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### Running command:
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###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:decoupleR.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings decoupleR_2.16.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/decoupleR.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 ‘decoupleR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘decoupleR’ version ‘2.16.0’
* 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 for sufficient/correct file permissions ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
[2025-11-18 02:52:05] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-18 02:52:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-18 02:52:05] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-11-18 02:52:05] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-11-18 02:52:05] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-11-17
[2025-11-18 02:52:05] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2025-11-17 22:04:20 UTC; unix
[2025-11-18 02:52:05] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.18.2
[2025-11-18 02:52:05] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-11-18 02:52:06] [INFO]    [OmnipathR] Session info: [version=R version 4.5.2 (2025-10-31); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-11-18; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2025-11-18 02:52:06] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-11-18 02:52:06] [INFO]    [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); annotate 1.88.0(2025-11-17); AnnotationDbi 1.72.0(2025-11-17); AUCell 1.32.0(2025-11-17); backports 1.5.0(2024-05-23); beachmat 2.26.0(2025-11-17); Biobase 2.70.0(2025-11-17); BiocGenerics 0.56.0(2025-11-17); BiocParallel 1.44.0(2025-11-17); BiocSingular 1.26.1(2025-11-17); Biostrings 2.78.0(2025-11-17); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); codetools 0.2-20(2024-03-31); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); data.table 1.17.8(2025-07-10); DBI 1.2.3(2024-06-02); decoupleR 2.16.0(2025-11-17); DelayedArray 0.36.0(2025-11-17); DelayedMatrixStats 1.32.0(2025-11-17); digest 0.6.38(2025-11-12); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); GenomicRanges 1.62.0(2025-11-17); glue 1.8.0(2024-09-30); graph 1.88.0(2025-11-17); GSEABase 1.72.0(2025-11-17); GSVA 2.4.1(2025-11-17); h5mread 1.2.0(2025-11-17); HDF5Array 1.38.0(2025-11-17); hms 1.1.4(2025-10-17); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.2.1(2025-10-27); IRanges 2.44.0(2025-11-17); irlba 2.3.5.1(2022-10-03); jsonlite 2.0.0(2025-03-27); KEGGREST 1.50.0(2025-11-17); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lattice 0.22-7(2025-04-02); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magick 2.9.0(2025-09-08); magrittr 2.0.4(2025-09-12); Matrix 1.7-4(2025-08-28); MatrixGenerics 1.22.0(2025-11-17); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); OmnipathR 3.18.2(2025-11-17); otel 0.2.0(2025-08-29); parallelly 1.45.1(2025-07-24); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); png 0.1-8(2022-11-29); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.0(2025-11-04); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); rhdf5 2.54.0(2025-11-17); rhdf5filters 1.22.0(2025-11-17); Rhdf5lib 1.32.0(2025-11-17); rjson 0.2.23(2024-09-16); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.4(2025-11-10); rsvd 1.0.5(2021-04-16); rvest 1.0.5(2025-08-29); S4Arrays 1.10.0(2025-11-17); S4Vectors 0.48.0(2025-11-17); ScaledMatrix 1.18.0(2025-11-17); Seqinfo 1.0.0(2025-11-17); sessioninfo 1.2.3(2025-02-05); SingleCellExperiment 1.32.0(2025-11-17); SparseArray 1.10.2(2025-11-17); sparseMatrixStats 1.22.0(2025-11-17); SpatialExperiment 1.20.0(2025-11-17); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); SummarizedExperiment 1.40.0(2025-11-17); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.5.0(2025-11-17); xtable 1.8-4(2019-04-21); XVector 0.50.0(2025-11-17); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-11-18 02:52:06] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: GnuTLS/3.8.3; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-11-18 02:52:06] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-11-18 02:52:06] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-11-18 02:52:06] [TRACE]   [OmnipathR] Contains 9 files.
[2025-11-18 02:52:06] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-11-18 02:52:06] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-18 02:52:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-18 02:52:06] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-11-18 02:52:06] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-11-18 02:52:06] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-11-18 02:52:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-18 02:52:06] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-11-18 02:52:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-18 02:52:06] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-11-18 02:52:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-18 02:52:06] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-11-18 02:52:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-18 02:52:06] [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’

Non-topic package-anchored link(s) in Rd file 'pipe.Rd':
  ‘[magrittr:pipe]{%>%}’

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 ... ERROR
Running examples in ‘decoupleR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: get_resource
> ### Title: Wrapper to access resources inside Omnipath. This wrapper allows
> ###   to easily query different prior knowledge resources. To check
> ###   available resources run 'decoupleR::show_resources()'. For more
> ###   information visit the official website for Omnipath.
> ### Aliases: get_resource
> 
> ### ** Examples
> 
> df <- decoupleR::get_resource('SIGNOR')
Warning in OmnipathR::get_annotation_resources() :
  'OmnipathR::get_annotation_resources' is deprecated.
Use 'annotation_resources' instead.
See help("Deprecated")
[2025-11-18 03:17:04] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
Warning in readLines(con = path, encoding = encoding) :
  incomplete final line found on 'https://omnipathdb.org/resources'
[2025-11-18 03:17:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
Warning in OmnipathR::import_omnipath_annotations(resources = name, ...,  :
  'OmnipathR::import_omnipath_annotations' is deprecated.
Use 'annotations' instead.
See help("Deprecated")
[2025-11-18 03:17:06] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-11-18 03:17:06] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SIGNOR,query_type=annotations]
[2025-11-18 03:17:06] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-11-18 03:17:06] [TRACE]   [OmnipathR] Orthology targets: 
[2025-11-18 03:17:06] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
Warning in file(con, "r") :
  URL 'https://omnipathdb.org/resources': status was 'SSL connect error'
[2025-11-18 03:17:13] [WARN]    [OmnipathR] Accessing `SIGNOR` as a static table: this is not the recommended way to access OmniPath data; it is only a backup plan for situations when our server or your computer is experiencing issues.
[2025-11-18 03:17:13] [ERROR]   [OmnipathR] [decoupleR] Failed to download annotation resource `SIGNOR` from OmniPath. For more information, see the OmnipathR log.
Error in value[[3L]](cond) : 
  [decoupleR] Failed to download annotation resource `SIGNOR` from OmniPath. For more information, see the OmnipathR log.
Calls: <Anonymous> ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
get_collectri 30.015  2.527 446.839
get_dorothea  23.948  2.137 699.570
get_progeny    3.403  0.738 326.830
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’