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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:netZooR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings netZooR_1.13.8.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/netZooR.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘netZooR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘netZooR’ version ‘1.13.8’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 38 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 ‘netZooR’ can be installed ... OK
* checking installed package size ... INFO
  installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data      1.7Mb
    extdata   2.8Mb
* 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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... WARNING
'::' or ':::' import not declared from: ‘cmdstanr’
* 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 ... WARNING
Missing link(s) in Rd file 'normalizeTissueAware.Rd':
  ‘limma::qsmooth’ ‘limma::normalizeQuantiles’

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

Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  bladder.Rd: ExpressionSet-class
  normalizeTissueAware.Rd: limma::qsmooth, limma::normalizeQuantiles
  skin.Rd: ExpressionSet-class
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 ... WARNING
Data with usage in Rd file 'bladder.Rd' but not in code:
  ‘bladder’

Data with usage in Rd file 'skin.Rd' but not in code:
  ‘skin’

* 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 data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘netZooR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: annotateFromBiomart
> ### Title: Annotate your Expression Set with biomaRt
> ### Aliases: annotateFromBiomart
> 
> ### ** Examples
> 
> u <- 'https://netzoo.s3.us-east-2.amazonaws.com/netZooR/unittest_datasets/'
> bladder <- paste0(u, 'yarn/bladder.rdata')
> skin <- paste0(u, 'yarn/skin.rdata')
> download.file(bladder, destfile='data/bladder.rdata')
Warning in download.file(bladder, destfile = "data/bladder.rdata") :
  URL https://netzoo.s3.us-east-2.amazonaws.com/netZooR/unittest_datasets/yarn/bladder.rdata: cannot open destfile 'data/bladder.rdata', reason 'No such file or directory'
Warning in download.file(bladder, destfile = "data/bladder.rdata") :
  download had nonzero exit status
> download.file(skin, destfile='data/skin.rdata')
Warning in download.file(skin, destfile = "data/skin.rdata") :
  URL https://netzoo.s3.us-east-2.amazonaws.com/netZooR/unittest_datasets/yarn/skin.rdata: cannot open destfile 'data/skin.rdata', reason 'No such file or directory'
Warning in download.file(skin, destfile = "data/skin.rdata") :
  download had nonzero exit status
> data(skin)
Warning in data(skin) : data set ‘skin’ not found
> # subsetting and changing column name just for a silly example
> skin <- skin[1:10,]
Error in skin[1:10, ] : incorrect number of dimensions
Execution halted
* 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:
  [ FAIL 1 | WARN 1 | SKIP 1 | PASS 103 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • empty test (1): 'test-lioness.R:45:1'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-monster.R:6:3'): MONSTER function works ────────────────────────
  Error in `load("./testDatasetMonster.RData")`: bad restore file magic number (file may be corrupted) -- no data loaded
  Backtrace:
      ▆
   1. └─base::load("./testDatasetMonster.RData") at test-monster.R:6:3
  
  [ FAIL 1 | WARN 1 | SKIP 1 | PASS 103 ]
  Error: Test failures
  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: 2 ERRORs, 3 WARNINGs
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/netZooR.Rcheck/00check.log’
for details.