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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:gINTomics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings gINTomics_1.3.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/gINTomics.Rcheck’
* using R Under development (unstable) (2025-01-22 r87618)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* 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 ... 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 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
[2025-02-04 20:53:52] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-04 20:53:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-04 20:53:52] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-02-04 20:53:52] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-02-04 20:53:52] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-02-04
[2025-02-04 20:53:52] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-02-04 20:26:57 UTC; unix
[2025-02-04 20:53:52] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.6
[2025-02-04 20:53:52] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-02-04 20:53:53] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2025-01-22 r87618); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-02-04; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown)]
[2025-02-04 20:53:53] [INFO]    [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.42 2022-12-11; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.0]
[2025-02-04 20:53:53] [INFO]    [OmnipathR] CURL: version: 8.11.1; headers: 8.11.1; ssl_version: OpenSSL/3.3.2 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-02-04 20:53:53] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-02-04 20:53:53] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-02-04 20:53:53] [TRACE]   [OmnipathR] Contains 1 files.
[2025-02-04 20:53:53] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-02-04 20:53:53] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-04 20:53:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-04 20:53:53] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-02-04 20:53:53] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-02-04 20:53:53] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-02-04 20:53:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-04 20:53:53] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-02-04 20:53:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-04 20:53:53] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-02-04 20:53:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-04 20:53:53] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-02-04 20:53:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-04 20:53:53] [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       22.338  1.980  36.516
extract_model_res  10.936  1.141  12.147
plot_ridge         10.057  1.215  13.551
run_multiomics      6.028  0.796   8.947
run_tf_integration  3.505  0.294   5.088
* 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
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/gINTomics.Rcheck/00check.log’
for details.