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###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:phantasus.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings phantasus_1.24.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/phantasus.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘phantasus/DESCRIPTION’ ... OK
* this is package ‘phantasus’ version ‘1.24.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .env
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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 29.2Mb
  sub-directories of 1Mb or more:
    testdata   5.1Mb
    www       23.6Mb
* 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 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
Namespace in Imports field not imported from: 'rhdf5client'
  All declared Imports should be used.
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'
getFileIndexDF: no visible global function definition for '.'
getFileIndexDF: no visible binding for global variable 'Name'
getFileIndexDF: no visible binding for global variable 'Last modified'
getFileIndexDF: no visible binding for global variable 'Size'
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'
servePhantasus: no visible global function definition for 'menu'
servePhantasus: no visible global function definition for
  'install.packages'
setupPhantasus: no visible global function definition for 'menu'
setupPhantasus: no visible global function definition for
  'install.packages'
validateCountsCollection: no visible binding for global variable
  'file_name'
Undefined global functions or variables:
  . ComparisonReference ComparisonTarget DT_counts_meta Last modified
  Name Size accession collection_type directory es file_name
  heatmapJson id install.packages menu
Consider adding
  importFrom("utils", "install.packages", "menu")
to your NAMESPACE file.
* checking Rd files ... NOTE
prepare_Rd: convertByAnnotationDB.Rd:35-40: 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 ... OK
* 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:
    1. └─phantasus:::loadGEO("GSE27112") at testloadGEO.R:9:5
    2.   └─phantasus::getES(name, type, destdir = cacheDir, mirrorPath = mirrorPath)
    3.     └─phantasus::getGSE(name, destdir, mirrorPath)
    4.       └─phantasus::getGSE(gpls[[i]], destdir = destdir, mirrorPath = mirrorPath)
    5.         └─phantasus:::annotateFeatureData(ess[[i]], destdir)
    6.           └─phantasus:::getGPLAnnotation(platform, destdir)
    7.             └─phantasus:::downloadGPL(GPL, destdir)
    8.               └─base::tryCatch(...)
    9.                 └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   10.                   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   11.                     └─value[[3L]](cond)
  
  [ FAIL 1 | WARN 2 | SKIP 0 | PASS 108 ]
  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, 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/phantasus.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL phantasus
###
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* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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(phantasus)
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Loading config from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/opencpu/config/defaults.conf
Loading config from /home/biocbuild/.config/R/opencpu/user.conf
> 
> test_check("phantasus")
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE53nnn/GSE53986/matrix/GSE53986_series_matrix.txt.gz'
Content type 'application/x-gzip' length 2848655 bytes (2.7 MB)
==================================================
downloaded 2.7 MB

trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/platforms/GPL1nnn/GPL1261/annot/GPL1261.annot.gz'
Content type 'application/x-gzip' length 8389179 bytes (8.0 MB)
==================================================
downloaded 8.0 MB

trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE107nnn/GSE107746/matrix/GSE107746_series_matrix.txt.gz'
Content type 'application/x-gzip' length 7196 bytes
==================================================
downloaded 7196 bytes

trying URL 'https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?targ=self&acc=GPL20795&form=text&view=data'
downloaded 48 bytes

trying URL 'https://alserglab.wustl.edu/files/phantasus/geo/series/GSE27nnn/GSE27112/matrix/GSE27112_series_matrix.txt.gz'
trying URL 'https://alserglab.wustl.edu/files/phantasus/geo/series/GSE27nnn/GSE27112/matrix/GSE27112-GPL6103_series_matrix.txt.gz'
Content type 'application/x-gzip' length 596707 bytes (582 KB)
==================================================
downloaded 582 KB

trying URL 'https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?targ=self&acc=GPL6103&form=text&view=data'
downloaded 3.4 MB

trying URL 'https://alserglab.wustl.edu/files/phantasus/geo/series/GSE27nnn/GSE27112/matrix/GSE27112-GPL6885_series_matrix.txt.gz'
Content type 'application/x-gzip' length 1273889 bytes (1.2 MB)
==================================================
downloaded 1.2 MB

trying URL 'https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?targ=self&acc=GPL6885&form=text&view=data'
trying URL 'https://alserglab.wustl.edu/files/phantasus/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://ftp.ncbi.nlm.nih.gov/geo/series/GSE14nnn/GSE14308/matrix/GSE14308_series_matrix.txt.gz'
Content type 'application/x-gzip' length 1807570 bytes (1.7 MB)
==================================================
downloaded 1.7 MB

trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE99nnn/GSE99709/matrix/GSE99709_series_matrix.txt.gz'
Content type 'application/x-gzip' length 3386 bytes
==================================================
downloaded 3386 bytes

trying URL 'https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?targ=self&acc=GPL17021&form=text&view=data'
downloaded 48 bytes

trying URL 'https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?targ=self&acc=GPL17021&form=text&view=data'
downloaded 48 bytes

[ FAIL 1 | WARN 2 | SKIP 0 | PASS 108 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('testloadGEO.R:9:5'): loadGEO finishes with result ───────────────────
Error in `value[[3L]](cond)`: Could not download GPL GPL6885Error 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=GPL6885&form=text&view=data'

Backtrace:
     ▆
  1. └─phantasus:::loadGEO("GSE27112") at testloadGEO.R:9:5
  2.   └─phantasus::getES(name, type, destdir = cacheDir, mirrorPath = mirrorPath)
  3.     └─phantasus::getGSE(name, destdir, mirrorPath)
  4.       └─phantasus::getGSE(gpls[[i]], destdir = destdir, mirrorPath = mirrorPath)
  5.         └─phantasus:::annotateFeatureData(ess[[i]], destdir)
  6.           └─phantasus:::getGPLAnnotation(platform, destdir)
  7.             └─phantasus:::downloadGPL(GPL, destdir)
  8.               └─base::tryCatch(...)
  9.                 └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 10.                   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 11.                     └─value[[3L]](cond)

[ FAIL 1 | WARN 2 | SKIP 0 | PASS 108 ]
Error: Test failures
Execution halted