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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:decoupleR.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings decoupleR_2.13.0.tar.gz
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* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/decoupleR.Rcheck'
* using R Under development (unstable) (2025-01-21 r87610 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'decoupleR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'decoupleR' version '2.13.0'
* 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 'decoupleR' 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 ... NOTE
[2025-02-13 00:27:02] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-13 00:27:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-13 00:27:02] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-02-13 00:27:02] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-02-13 00:27:02] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-02-12
[2025-02-13 00:27:02] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-02-12 20:50:39 UTC; windows
[2025-02-13 00:27:02] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.8
[2025-02-13 00:27:02] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-02-13 00:27:04] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2025-01-21 r87610 ucrt); os=Windows Server 2022 x64 (build 20348); system=x86_64, mingw32; ui=RTerm; language=(EN); collate=C; ctype=English_United States.utf8; tz=America/New_York; date=2025-02-13; pandoc=2.7.3 @ C:/PROGRA~1/Pandoc/ (via rmarkdown); quarto=NA]
[2025-02-13 00:27:04] [INFO]    [OmnipathR] External libraries: [cairo=1.18.2; cairoFT=; pango=; png=1.6.44; jpeg=9.6; tiff=LIBTIFF, Version 4.7.0; tcl=8.6.13; curl=8.10.1; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.22; PCRE=10.44 2024-06-07; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=win_iconv; readline=; BLAS=; lapack=; lapack_version=3.12.0]
[2025-02-13 00:27:04] [INFO]    [OmnipathR] CURL: version: 8.10.1; headers: 8.10.1; ssl_version: (OpenSSL/3.4.0) Schannel; libz_version: 1.3; libssh_version: libssh2/1.11.0; libidn_version: NA; host: x86_64-w64-mingw32; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-02-13 00:27:04] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-02-13 00:27:04] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-02-13 00:27:04] [TRACE]   [OmnipathR] Contains 8 files.
[2025-02-13 00:27:04] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-02-13 00:27:04] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-13 00:27:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-13 00:27:04] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-02-13 00:27:04] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-02-13 00:27:04] [TRACE]   [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-02-13 00:27:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-13 00:27:04] [TRACE]   [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-02-13 00:27:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-13 00:27:04] [TRACE]   [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-02-13 00:27:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-13 00:27:04] [TRACE]   [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-02-13 00:27:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-13 00:27:04] [TRACE]   [OmnipathR] Cache locked: FALSE
* 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 'run_gsva.Rd':
  'GSVA::gsva' 'GeneSetCollection'

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

Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  run_gsva.Rd: GSVA::gsva, GeneSetCollection
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
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
run_fgsea     23.69   0.07   23.78
get_dorothea  22.82   0.53   23.68
get_collectri  8.60   0.64   12.57
run_aucell     8.55   0.47    9.03
get_progeny    6.32   0.38    8.03
* 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: 1 WARNING, 1 NOTE
See
  'E:/biocbuild/bbs-3.21-bioc/meat/decoupleR.Rcheck/00check.log'
for details.