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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:decoupleR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings decoupleR_2.13.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/decoupleR.Rcheck’
* using R Under development (unstable) (2025-03-02 r87868)
* using platform: aarch64-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 Ventura 13.7.1
* 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 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 dependencies in R code ... NOTE
[2025-03-10 19:35:35] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-10 19:35:35] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-10 19:35:35] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-10 19:35:35] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-03-10 19:35:35] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-03-10
[2025-03-10 19:35:35] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-03-10 19:04:43 UTC; unix
[2025-03-10 19:35:35] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.11
[2025-03-10 19:35:35] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-03-10 19:35:35] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-03-02 r87868); os=macOS Ventura 13.7.1; system=aarch64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-03-10; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.4.552 @ /usr/local/bin/quarto]
[2025-03-10 19:35:35] [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=10.44 2024-06-07; ICU=70.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib; lapack_version=3.12.0]
[2025-03-10 19:35:35] [INFO] [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); annotate 1.85.0(2025-03-10); AnnotationDbi 1.69.0(2025-03-10); AUCell 1.29.0(2025-03-10); backports 1.5.0(2024-05-23); beachmat 2.23.6(2025-03-10); Biobase 2.67.0(2025-03-10); BiocGenerics 0.53.6(2025-03-10); BiocParallel 1.41.2(2025-03-10); BiocSingular 1.23.0(2025-03-10); Biostrings 2.75.4(2025-03-10); 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 2.3.2(2024-07-29); chromote 0.4.0(2025-01-25); cli 3.6.4(2025-02-13); codetools 0.2-20(2024-03-31); crayon 1.5.3(2024-06-20); curl 6.2.1(2025-02-19); data.table 1.17.0(2025-02-22); DBI 1.2.3(2024-06-02); decoupleR 2.13.0(2025-03-10); DelayedArray 0.33.6(2025-03-10); DelayedMatrixStats 1.29.1(2025-03-10); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.3(2025-01-10); fastmap 1.2.0(2024-05-15); fs 1.6.5(2024-10-30); generics 0.1.3(2022-07-05); GenomeInfoDb 1.43.4(2025-03-10); GenomeInfoDbData 1.2.13(2025-03-03); GenomicRanges 1.59.1(2025-03-10); glue 1.8.0(2024-09-30); graph 1.85.2(2025-03-10); GSEABase 1.69.1(2025-03-10); GSVA 2.1.7(2025-03-10); h5mread 0.99.4(2025-03-10); HDF5Array 1.35.15(2025-03-10); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.1.1(2025-03-08); igraph 2.1.4(2025-01-23); IRanges 2.41.3(2025-03-10); irlba 2.3.5.1(2022-10-03); jsonlite 1.9.1(2025-03-03); KEGGREST 1.47.0(2025-03-10); knitr 1.49(2024-11-08); later 1.4.1(2024-11-27); lattice 0.22-6(2024-03-20); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magick 2.8.5(2024-09-20); magrittr 2.0.3(2022-03-30); Matrix 1.7-2(2025-01-23); MatrixGenerics 1.19.1(2025-03-10); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); OmnipathR 3.15.11(2025-03-10); parallelly 1.42.0(2025-01-30); pillar 1.10.1(2025-01-07); 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 1.3.2(2024-11-28); ps 1.9.0(2025-02-18); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.0(2024-11-01); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.0.14(2025-01-12); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rhdf5 2.51.2(2025-03-10); rhdf5filters 1.19.2(2025-03-10); Rhdf5lib 1.29.1(2025-03-10); rjson 0.2.23(2024-09-16); rlang 1.1.5(2025-01-17); rmarkdown 2.29(2024-11-04); RSQLite 2.3.9(2024-12-03); rsvd 1.0.5(2021-04-16); rvest 1.0.4(2024-02-12); S4Arrays 1.7.3(2025-03-10); S4Vectors 0.45.4(2025-03-10); ScaledMatrix 1.15.0(2025-03-10); sessioninfo 1.2.3(2025-02-05); SingleCellExperiment 1.29.2(2025-03-10); SparseArray 1.7.6(2025-03-10); sparseMatrixStats 1.19.0(2025-03-10); SpatialExperiment 1.17.0(2025-03-10); stringi 1.8.4(2024-05-06); stringr 1.5.1(2023-11-14); SummarizedExperiment 1.37.0(2025-03-10); tibble 3.2.1(2023-03-20); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.4.0(2023-05-12); UCSC.utils 1.3.1(2025-03-10); vctrs 0.6.5(2023-12-01); websocket 1.4.2(2024-07-22); withr 3.0.2(2024-10-28); xfun 0.51(2025-02-19); XML 3.99-0.18(2025-01-01); xml2 1.3.7(2025-02-28); xtable 1.8-4(2019-04-21); XVector 0.47.2(2025-03-10); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01)
[2025-03-10 19:35:35] [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: aarch64-apple-darwin23.6.0; 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
[2025-03-10 19:35:35] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-03-10 19:35:35] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-10 19:35:35] [TRACE] [OmnipathR] Contains 8 files.
[2025-03-10 19:35:35] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-03-10 19:35:35] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-10 19:35:35] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-10 19:35:35] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-10 19:35:35] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`.
[2025-03-10 19:35:35] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-10 19:35:35] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-10 19:35:35] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-10 19:35:35] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-10 19:35:36] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-10 19:35:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-10 19:35:36] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-10 19:35:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-10 19:35:36] [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 10.011 0.678 13.513
get_dorothea 7.823 0.678 22.559
run_aucell 4.034 2.084 17.521
get_collectri 2.999 0.338 9.687
get_progeny 2.733 0.217 11.327
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
[120] 0.112 | 0.112 [120]
[121] 0.991 - 1.000 [121]
[122] 0.991 - 1.000 [122]
[123] 0.123 - 0.126 [123]
[124] 0.123 - 0.126 [124]
[125] 0.156 | 0.156 [125]
[126] 0.156 | 0.156 [126]
[127] 0.592 | 0.592 [127]
`actual$p_value[132:139]`: 0.125 0.592 0.592 0.175 0.175 0.198 0.198 0.592
`expected$p_value[132:139]`: 0.125 0.592 0.592 0.184 0.184 0.198 0.198 0.592
[ FAIL 1 | WARN 9 | SKIP 0 | PASS 34 ]
Error: Test failures
Execution halted
* 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 ERROR, 1 WARNING, 1 NOTE
See
‘/Users/biocbuild/bbs-3.21-bioc/meat/decoupleR.Rcheck/00check.log’
for details.