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### Running command:
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###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:crossmeta.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --timings crossmeta_1.27.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/crossmeta.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
* checking for file ‘crossmeta/DESCRIPTION’ ... OK
* this is package ‘crossmeta’ 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 ... 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 loading without being on the library search path ... 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
symbol_annot 21.422  2.475  28.357
diff_expr    22.330  1.272  24.047
es_meta      14.141  0.469  14.702
setup_prev    6.013  1.385   8.270
get_raw       0.595  0.065   9.218
* 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:
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-two-channel.R:60:3'): crossmeta produces similar results to limma ──
  Error in `limma::intraspotCorrelation(MA, mod)`: statmod package required but is not installed
  Backtrace:
      ▆
   1. └─crossmeta::diff_expr(...) at test-two-channel.R:60:2
   2.   └─crossmeta::run_limma(eset, annot, svobj, numsv)
   3.     └─crossmeta:::fit_lm(...)
   4.       └─crossmeta:::run_lmfit(eset, mod, rna_seq)
   5.         └─limma::intraspotCorrelation(MA, mod)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 19 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘crossmeta-vignette.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘crossmeta-vignette.Rmd’ using rmarkdown
add_sources             package:crossmeta              R Documentation

_A_d_d _s_a_m_p_l_e _s_o_u_r_c_e _i_n_f_o_r_m_a_t_i_o_n _f_o_r _m_e_t_a-_a_n_a_l_y_s_i_s.

_D_e_s_c_r_i_p_t_i_o_n:

     User selects a tissue source for each contrast and indicates any
     sources that should be paired. This step is required if you would
     like to perform source-specific effect-size/pathway meta-analyses.

_U_s_a_g_e:

     add_sources(diff_exprs, data_dir = getwd(), postfix = NULL)
     
_A_r_g_u_m_e_n_t_s:

diff_exprs: Previous result of 'diff_expr', which can be reloaded using
          'load_diff'.

data_dir: String specifying directory of GSE folders.

 postfix: Optional string to append to saved results. Useful if need to
          run multiple meta-analyses on the same series but with
          different contrasts.

_D_e_t_a_i_l_s:

     The *Sources* tab is used to add a source for each contrast. To do
     so: click the relevant contrast rows, search for a source in the
     _Sample source_ dropdown box, and then click the _Add_ button.

     The *Pairs* tab is used to indicate sources that should be paired
     (treated as the same source for subsequent effect-size and pathway
     meta-analyses). To do so: select at least two sources from the
     _Paired sources_ dropdown box, and then click the _Add_ button.

     For each GSE, analysis results with added sources/pairs are saved
     in the corresponding GSE folder (in 'data_dir') that was created
     by 'get_raw'.

_V_a_l_u_e:

     Same as 'diff_expr' with added slots for each GSE in 'diff_exprs':

 sources: Named vector specifying selected sample source for each
          contrast.  Vector names identify the contrast.

   pairs: List of character vectors indicating tissue sources that
          should be treated as the same source for subsequent
          effect-size and pathway meta-analyses.

_E_x_a_m_p_l_e_s:

     library(lydata)
     
     # load result of previous call to diff_expr:
     data_dir  <- system.file("extdata", package = "lydata")
     gse_names <- c("GSE9601", "GSE34817")
     anals     <- load_diff(gse_names, data_dir)
     
     # run shiny GUI to add tissue sources
     # anals <- add_sources(anals, data_dir)
     


* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/crossmeta.Rcheck/00check.log’
for details.

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### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL crossmeta
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* installing to library ‘/home/biocbuild/R/R-4.3.1/site-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: 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.

> 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
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 19 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-two-channel.R:60:3'): crossmeta produces similar results to limma ──
Error in `limma::intraspotCorrelation(MA, mod)`: statmod package required but is not installed
Backtrace:
    ▆
 1. └─crossmeta::diff_expr(...) at test-two-channel.R:60:2
 2.   └─crossmeta::run_limma(eset, annot, svobj, numsv)
 3.     └─crossmeta:::fit_lm(...)
 4.       └─crossmeta:::run_lmfit(eset, mod, rna_seq)
 5.         └─limma::intraspotCorrelation(MA, mod)

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 19 ]
Error: Test failures
Execution halted