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Merged
msraredon merged 1 commit into from
Jan 29, 2026
Merged

v1.2.2 #68

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4 changes: 2 additions & 2 deletions DESCRIPTION
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
Package: NICHES
Version: 1.2.1
Date: 2025-11-22
Version: 1.2.2
Date: 2029-01-29
Title: Niche Interactions and Communication Heterogeneity in Extracellular Signaling
Authors@R: c(person("Micha Sam", "Brickman Raredon", email = "michasam.raredon@yale.edu", role = c("aut", "cre")),person("Junchen", "Yang", email = "junchen.yang@yale.edu", role = c("aut")),person("Aaron", "Osgood-Zimmerman", email = "aeoz001@bucknell.edu", role = c("aut")))
Description: Cell-cell Interactions at Single-Cell Resolution
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2 changes: 1 addition & 1 deletion NAMESPACE
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Expand Up @@ -12,7 +12,7 @@ export(LoadFantom5)
export(LoadGroundTruth)
export(LoadOmniPath)
export(PrepNodeObject)
export(ReturnCelltypes)
export(ReturnCellTypes)
export(RunCellToCell)
export(RunCellToCellSpatial)
export(RunCellToNeighborhood)
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6 changes: 3 additions & 3 deletions man/ReturnCelltypes.Rd
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20 changes: 20 additions & 0 deletions omnipathr-log/omnipathr-20260129-1411.log
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[2026-01-29 14:11:47] [TRACE] [OmnipathR] Reading JSON from `/Users/msbr/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-01-29 14:11:47] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-01-29 14:11:47] [INFO] [OmnipathR] Initialized cache: `/Users/msbr/Library/Caches/OmnipathR`.
[2026-01-29 14:11:47] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-12-12 11:10:44 UTC; biocbuild
[2026-01-29 14:11:47] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-12-11
[2026-01-29 14:11:47] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2025-12-14 16:21:52 UTC; unix
[2026-01-29 14:11:47] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.3
[2026-01-29 14:11:47] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2026-01-29 14:11:50] [INFO] [OmnipathR] Session info: [version=R version 4.5.2 (2025-10-31); os=macOS Sonoma 14.6.1; system=aarch64, darwin20; ui=RStudio; language=(EN); collate=en_US.UTF-8; ctype=en_US.UTF-8; tz=America/New_York; date=2026-01-29; rstudio=2026.01.0+392 Apple Blossom (desktop); pandoc=3.8.2 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.8.25 @ /Applications/RStudio.app/Contents/Resources/app/quarto/bin/quarto]
[2026-01-29 14:11:56] [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=1.2.12; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=74.1; 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=/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2026-01-29 14:11:56] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.3.0(2026-01-14); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); desc 1.4.3(2023-12-10); devtools 2.4.6(2025-10-03); digest 0.6.39(2025-11-19); dplyr 1.1.4(2023-11-17); ellipsis 0.3.2(2021-04-29); 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); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.7(2023-08-15); httr2 1.2.2(2025-12-08); igraph 2.2.1(2025-10-27); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.5(2026-01-08); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); NICHES 1.2.1(2026-01-29); OmnipathR 3.18.3(2025-12-11); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgbuild 1.4.8(2025-05-26); pkgconfig 2.0.3(2019-09-22); pkgdown 2.1.3(2025-05-25); pkgload 1.4.1(2025-09-23); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.2.1(2026-01-09); 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 0.3.4(2026-01-17); Rcpp 1.1.1(2026-01-10); readr 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); remotes 2.5.0(2024-03-17); rlang 1.1.7(2026-01-09); rmarkdown 2.30(2025-09-28); roxygen2 7.3.3(2025-09-03); rprojroot 2.1.1(2025-08-26); RSQLite 2.4.5(2025-11-30); rstudioapi 0.17.1(2024-10-22); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); usethis 3.2.1(2025-09-06); vctrs 0.7.1(2026-01-23); withr 3.0.2(2024-10-28); xfun 0.56(2026-01-18); XML 3.99-0.20(2025-11-08); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-01-29 14:11:56] [INFO] [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.12; 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
[2026-01-29 14:11:56] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-01-29 14:11:56] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-01-29 14:11:56] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-01-29 14:11:56] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-01-29 14:11:56] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-01-29 14:11:56] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-01-29 14:11:56] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-01-29 14:11:56] [TRACE] [OmnipathR] JSON validation successful: TRUE
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