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### Running command:
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###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:gINTomics.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings gINTomics_1.3.0.tar.gz
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* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/gINTomics.Rcheck'
* using R Under development (unstable) (2024-10-26 r87273 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'gINTomics/DESCRIPTION' ... OK
* this is package 'gINTomics' version '1.3.0'
* 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 whether package 'gINTomics' 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 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 ... NOTE
[2024-12-12 01:28:16] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-12 01:28:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-12 01:28:16] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-12-12 01:28:16] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-12-12 01:28:16] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-12-12 01:28:16] [TRACE]   [OmnipathR] Contains 1 files.
[2024-12-12 01:28:16] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-12-12 01:28:16] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-12 01:28:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-12 01:28:16] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-12-12 01:28:16] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-12-12 01:28:16] [TRACE]   [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-12-12 01:28:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-12 01:28:16] [TRACE]   [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-12-12 01:28:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-12 01:28:16] [TRACE]   [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-12-12 01:28:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-12 01:28:16] [TRACE]   [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-12-12 01:28:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-12 01:28:16] [TRACE]   [OmnipathR] Cache locked: FALSE
.build_histo: no visible binding for global variable 'chr_cov'
.build_histo: no visible binding for global variable 'significance'
.build_ridge: no visible binding for global variable 'coef'
.build_ridge: no visible binding for global variable 'significance'
.circos_preprocess: no visible binding for global variable 'cnv_met'
.prepare_cnv_heatmap: no visible binding for global variable 'cnv'
.prepare_gen_heatmap: no visible binding for global variable 'met'
.prepare_gen_heatmap: no visible binding for global variable 'cnv'
.prepare_met_heatmap: no visible binding for global variable 'met'
.prepare_mirna_heatmap: no visible binding for global variable
  'mirna_cnv'
.prepare_network: no visible binding for global variable 'omics'
.prepare_reactive_histo_tf: no visible binding for global variable
  'Freq'
.prepare_reactive_venn: no visible binding for global variable
  'cnv_met'
.prepare_reactive_venn: no visible binding for global variable 'pval'
.shiny_preprocess: no visible binding for global variable 'cov'
plot_tf_distribution: no visible binding for global variable 'Freq'
Undefined global functions or variables:
  Freq chr_cov cnv cnv_met coef cov met mirna_cnv omics pval
  significance
Consider adding
  importFrom("stats", "coef", "cov")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  mmultiassay_ov.Rd: MultiAssayExperiment-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 ... 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 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
plot_volcano      14.22   0.90   26.20
extract_model_res 11.31   0.71   12.05
plot_ridge         8.89   0.58    9.46
run_multiomics     4.69   0.08    5.17
* 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: 2 NOTEs
See
  'E:/biocbuild/bbs-3.21-bioc/meat/gINTomics.Rcheck/00check.log'
for details.