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### Running command:
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###   /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.