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### Running command:
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###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:omicsViewer.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings omicsViewer_1.14.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/omicsViewer.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘omicsViewer/DESCRIPTION’ ... OK
* this is package ‘omicsViewer’ version ‘1.14.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 33 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 ... NOTE
Found the following hidden files and directories:
  .claude
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘omicsViewer’ can be installed ... OK
* checking installed package size ... INFO
  installed size is  5.5Mb
  sub-directories of 1Mb or more:
    extdata   4.9Mb
* 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 dependencies in R code ... OK
* 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 'app_module.Rd':
  ‘L1_data_space_module’ ‘L1_result_space_module’

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

Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  app_module.Rd: L1_data_space_module, L1_result_space_module
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 files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test_auxi_sparse_converter.R’
 ERROR
Running the tests in ‘tests/test_auxi_sparse_converter.R’ failed.
Last 13 lines of output:
  > csc2 <- omicsViewer:::list2csc(scc, dimnames = list(rownames(m)))
  Error in (function (i, j, p, x, dims, dimnames, symmetric = FALSE, triangular = FALSE,  : 
    'i' and 'j' must not contain NA
  Calls: <Anonymous> -> do.call -> <Anonymous>
  Bail out! Looks like 1 tests ran, but script ended prematurely
  # Error in (function (i, j, p, x, dims, dimnames, symmetric = FALSE, triangular = FALSE,  : 
  #   'i' and 'j' must not contain NA
  # Calls: <Anonymous> -> do.call -> <Anonymous>
  # Traceback:
  #  1: omicsViewer:::list2csc(scc, dimnames = list(rownames(m)))
  #  2: do.call(sparseMatrix, args)
  #  3: (function (i, j, p, x, dims, dimnames, symmetric = FALSE, triangular = FALSE, 
  #       index1 = TRUE, repr = c("C", "R", "T"), giveCsparse, check = TRUE, 
  #       use.last.ij = FALSE) 
  #  4: stop("'i' and 'j' must not contain NA")
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/omicsViewer.Rcheck/00check.log’
for details.