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### Running command:
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###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:gINTomics.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings gINTomics_1.3.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/gINTomics.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* 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 ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 INFO
Imports includes 40 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 ‘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 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 ... NOTE
[2024-12-12 00:33:44] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-12 00:33:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-12 00:33:44] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-12-12 00:33:44] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-12-12 00:33:44] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-12-12 00:33:44] [TRACE]   [OmnipathR] Contains 1 files.
[2024-12-12 00:33:44] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-12-12 00:33:44] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-12 00:33:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-12 00:33:44] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-12-12 00:33:44] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2024-12-12 00:33:45] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-12-12 00:33:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-12 00:33:45] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-12-12 00:33:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-12 00:33:45] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-12-12 00:33:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-12 00:33:45] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-12-12 00:33:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-12 00:33:45] [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      10.851  1.375  17.998
extract_model_res  8.939  0.688   9.632
plot_ridge         6.323  0.401   6.725
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/gINTomics.Rcheck/00check.log’
for details.