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### Running command:
###
###   /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.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL omicsViewer
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘omicsViewer’ ...
** this is package ‘omicsViewer’ version ‘1.14.0’
** using staged installation
** R
** 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 (omicsViewer)

R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-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(omicsViewer)
> library(Matrix)
> library(unittest, quietly = TRUE)
> 
> # source("R/auxi_sparse_converter.R")
> 
> m <- matrix(0, 10, 5, dimnames = list(paste0("R", 1:10), paste0("C", 1:5)))
> for (i in 2:ncol(m)) {
+    m[i*2, i] <- 1
+ }
> 
> csc <- as(m, "dgCMatrix")
> ok(ut_cmp_equal(colSums(csc), colSums(m)), "as sparse")
ok - as sparse
> 
> scc <- omicsViewer:::csc2list(csc)
> 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")