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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:crossmeta.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings crossmeta_1.34.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/crossmeta.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘crossmeta/DESCRIPTION’ ... OK
* this is package ‘crossmeta’ version ‘1.34.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 30 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... WARNING
Namespaces in Imports field not imported from:
  ‘RCurl’ ‘XML’
  All declared Imports should be used.
Missing or unexported object: ‘GEOquery::gunzip’
* 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 ... NOTE
Non-topic package-anchored link(s) in Rd file 'get_top_table.Rd':
  ‘[limma]{toptable}’

See section 'Cross-references' in the 'Writing R Extensions' manual.

Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  fix_illum_headers.Rd: getGEO
  load_agil_plat.Rd: getGEO
  run_lmfit.Rd: duplicateCorrelation
  to_eset.Rd: getGEO
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 ... ERROR
Running examples in ‘crossmeta-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: get_raw
> ### Title: Download and unpack microarray supplementary files from GEO.
> ### Aliases: get_raw
> 
> ### ** Examples
> 
> get_raw("GSE41845")
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE41nnn/GSE41845/suppl//GSE41845_RAW.tar?tool=geoquery'
Content type 'application/x-tar' length 71680 bytes (70 KB)
==================================================
downloaded 70 KB

trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE41nnn/GSE41845/suppl//GSE41845_non-normalized_data.txt.gz?tool=geoquery'
Content type 'application/x-gzip' length 19149 bytes (18 KB)
==================================================
downloaded 18 KB

Error: 'gunzip' is not an exported object from 'namespace:GEOquery'
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
diff_expr 21.755  0.455  22.327
es_meta   17.400  0.451  17.873
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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, 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/crossmeta.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL crossmeta
###
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* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘crossmeta’ ...
** this is package ‘crossmeta’ version ‘1.34.0’
** 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
Warning in fun(libname, pkgname) :
  Package 'crossmeta' is deprecated and will be removed from Bioconductor
  version 3.22
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'crossmeta' is deprecated and will be removed from Bioconductor
  version 3.22
** testing if installed package keeps a record of temporary installation path
* DONE (crossmeta)

R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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)
Warning message:
In fun(libname, pkgname) :
  Package 'crossmeta' is deprecated and will be removed from Bioconductor
  version 3.22
> 
> test_check("crossmeta")
GSE1_disease-healthy (# p < 0.05): 0 
GSE1_disease-healthy (# p < 0.05): 1 
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 
 30.468   0.667  31.177