############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:gINTomics.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings gINTomics_1.5.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.22-bioc/meat/gINTomics.Rcheck' * using R version 4.5.1 (2025-06-13 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'gINTomics/DESCRIPTION' ... OK * this is package 'gINTomics' version '1.5.0' * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 42 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 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 ... NOTE ERROR: Unknown command "TMPDIR=F:/biocbuild/bbs-3.22-bioc/tmpdir/RtmpWGZ6nQ/file1bdfc1118108f". Did you mean command "update"? * checking S3 generic/method consistency ... WARNING ERROR: Unknown command "TMPDIR=F:/biocbuild/bbs-3.22-bioc/tmpdir/RtmpGwQ4CX/file1b8fc76831242". Did you mean command "update"? See section 'Generic functions and methods' in the 'Writing R Extensions' manual. * checking replacement functions ... WARNING ERROR: Unknown command "TMPDIR=F:/biocbuild/bbs-3.22-bioc/tmpdir/RtmpgHAAuG/filef4dc61071df0". Did you mean command "update"? The argument of a replacement function which corresponds to the right hand side must be named 'value'. * checking foreign function calls ... NOTE ERROR: Unknown command "TMPDIR=F:/biocbuild/bbs-3.22-bioc/tmpdir/RtmpI1BD14/file2164c3131228d". Did you mean command "update"? See chapter 'System and foreign language interfaces' in the 'Writing R Extensions' manual. * checking R code for possible problems ... NOTE [2025-07-24 02:46:40] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2025-07-24 02:46:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-24 02:46:40] [INFO] [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2025-07-24 02:46:40] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-07-24 02:46:40] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-07-23 [2025-07-24 02:46:40] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-07-23 19:54:48 UTC; windows [2025-07-24 02:46:40] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.4 [2025-07-24 02:46:40] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22 ERROR: Unknown command "TMPDIR=F:/biocbuild/bbs-3.22-bioc/tmpdir/RtmpsTSW1B/file10398401e167a". Did you mean command "update"? [2025-07-24 02:46:42] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13 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=2025-07-24; pandoc=2.7.3 @ C:/PROGRA~1/Pandoc/ (via rmarkdown); quarto=NA @ C:\PROGRA~1\Quarto\bin\quarto.exe] [2025-07-24 02:46:42] [INFO] [OmnipathR] External libraries: [cairo=1.18.4; cairoFT=; pango=; png=1.6.48; jpeg=9.6; tiff=LIBTIFF, Version 4.7.0; tcl=8.6.16; curl=8.13.0; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.8.1; deflate=1.24; PCRE=10.45 2025-02-05; ICU=77.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=win_iconv; readline=; BLAS=; lapack=; lapack_version=3.12.1] [2025-07-24 02:46:43] [INFO] [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.71.0(2025-07-23); backports 1.5.0(2024-05-23); Biobase 2.69.0(2025-07-23); BiocBaseUtils 1.11.2(2025-07-23); BiocGenerics 0.55.0(2025-07-23); BiocIO 1.19.0(2025-07-23); BiocParallel 1.43.4(2025-07-23); Biostrings 2.77.2(2025-07-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); bitops 1.0-9(2024-10-03); 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 0.5.1(2025-04-24); circlize 0.4.16(2024-02-20); cli 3.6.5(2025-04-23); clisymbols 1.2.0(2017-05-21); clue 0.3-66(2024-11-13); cluster 2.1.8.1(2025-03-12); codetools 0.2-20(2024-03-31); colorspace 2.1-1(2024-07-26); ComplexHeatmap 2.25.2(2025-07-23); crayon 1.5.3(2024-06-20); curl 6.4.0(2025-06-22); DBI 1.2.3(2024-06-02); DelayedArray 0.35.2(2025-07-23); dichromat 2.0-0.1(2022-05-02); digest 0.6.37(2024-08-19); doParallel 1.0.17(2022-02-07); dplyr 1.1.4(2023-11-17); DT 0.33(2024-04-04); evaluate 1.0.4(2025-06-18); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fontawesome 0.5.3(2024-11-16); foreach 1.5.2(2022-02-02); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); GenomicAlignments 1.45.1(2025-07-23); GenomicFeatures 1.61.5(2025-07-23); GenomicRanges 1.61.1(2025-07-23); GetoptLong 1.0.5(2020-12-15); ggplot2 3.5.2(2025-04-09); gINTomics 1.5.0(2025-07-23); GlobalOptions 0.1.2(2020-06-10); glue 1.8.0(2024-09-30); gtable 0.3.6(2024-10-25); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); htmlwidgets 1.6.4(2023-12-06); httpuv 1.6.16(2025-04-16); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.1.4(2025-01-23); InteractiveComplexHeatmap 1.17.0(2025-07-23); IRanges 2.43.0(2025-07-23); iterators 1.0.14(2022-02-05); jsonlite 2.0.0(2025-03-27); kableExtra 1.4.0(2024-01-24); KEGGREST 1.49.1(2025-07-23); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lattice 0.22-7(2025-04-02); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); MASS 7.3-65(2025-02-28); Matrix 1.7-3(2025-03-11); MatrixGenerics 1.21.0(2025-07-23); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); MethylMix 2.39.0(2025-07-23); mime 0.13(2025-03-17); MultiAssayExperiment 1.35.6(2025-07-23); OmnipathR 3.17.4(2025-07-23); pillar 1.11.0(2025-07-04); 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 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); 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); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.0(2025-07-02); RCurl 1.98-1.17(2025-03-22); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); restfulr 0.0.16(2025-06-27); rjson 0.2.23(2024-09-16); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); Rsamtools 2.25.1(2025-07-23); RSQLite 2.4.2(2025-07-18); rstudioapi 0.17.1(2024-10-22); rtracklayer 1.69.1(2025-07-23); rvest 1.0.4(2024-02-12); S4Arrays 1.9.1(2025-07-23); S4Vectors 0.47.0(2025-07-23); scales 1.4.0(2025-04-24); Seqinfo 0.99.2(2025-07-23); sessioninfo 1.2.3(2025-02-05); shape 1.4.6.1(2024-02-23); shiny 1.11.1(2025-07-03); SparseArray 1.9.1(2025-07-23); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); SummarizedExperiment 1.39.1(2025-07-23); svglite 2.2.1(2025-05-12); systemfonts 1.2.3(2025-04-30); textshaping 1.0.1(2025-05-01); 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); viridisLite 0.4.2(2023-05-02); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); xtable 1.8-4(2019-04-21); XVector 0.49.0(2025-07-23); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13) [2025-07-24 02:46:43] [INFO] [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: (OpenSSL/3.5.0) 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, ws, wss; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2025-07-24 02:46:43] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-07-24 02:46:43] [TRACE] [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2025-07-24 02:46:43] [TRACE] [OmnipathR] Contains 1 files. [2025-07-24 02:46:43] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-07-24 02:46:43] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2025-07-24 02:46:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-24 02:46:43] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2025-07-24 02:46:43] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-07-24 02:46:43] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-07-24 02:46:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-24 02:46:43] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-07-24 02:46:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-24 02:46:43] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-07-24 02:46:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-24 02:46:43] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-07-24 02:46:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-24 02:46:43] [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' .find_deg: no visible global function definition for 'combn' .find_deg: no visible global function definition for 'contrasts.fit' .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' .reactive_cnv_test_plots: no visible binding for global variable 'x' .reactive_cnv_test_plots: no visible binding for global variable 'y' .reactive_transcExpr_plots: no visible binding for global variable 'x' .reactive_transcExpr_plots: no visible binding for global variable 'y' .run_reactive_tf_enrich: no visible binding for '<<-' assignment to 'bg_process' .server_enrich_bg : : no visible binding for global variable 'bg_process' .server_enrich_bgTF: no visible binding for '<<-' assignment to 'bg_process' .server_enrich_bgTF : : no visible binding for global variable 'bg_process' .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 bg_process chr_cov cnv cnv_met coef combn contrasts.fit cov met mirna_cnv omics pval significance x y Consider adding importFrom("stats", "coef", "cov") importFrom("utils", "combn") 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 ... WARNING ERROR: Unknown command "TMPDIR=F:/biocbuild/bbs-3.22-bioc/tmpdir/Rtmp4YDl7M/file1d8606abc33ca". Did you mean command "update"? All user-level objects in a package should have documentation entries. See chapter 'Writing R documentation files' in the 'Writing R Extensions' manual. * checking for code/documentation mismatches ... WARNING ERROR: Unknown command "TMPDIR=F:/biocbuild/bbs-3.22-bioc/tmpdir/RtmpgXz4Sv/file229e81d427dc0". Did you mean command "preview"? ERROR: Unknown command "TMPDIR=F:/biocbuild/bbs-3.22-bioc/tmpdir/RtmpEvmyrY/file13074733d74ea". Did you mean command "preview"? ERROR: Unknown command "TMPDIR=F:/biocbuild/bbs-3.22-bioc/tmpdir/RtmpkjtnZ0/file1dfcc72d93332". Did you mean command "update"? * checking Rd \usage sections ... NOTE ERROR: Unknown command "TMPDIR=F:/biocbuild/bbs-3.22-bioc/tmpdir/Rtmp024O4B/file1158845ecf81". Did you mean command "update"? The \usage entries for S3 methods should use the \method markup and not their full name. See chapter 'Writing R documentation files' in the 'Writing R Extensions' manual. * 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 48.20 3.17 60.17 extract_model_res 14.32 0.62 14.98 plot_ridge 9.95 0.85 10.83 run_multiomics 6.50 0.22 7.20 * 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: 4 WARNINGs, 5 NOTEs See 'F:/biocbuild/bbs-3.22-bioc/meat/gINTomics.Rcheck/00check.log' for details.