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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:crossmeta.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings crossmeta_1.26.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/crossmeta.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘crossmeta/DESCRIPTION’ ... OK
* this is package ‘crossmeta’ version ‘1.26.0’
* 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 ‘crossmeta’ 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 dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
  ‘RCurl’ ‘XML’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
diff_expr   52.269  2.117  72.982
es_meta     50.981  1.748  70.792
setup_prev   9.190  0.693  12.852
load_diff    8.078  0.266  10.944
add_sources  7.246  0.316   9.861
get_raw      1.071  0.103   5.014
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.17-bioc/meat/crossmeta.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL crossmeta
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’
* installing *source* package ‘crossmeta’ ...
** 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 (crossmeta)

R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-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(crossmeta)
> 
> test_check("crossmeta")
GSE1_disease-healthy (# p < 0.05): 0 
GSE1_disease-healthy (# p < 0.05): 2 
Illumina samples matched by pdata column.
Illumina samples matched by pdata column.
Illumina samples matched by pdata column.
Illumina samples matched by pdata column.
Illumina samples matched by column names.
Illumina samples matched by pdata column.
Illumina samples matched by pdata column.
Illumina samples matched by pdata column.
Illumina samples matched by pdata column.
Array 1 corrected
Array 2 corrected
Array 3 corrected
Array 4 corrected
Array 5 corrected
Array 6 corrected
Array 7 corrected
Array 8 corrected
Array 9 corrected
Array 10 corrected
Array 11 corrected
Array 12 corrected
Array 13 corrected
Array 14 corrected
Array 15 corrected
Array 16 corrected
Array 1 corrected
Array 2 corrected
Array 3 corrected
Array 4 corrected
Array 5 corrected
Array 6 corrected
Array 7 corrected
Array 8 corrected
Array 9 corrected
Array 10 corrected
Array 11 corrected
Array 12 corrected
Array 13 corrected
Array 14 corrected
Array 15 corrected
Array 16 corrected
Apoa1_ApoAI...-C57BL.6 (# p < 0.05): 20 
Array 1 corrected
Array 2 corrected
Array 3 corrected
Array 4 corrected
Array 5 corrected
Array 6 corrected
Array 7 corrected
Array 8 corrected
Array 9 corrected
Array 10 corrected
Array 11 corrected
Array 12 corrected
Array 13 corrected
Array 14 corrected
Array 15 corrected
Array 16 corrected
Array 1 corrected
Array 2 corrected
Array 3 corrected
Array 4 corrected
Array 5 corrected
Array 6 corrected
Array 7 corrected
Array 8 corrected
Array 9 corrected
Array 10 corrected
Array 11 corrected
Array 12 corrected
Array 13 corrected
Array 14 corrected
Array 15 corrected
Array 16 corrected
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 21 ]
> 
> proc.time()
   user  system elapsed 
 47.584   1.566  64.906