##############################################################################
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###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:phantasus.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings phantasus_1.27.0.tar.gz
###
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* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/phantasus.Rcheck'
* using R Under development (unstable) (2024-10-26 r87273 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'phantasus/DESCRIPTION' ... OK
* this is package 'phantasus' version '1.27.0'
* 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 whether package 'phantasus' can be installed ... OK
* checking installed package size ... INFO
  installed size is 28.9Mb
  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 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 ... 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
filterPhenoAnnotations : parsePData: no visible binding for global
  variable 'value'
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 value
Consider adding
  importFrom("utils", "install.packages", "menu")
to your NAMESPACE file.
* checking Rd files ... NOTE
prepare_Rd: convertByAnnotationDB.Rd:35-39: 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:
  Error in `readLines(con, n = 100)`: error reading from the connection
  Backtrace:
      ▆
   1. └─phantasus::getGSE("GSE120978") at testloadGEO.R:146:5
   2.   └─phantasus:::annotateFeatureData(ess[[i]], destdir)
   3.     └─phantasus:::getGPLAnnotation(platform, destdir)
   4.       └─phantasus:::downloadGPL(GPL, destdir)
   5.         └─base::readLines(con, n = 100)
  
  [ FAIL 2 | WARN 2 | SKIP 0 | PASS 103 ]
  Error: Test failures
  In addition: Warning message:
  In for (getMethodName in getMethodNames) { :
    closing unused connection 4 (E:\biocbuild\bbs-3.21-bioc\tmpdir\RtmpUFYxdZ/geo/platforms/GPL6nnn/GPL6103/annot/GPL6103.soft.gz)
  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, 4 NOTEs
See
  'E:/biocbuild/bbs-3.21-bioc/meat/phantasus.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL phantasus
###
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* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/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 Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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 E:/biocbuild/bbs-3.21-bioc/R/library/opencpu/config/defaults.conf
Loading config from C:\Users\biocbuild\AppData\Roaming/R/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/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

trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120978/matrix/GSE120978_series_matrix.txt.gz'
Content type 'application/x-gzip' length 4192282 bytes (4.0 MB)
==================================================
downloaded 4.0 MB

trying URL 'https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?targ=self&acc=GPL16985&form=text&view=data'
downloaded 6.3 MB

[ FAIL 2 | WARN 2 | SKIP 0 | PASS 103 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('testloadGEO.R:9:5'): loadGEO finishes with result ───────────────────
Error in `readLines(con, n = 100)`: error reading from the connection
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::readLines(con, n = 100)
── Error ('testloadGEO.R:146:5'): filterPhenoAnnotations does not split title ──
Error in `readLines(con, n = 100)`: error reading from the connection
Backtrace:
    ▆
 1. └─phantasus::getGSE("GSE120978") at testloadGEO.R:146:5
 2.   └─phantasus:::annotateFeatureData(ess[[i]], destdir)
 3.     └─phantasus:::getGPLAnnotation(platform, destdir)
 4.       └─phantasus:::downloadGPL(GPL, destdir)
 5.         └─base::readLines(con, n = 100)

[ FAIL 2 | WARN 2 | SKIP 0 | PASS 103 ]
Error: Test failures
In addition: Warning message:
In for (getMethodName in getMethodNames) { :
  closing unused connection 4 (E:\biocbuild\bbs-3.21-bioc\tmpdir\RtmpUFYxdZ/geo/platforms/GPL6nnn/GPL6103/annot/GPL6103.soft.gz)
Execution halted