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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:phantasusLite.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings phantasusLite_1.0.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/phantasusLite.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* 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 ‘phantasusLite/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘phantasusLite’ version ‘1.0.0’
* 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 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 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
createIndexH5: no visible global function definition for ‘h5closeAll’
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
  h5closeAll 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
inferCondition           2.598  0.164   9.188
loadCountsFromH5FileHSDS 1.198  0.335  19.596
loadCountsFromHSDS       1.013  0.147  13.632
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/phantasusLite.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL phantasusLite
###
##############################################################################
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* installing to library ‘/home/biocbuild/R/R-4.3.1/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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (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.

> # 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, setdiff, sort, 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)
GSE10010_series_matrix.txt.gz
Found 1 file(s)
GSE85653_series_matrix.txt.gz
Using locally cached version: /home/biocbuild/tmp/RtmpyDGgHo/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/tmp/RtmpyDGgHo/GPL13222.soft.gz 
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 25 ]
> 
> proc.time()
   user  system elapsed 
 20.265   2.324 104.444