(s)
NA
HTTP 404 Not Found.File stored at:
/home/biocbuild/bbs-3.20-bioc/tmpdir/Rtmp2MvpY2/NA
Error in downloadFile(url, destfile = destfile, mode = "wb") : 
  Failed to download /home/biocbuild/bbs-3.20-bioc/tmpdir/Rtmp2MvpY2/NA!
Calls: <Anonymous> -> getAndParseGSEMatrices -> downloadFile
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:
    2.   └─GEOquery:::getAndParseGSEMatrices(...)
    3.     └─GEOquery:::getDirListing(sprintf(gdsurl, stub, GEO))
    4.       ├─xml2::read_html(url)
    5.       └─xml2:::read_html.default(url)
    6.         ├─base::suppressWarnings(...)
    7.         │ └─base::withCallingHandlers(...)
    8.         ├─xml2::read_xml(x, encoding = encoding, ..., as_html = TRUE, options = options)
    9.         └─xml2:::read_xml.character(...)
   10.           └─xml2:::read_xml.connection(...)
   11.             ├─base::open(x, "rb")
   12.             └─base::open.connection(x, "rb")
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 25 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/phantasusLite.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL phantasusLite
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘phantasusLite’ ...
** using staged installation
** R
** 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 (phantasusLite)

R version 4.4.3 (2025-02-28) -- "Trophy Case"
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.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
> 
> library(testthat)
> library(phantasusLite)
> 
> test_check("phantasusLite")
Loading required package: Biobase
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table,
    tapply, union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Found 1 file(s)
GSE85653_series_matrix.txt.gz
Annotation GPL not available, so will use submitter GPL instead
Found 1 file(s)
GSE53053_series_matrix.txt.gz
Annotation GPL not available, so will use submitter GPL instead
Found 1 file(s)
GSE85653_series_matrix.txt.gz
Using locally cached version: /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpvBY9Qc/GSE85653_series_matrix.txt.gz
Annotation GPL not available, so will use submitter GPL instead
Using locally cached version of GPL13222 found here:
/home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpvBY9Qc/GPL13222.soft.gz 
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 25 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-loadCountsFromH5file.R:25:3'): loadCountsFromHSDS returns the same ExpressionSet, if it contains counts matrix ──
Error in `open.connection(x, "rb")`: cannot open the connection
Backtrace:
     ▆
  1. └─GEOquery::getGEO("GSE10010") at test-loadCountsFromH5file.R:25:3
  2.   └─GEOquery:::getAndParseGSEMatrices(...)
  3.     └─GEOquery:::getDirListing(sprintf(gdsurl, stub, GEO))
  4.       ├─xml2::read_html(url)
  5.       └─xml2:::read_html.default(url)
  6.         ├─base::suppressWarnings(...)
  7.         │ └─base::withCallingHandlers(...)
  8.         ├─xml2::read_xml(x, encoding = encoding, ..., as_html = TRUE, options = options)
  9.         └─xml2:::read_xml.character(...)
 10.           └─xml2:::read_xml.connection(...)
 11.             ├─base::open(x, "rb")
 12.             └─base::open.connection(x, "rb")

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 25 ]
Error: Test failures
Execution halted