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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:phantasus.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings phantasus_1.22.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/phantasus.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* 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 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘phantasus/DESCRIPTION’ ... OK
* this is package ‘phantasus’ version ‘1.22.2’
* 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 ‘phantasus’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 29.0Mb
  sub-directories of 1Mb or more:
    testdata   5.0Mb
    www       23.5Mb
* checking package 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 R 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 ... NOTE
Unexported objects imported by ':::' calls:
  'GEOquery:::.parseGPLTxt' 'GEOquery:::getDirListing'
  'opencpu:::rookhandler' 'opencpu:::tmp_root' 'opencpu:::win_or_mac'
  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
generatePreloadedSession: no visible binding for global variable 'es'
generatePreloadedSession: no visible binding for global variable
  'heatmapJson'
getCountsMetaPart: no visible binding for global variable 'file_name'
getDesignMatrix: no visible binding for global variable 'id'
limmaAnalysisSimpleImpl: no visible binding for global variable
  'ComparisonTarget'
limmaAnalysisSimpleImpl: no visible binding for global variable
  'ComparisonReference'
loadCounts: no visible global function definition for '.'
loadCounts: no visible binding for global variable 'directory'
loadCounts: no visible binding for global variable 'DT_counts_meta'
loadCounts: no visible binding for global variable 'accession'
loadCounts: no visible binding for global variable 'collection_type'
loadCounts: no visible binding for global variable 'file_name'
loadSession: no visible binding for global variable 'es'
safeDownload: no visible binding for global variable 'tempDestFile'
validateCountsCollection: no visible binding for global variable
  'file_name'
Undefined global functions or variables:
  . ComparisonReference ComparisonTarget DT_counts_meta accession
  collection_type directory es file_name heatmapJson id tempDestFile
* checking Rd files ... NOTE
prepare_Rd: convertByAnnotationDB.Rd:36-41: Dropping empty section \examples
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘phantasus-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getGSE
> ### Title: Load ExpressionSet from GEO Series
> ### Aliases: getGSE
> 
> ### ** Examples
> 
> ## Not run: 
> ##D     getGSE('GSE14308', destdir = 'cache')
> ##D     getGSE('GSE27112')
> ## End(Not run)
> getGSE('GSE53986')
Trying https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE53986&targ=self&form=text&view=brief
No encoding supplied: defaulting to UTF-8.
No such dataset: GSE53986
Error in getBriefData(name, destDir) : 
  Failed to download brief data on: GSE53986. No such dataset
Calls: getGSE -> checkGSEType -> getBriefData
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:
   5.         └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   6.           └─value[[3L]](cond)
  ── Error ('testloadGEO.R:132:5'): getGSEType works ─────────────────────────────
  Error in `getBriefData(name, destDir)`: Failed to download brief data on: GSE53986. No such dataset
  Backtrace:
      ▆
   1. ├─testthat::expect_true(checkGSEType("GSE53986", tempdir())) at testloadGEO.R:132:5
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─phantasus:::checkGSEType("GSE53986", tempdir())
   5.   └─phantasus:::getBriefData(name, destDir)
  
  [ FAIL 8 | WARN 4 | SKIP 0 | PASS 95 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/phantasus.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL phantasus
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘phantasus’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (phantasus)

R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (64-bit)

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(phantasus)
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Loading config from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/opencpu/config/defaults.conf
Loading config from /Users/biocbuild/Library/Preferences/org.R-project.R/R/opencpu/user.conf
> 
> test_check("phantasus")
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/datasets/GDS4nnn/GDS4885/soft/GDS4885.soft.gz'
Content type 'application/x-gzip' length 1250109 bytes (1.2 MB)
==================================================
downloaded 1.2 MB

trying URL 'https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?targ=self&acc=GPL17021&form=text&view=data'
[ FAIL 8 | WARN 4 | SKIP 0 | PASS 95 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('testCollapse.R:64:5'): Collapse strip unannotated rows ──────────────
Error in `getBriefData(name, destDir)`: Failed to download brief data on: GSE53986. No such dataset
Backtrace:
    ▆
 1. └─phantasus::getGSE("GSE53986") at testCollapse.R:64:5
 2.   └─phantasus:::checkGSEType(name, destdir)
 3.     └─phantasus:::getBriefData(name, destDir)
── Error ('testcounts.R:87:5'): loadCounts returns result ──────────────────────
Error in `getBriefData(name, destDir)`: Failed to download brief data on: GSE107746. No such dataset
Backtrace:
    ▆
 1. └─phantasus::getGSE(test_gse, destdir = tmp_dir) at testcounts.R:87:5
 2.   └─phantasus:::checkGSEType(name, destdir)
 3.     └─phantasus:::getBriefData(name, destDir)
── Error ('testloadGEO.R:11:5'): loadGEO finishes with result ──────────────────
Error in `getBriefData(name, destDir)`: Failed to download brief data on: GSE27112. No such dataset
Backtrace:
    ▆
 1. └─phantasus:::loadGEO("GSE27112") at testloadGEO.R:11:5
 2.   └─phantasus::getES(name, type, destdir = cacheDir, mirrorPath = mirrorPath)
 3.     └─phantasus::getGSE(name, destdir, mirrorPath)
 4.       └─phantasus:::checkGSEType(name, destdir)
 5.         └─phantasus:::getBriefData(name, destDir)
── Error ('testloadGEO.R:41:5'): filterPhenoAnnotations saves colnames ─────────
Error in `getBriefData(name, destDir)`: Failed to download brief data on: GSE53986. No such dataset
Backtrace:
    ▆
 1. └─phantasus::getES("GSE53986", destdir = cacheDir) at testloadGEO.R:41:5
 2.   └─phantasus::getGSE(name, destdir, mirrorPath)
 3.     └─phantasus:::checkGSEType(name, destdir)
 4.       └─phantasus:::getBriefData(name, destDir)
── Error ('testloadGEO.R:47:5'): reparseCachedGSEs works ───────────────────────
Error in `getBriefData(name, destDir)`: Failed to download brief data on: GSE14308. No such dataset
Backtrace:
    ▆
 1. └─phantasus::getES("GSE14308", destdir = cacheDir) at testloadGEO.R:47:5
 2.   └─phantasus::getGSE(name, destdir, mirrorPath)
 3.     └─phantasus:::checkGSEType(name, destdir)
 4.       └─phantasus:::getBriefData(name, destDir)
── Error ('testloadGEO.R:87:5'): getGSE works with ARCHS4 ──────────────────────
Error in `getBriefData(gpl, destdir = destDir)`: Failed to download brief data on: GPL17021. No such dataset
Backtrace:
    ▆
 1. └─phantasus::getGSE(...) at testloadGEO.R:87:5
 2.   └─phantasus:::checkGSEType(name, destdir)
 3.     └─base::sapply(...)
 4.       └─base::lapply(X = X, FUN = FUN, ...)
 5.         └─phantasus (local) FUN(X[[i]], ...)
 6.           └─phantasus:::getBriefData(gpl, destdir = destDir)
── Error ('testloadGEO.R:127:5'): getGPLAnnotation works with errorneous empty annotation files ──
Error in `value[[3L]](cond)`: Could not download GPL GPL17021Error in download.file(submitterURL, tmp, headers = c(`accept-encoding` = "gzip")): cannot open URL 'https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?targ=self&acc=GPL17021&form=text&view=data'

Backtrace:
    ▆
 1. └─phantasus:::getGPLAnnotation(GPL, destdir) at testloadGEO.R:127:5
 2.   └─phantasus:::downloadGPL(GPL, destdir)
 3.     └─base::tryCatch(...)
 4.       └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 5.         └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 6.           └─value[[3L]](cond)
── Error ('testloadGEO.R:132:5'): getGSEType works ─────────────────────────────
Error in `getBriefData(name, destDir)`: Failed to download brief data on: GSE53986. No such dataset
Backtrace:
    ▆
 1. ├─testthat::expect_true(checkGSEType("GSE53986", tempdir())) at testloadGEO.R:132:5
 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
 3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
 4. └─phantasus:::checkGSEType("GSE53986", tempdir())
 5.   └─phantasus:::getBriefData(name, destDir)

[ FAIL 8 | WARN 4 | SKIP 0 | PASS 95 ]
Error: Test failures
Execution halted