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bioc support 9158418
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| ## R 4.3.2 bioc 3.18 test | |
| ```R | |
| > library("recount3") | |
| > args(recount3_cache) | |
| function (cache_dir = getOption("recount3_cache", NULL)) | |
| NULL | |
| > rse_data <- recount3::create_rse_manual( | |
| + project = "SRP045225", | |
| + project_home = "data_sources/sra", | |
| + organism = "human", | |
| + annotation = "gencode_v29", | |
| + type = "gene", | |
| + bfc = recount3_cache(cache_dir = "~/Desktop/test_recount3_bioc3.18") | |
| + ) | |
| 2024-05-21 13:36:00.36106 downloading and reading the metadata. | |
| ~/Desktop/test_recount3_bioc3.18 | |
| does not exist, create directory? (yes/no): y | |
| 2024-05-21 13:36:02.590832 caching file sra.sra.SRP045225.MD.gz. | |
| adding rname 'http://duffel.rail.bio/recount3/human/data_sources/sra/metadata/25/SRP045225/sra.sra.SRP045225.MD.gz' | |
| |======================================================================| 100% | |
| |======================================================================| 100% | |
| 2024-05-21 13:36:03.456706 caching file sra.recount_project.SRP045225.MD.gz. | |
| adding rname 'http://duffel.rail.bio/recount3/human/data_sources/sra/metadata/25/SRP045225/sra.recount_project.SRP045225.MD.gz' | |
| |======================================================================| 100% | |
| |======================================================================| 100% | |
| 2024-05-21 13:36:04.355192 caching file sra.recount_qc.SRP045225.MD.gz. | |
| adding rname 'http://duffel.rail.bio/recount3/human/data_sources/sra/metadata/25/SRP045225/sra.recount_qc.SRP045225.MD.gz' | |
| |======================================================================| 100% | |
| |======================================================================| 100% | |
| 2024-05-21 13:36:05.320262 caching file sra.recount_seq_qc.SRP045225.MD.gz. | |
| adding rname 'http://duffel.rail.bio/recount3/human/data_sources/sra/metadata/25/SRP045225/sra.recount_seq_qc.SRP045225.MD.gz' | |
| |======================================================================| 100% | |
| |======================================================================| 100% | |
| 2024-05-21 13:36:06.314343 caching file sra.recount_pred.SRP045225.MD.gz. | |
| adding rname 'http://duffel.rail.bio/recount3/human/data_sources/sra/metadata/25/SRP045225/sra.recount_pred.SRP045225.MD.gz' | |
| |======================================================================| 100% | |
| |======================================================================| 100% | |
| 2024-05-21 13:36:07.04605 downloading and reading the feature information. | |
| 2024-05-21 13:36:07.288423 caching file human.gene_sums.G029.gtf.gz. | |
| adding rname 'http://duffel.rail.bio/recount3/human/annotations/gene_sums/human.gene_sums.G029.gtf.gz' | |
| |======================================================================| 100% | |
| |======================================================================| 100% | |
| 2024-05-21 13:36:08.476343 downloading and reading the counts: 86 samples across 64837 features. | |
| 2024-05-21 13:36:08.731985 caching file sra.gene_sums.SRP045225.G029.gz. | |
| adding rname 'http://duffel.rail.bio/recount3/human/data_sources/sra/gene_sums/25/SRP045225/sra.gene_sums.SRP045225.G029.gz' | |
| |======================================================================| 100% | |
| |======================================================================| 100% | |
| 2024-05-21 13:36:10.926105 constructing the RangedSummarizedExperiment (rse) object. | |
| > rse_data | |
| class: RangedSummarizedExperiment | |
| dim: 64837 86 | |
| metadata(8): time_created recount3_version ... annotation recount3_url | |
| assays(1): raw_counts | |
| rownames(64837): ENSG00000278704.1 ENSG00000277400.1 ... ENSG00000182484.15_PAR_Y ENSG00000227159.8_PAR_Y | |
| rowData names(10): source type ... havana_gene tag | |
| colnames(86): SRR1797218 SRR1797219 ... SRR1797300 SRR1797262 | |
| colData names(175): rail_id external_id ... recount_pred.curated.cell_line BigWigURL | |
| ## Clean up | |
| > recount3_cache_rm(recount3_cache(cache_dir = "~/Desktop/test_recount3_bioc3.18")) | |
| ## R Session info | |
| > options(width = 120) | |
| > sessioninfo::session_info() | |
| ─ Session info ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── | |
| setting value | |
| version R version 4.3.2 (2023-10-31) | |
| os macOS Sonoma 14.5 | |
| system aarch64, darwin20 | |
| ui X11 | |
| language (EN) | |
| collate en_US.UTF-8 | |
| ctype en_US.UTF-8 | |
| tz America/New_York | |
| date 2024-05-21 | |
| pandoc 3.1.12.1 @ /opt/homebrew/bin/pandoc | |
| ─ Packages ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── | |
| package * version date (UTC) lib source | |
| abind 1.4-5 2016-07-21 [1] CRAN (R 4.3.0) | |
| Biobase * 2.62.0 2023-10-26 [1] Bioconductor | |
| BiocFileCache 2.10.2 2024-03-30 [1] Bioconductor 3.18 (R 4.3.3) | |
| BiocGenerics * 0.48.1 2023-11-02 [1] Bioconductor | |
| BiocIO 1.12.0 2023-10-26 [1] Bioconductor | |
| BiocParallel 1.36.0 2023-10-26 [1] Bioconductor | |
| Biostrings 2.70.3 2024-03-16 [1] Bioconductor 3.18 (R 4.3.3) | |
| bit 4.0.5 2022-11-15 [1] CRAN (R 4.3.0) | |
| bit64 4.0.5 2020-08-30 [1] CRAN (R 4.3.0) | |
| bitops 1.0-7 2021-04-24 [1] CRAN (R 4.3.0) | |
| blob 1.2.4 2023-03-17 [1] CRAN (R 4.3.0) | |
| brio 1.1.5 2024-04-24 [1] CRAN (R 4.3.1) | |
| cachem 1.1.0 2024-05-16 [1] CRAN (R 4.3.3) | |
| cli 3.6.2 2023-12-11 [1] CRAN (R 4.3.1) | |
| codetools 0.2-20 2024-03-31 [1] CRAN (R 4.3.1) | |
| colorout * 1.3-0.2 2024-02-27 [1] Github (jalvesaq/colorout@c6113a2) | |
| crayon 1.5.2 2022-09-29 [1] CRAN (R 4.3.0) | |
| curl 5.2.1 2024-03-01 [1] CRAN (R 4.3.1) | |
| data.table 1.15.4 2024-03-30 [1] CRAN (R 4.3.1) | |
| DBI 1.2.2 2024-02-16 [1] CRAN (R 4.3.1) | |
| dbplyr 2.5.0 2024-03-19 [1] CRAN (R 4.3.1) | |
| DelayedArray 0.28.0 2023-11-06 [1] Bioconductor | |
| devtools * 2.4.5 2022-10-11 [1] CRAN (R 4.3.0) | |
| digest 0.6.35 2024-03-11 [1] CRAN (R 4.3.1) | |
| dplyr 1.1.4 2023-11-17 [1] CRAN (R 4.3.1) | |
| ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.3.0) | |
| fansi 1.0.6 2023-12-08 [1] CRAN (R 4.3.1) | |
| fastmap 1.2.0 2024-05-15 [1] CRAN (R 4.3.3) | |
| filelock 1.0.3 2023-12-11 [1] CRAN (R 4.3.1) | |
| fs 1.6.4 2024-04-25 [1] CRAN (R 4.3.1) | |
| generics 0.1.3 2022-07-05 [1] CRAN (R 4.3.0) | |
| GenomeInfoDb * 1.38.8 2024-03-16 [1] Bioconductor 3.18 (R 4.3.3) | |
| GenomeInfoDbData 1.2.11 2024-02-27 [1] Bioconductor | |
| GenomicAlignments 1.38.2 2024-01-20 [1] Bioconductor 3.18 (R 4.3.2) | |
| GenomicRanges * 1.54.1 2023-10-30 [1] Bioconductor | |
| glue 1.7.0 2024-01-09 [1] CRAN (R 4.3.1) | |
| htmltools 0.5.8.1 2024-04-04 [1] CRAN (R 4.3.1) | |
| htmlwidgets 1.6.4 2023-12-06 [1] CRAN (R 4.3.1) | |
| httpuv 1.6.15 2024-03-26 [1] CRAN (R 4.3.1) | |
| httr 1.4.7 2023-08-15 [1] CRAN (R 4.3.0) | |
| IRanges * 2.36.0 2023-10-26 [1] Bioconductor | |
| later 1.3.2 2023-12-06 [1] CRAN (R 4.3.1) | |
| lattice 0.22-6 2024-03-20 [1] CRAN (R 4.3.1) | |
| lifecycle 1.0.4 2023-11-07 [1] CRAN (R 4.3.1) | |
| magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.3.0) | |
| Matrix 1.6-5 2024-01-11 [1] CRAN (R 4.3.2) | |
| MatrixGenerics * 1.14.0 2023-10-26 [1] Bioconductor | |
| matrixStats * 1.3.0 2024-04-11 [1] CRAN (R 4.3.1) | |
| memoise 2.0.1 2021-11-26 [1] CRAN (R 4.3.0) | |
| mime 0.12 2021-09-28 [1] CRAN (R 4.3.0) | |
| miniUI 0.1.1.1 2018-05-18 [1] CRAN (R 4.3.0) | |
| pillar 1.9.0 2023-03-22 [1] CRAN (R 4.3.0) | |
| pkgbuild 1.4.4 2024-03-17 [1] CRAN (R 4.3.1) | |
| pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.3.0) | |
| pkgload 1.3.4 2024-01-16 [1] CRAN (R 4.3.1) | |
| profvis 0.3.8 2023-05-02 [1] CRAN (R 4.3.0) | |
| promises 1.3.0 2024-04-05 [1] CRAN (R 4.3.1) | |
| prompt 1.0.2.9000 2024-02-27 [1] Github (gaborcsardi/prompt@17bd0e1) | |
| purrr 1.0.2 2023-08-10 [1] CRAN (R 4.3.0) | |
| R.methodsS3 1.8.2 2022-06-13 [1] CRAN (R 4.3.0) | |
| R.oo 1.26.0 2024-01-24 [1] CRAN (R 4.3.1) | |
| R.utils 2.12.3 2023-11-18 [1] CRAN (R 4.3.1) | |
| R6 2.5.1 2021-08-19 [1] CRAN (R 4.3.0) | |
| Rcpp 1.0.12 2024-01-09 [1] CRAN (R 4.3.1) | |
| RCurl 1.98-1.14 2024-01-09 [1] CRAN (R 4.3.1) | |
| recount3 * 1.12.0 2023-10-26 [1] Bioconductor | |
| remotes 2.5.0 2024-03-17 [1] CRAN (R 4.3.1) | |
| restfulr 0.0.15 2022-06-16 [1] CRAN (R 4.3.0) | |
| rjson 0.2.21 2022-01-09 [1] CRAN (R 4.3.0) | |
| rlang 1.1.3 2024-01-10 [1] CRAN (R 4.3.1) | |
| Rsamtools 2.18.0 2023-10-26 [1] Bioconductor | |
| RSQLite 2.3.6 2024-03-31 [1] CRAN (R 4.3.1) | |
| rsthemes 0.4.0 2024-02-27 [1] Github (gadenbuie/rsthemes@34a55a4) | |
| rstudioapi 0.16.0 2024-03-24 [1] CRAN (R 4.3.1) | |
| rtracklayer 1.62.0 2023-10-26 [1] Bioconductor | |
| S4Arrays 1.2.1 2024-03-05 [1] Bioconductor 3.18 (R 4.3.2) | |
| S4Vectors * 0.40.2 2023-11-25 [1] Bioconductor 3.18 (R 4.3.2) | |
| sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.3.0) | |
| shiny 1.8.1.1 2024-04-02 [1] CRAN (R 4.3.1) | |
| SparseArray 1.2.4 2024-02-10 [1] Bioconductor 3.18 (R 4.3.2) | |
| stringi 1.8.4 2024-05-06 [1] CRAN (R 4.3.1) | |
| stringr 1.5.1 2023-11-14 [1] CRAN (R 4.3.1) | |
| SummarizedExperiment * 1.32.0 2023-11-06 [1] Bioconductor | |
| testthat * 3.2.1.1 2024-04-14 [1] CRAN (R 4.3.1) | |
| tibble 3.2.1 2023-03-20 [1] CRAN (R 4.3.0) | |
| tidyselect 1.2.1 2024-03-11 [1] CRAN (R 4.3.1) | |
| urlchecker 1.0.1 2021-11-30 [1] CRAN (R 4.3.0) | |
| usethis * 2.2.3 2024-02-19 [1] CRAN (R 4.3.1) | |
| utf8 1.2.4 2023-10-22 [1] CRAN (R 4.3.1) | |
| vctrs 0.6.5 2023-12-01 [1] CRAN (R 4.3.1) | |
| withr 3.0.0 2024-01-16 [1] CRAN (R 4.3.1) | |
| XML 3.99-0.16.1 2024-01-22 [1] CRAN (R 4.3.1) | |
| xtable 1.8-4 2019-04-21 [1] CRAN (R 4.3.0) | |
| XVector 0.42.0 2023-10-26 [1] Bioconductor | |
| yaml 2.3.8 2023-12-11 [1] CRAN (R 4.3.1) | |
| zlibbioc 1.48.2 2024-03-19 [1] Bioconductor 3.18 (R 4.3.3) | |
| [1] /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library | |
| ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── | |
| > curl::curl_version() | |
| $version | |
| [1] "8.6.0" | |
| $ssl_version | |
| [1] "(SecureTransport) LibreSSL/3.3.6" | |
| $libz_version | |
| [1] "1.2.12" | |
| $libssh_version | |
| [1] NA | |
| $libidn_version | |
| [1] NA | |
| $host | |
| [1] "x86_64-apple-darwin23.0" | |
| $protocols | |
| [1] "dict" "file" "ftp" "ftps" "gopher" "gophers" "http" "https" "imap" "imaps" "ldap" | |
| [12] "ldaps" "mqtt" "pop3" "pop3s" "rtsp" "smb" "smbs" "smtp" "smtps" "telnet" "tftp" | |
| $ipv6 | |
| [1] TRUE | |
| $http2 | |
| [1] TRUE | |
| $idn | |
| [1] FALSE | |
| ``` |
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| # R 4.4.0 bioc 3.19 test | |
| ```R | |
| devel > library("recount3") | |
| devel > rse_data <- recount3::create_rse_manual( | |
| + project = "SRP045225", | |
| + project_home = "data_sources/sra", | |
| + organism = "human", | |
| + annotation = "gencode_v29", | |
| + type = "gene" | |
| + ) | |
| 2024-05-21 13:30:02.836616 downloading and reading the metadata. | |
| 2024-05-21 13:30:03.411725 caching file sra.sra.SRP045225.MD.gz. | |
| adding rname 'http://duffel.rail.bio/recount3/human/data_sources/sra/metadata/25/SRP045225/sra.sra.SRP045225.MD.gz' | |
| |===============================================================================================| 100% | |
| |===============================================================================================| 100% | |
| 2024-05-21 13:30:04.571391 caching file sra.recount_project.SRP045225.MD.gz. | |
| adding rname 'http://duffel.rail.bio/recount3/human/data_sources/sra/metadata/25/SRP045225/sra.recount_project.SRP045225.MD.gz' | |
| |===============================================================================================| 100% | |
| |===============================================================================================| 100% | |
| 2024-05-21 13:30:05.540178 caching file sra.recount_qc.SRP045225.MD.gz. | |
| adding rname 'http://duffel.rail.bio/recount3/human/data_sources/sra/metadata/25/SRP045225/sra.recount_qc.SRP045225.MD.gz' | |
| |===============================================================================================| 100% | |
| |===============================================================================================| 100% | |
| 2024-05-21 13:30:06.506624 caching file sra.recount_seq_qc.SRP045225.MD.gz. | |
| adding rname 'http://duffel.rail.bio/recount3/human/data_sources/sra/metadata/25/SRP045225/sra.recount_seq_qc.SRP045225.MD.gz' | |
| |===============================================================================================| 100% | |
| |===============================================================================================| 100% | |
| 2024-05-21 13:30:07.409781 caching file sra.recount_pred.SRP045225.MD.gz. | |
| adding rname 'http://duffel.rail.bio/recount3/human/data_sources/sra/metadata/25/SRP045225/sra.recount_pred.SRP045225.MD.gz' | |
| |===============================================================================================| 100% | |
| |===============================================================================================| 100% | |
| 2024-05-21 13:30:08.073772 downloading and reading the feature information. | |
| 2024-05-21 13:30:08.305467 caching file human.gene_sums.G029.gtf.gz. | |
| adding rname 'http://duffel.rail.bio/recount3/human/annotations/gene_sums/human.gene_sums.G029.gtf.gz' | |
| |===============================================================================================| 100% | |
| |===============================================================================================| 100% | |
| 2024-05-21 13:30:09.421889 downloading and reading the counts: 86 samples across 64837 features. | |
| 2024-05-21 13:30:09.738755 caching file sra.gene_sums.SRP045225.G029.gz. | |
| adding rname 'http://duffel.rail.bio/recount3/human/data_sources/sra/gene_sums/25/SRP045225/sra.gene_sums.SRP045225.G029.gz' | |
| |===============================================================================================| 100% | |
| |===============================================================================================| 100% | |
| 2024-05-21 13:30:11.773491 constructing the RangedSummarizedExperiment (rse) object. | |
| devel > rse_data | |
| class: RangedSummarizedExperiment | |
| dim: 64837 86 | |
| metadata(8): time_created recount3_version ... annotation recount3_url | |
| assays(1): raw_counts | |
| rownames(64837): ENSG00000278704.1 ENSG00000277400.1 ... ENSG00000182484.15_PAR_Y | |
| ENSG00000227159.8_PAR_Y | |
| rowData names(10): source type ... havana_gene tag | |
| colnames(86): SRR1797218 SRR1797219 ... SRR1797300 SRR1797262 | |
| colData names(175): rail_id external_id ... recount_pred.curated.cell_line BigWigURL | |
| devel > options(width = 120) | |
| devel > sessioninfo::session_info() | |
| ─ Session info ─────────────────────────────────────────────────────────────────────────────────────────────────────── | |
| setting value | |
| version R version 4.4.0 (2024-04-24) | |
| os macOS Sonoma 14.5 | |
| system aarch64, darwin20 | |
| ui RStudio | |
| language (EN) | |
| collate en_US.UTF-8 | |
| ctype en_US.UTF-8 | |
| tz America/New_York | |
| date 2024-05-21 | |
| rstudio 2024.04.0+735 Chocolate Cosmos (desktop) | |
| pandoc 3.1.12.1 @ /opt/homebrew/bin/pandoc | |
| ─ Packages ─────────────────────────────────────────────────────────────────────────────────────────────────────────── | |
| package * version date (UTC) lib source | |
| abind 1.4-5 2016-07-21 [1] CRAN (R 4.4.0) | |
| Biobase * 2.64.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0) | |
| BiocFileCache 2.12.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0) | |
| BiocGenerics * 0.50.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0) | |
| BiocIO 1.14.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0) | |
| BiocParallel 1.38.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0) | |
| biocthis 1.14.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0) | |
| Biostrings 2.72.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0) | |
| bit 4.0.5 2022-11-15 [1] CRAN (R 4.4.0) | |
| bit64 4.0.5 2020-08-30 [1] CRAN (R 4.4.0) | |
| bitops 1.0-7 2021-04-24 [1] CRAN (R 4.4.0) | |
| blob 1.2.4 2023-03-17 [1] CRAN (R 4.4.0) | |
| brio 1.1.5 2024-04-24 [1] CRAN (R 4.4.0) | |
| cachem 1.1.0 2024-05-16 [1] CRAN (R 4.4.0) | |
| cli 3.6.2 2023-12-11 [1] CRAN (R 4.4.0) | |
| codetools 0.2-20 2024-03-31 [1] CRAN (R 4.4.0) | |
| colorout * 1.3-0.2 2024-05-03 [1] Github (jalvesaq/colorout@c6113a2) | |
| crayon 1.5.2 2022-09-29 [1] CRAN (R 4.4.0) | |
| curl 5.2.1 2024-03-01 [1] CRAN (R 4.4.0) | |
| data.table 1.15.4 2024-03-30 [1] CRAN (R 4.4.0) | |
| DBI 1.2.2 2024-02-16 [1] CRAN (R 4.4.0) | |
| dbplyr 2.5.0 2024-03-19 [1] CRAN (R 4.4.0) | |
| DelayedArray 0.30.1 2024-05-07 [1] Bioconductor 3.19 (R 4.4.0) | |
| devtools * 2.4.5 2022-10-11 [1] CRAN (R 4.4.0) | |
| digest 0.6.35 2024-03-11 [1] CRAN (R 4.4.0) | |
| dplyr 1.1.4 2023-11-17 [1] CRAN (R 4.4.0) | |
| ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.4.0) | |
| fansi 1.0.6 2023-12-08 [1] CRAN (R 4.4.0) | |
| fastmap 1.2.0 2024-05-15 [1] CRAN (R 4.4.0) | |
| filelock 1.0.3 2023-12-11 [1] CRAN (R 4.4.0) | |
| fs 1.6.4 2024-04-25 [1] CRAN (R 4.4.0) | |
| generics 0.1.3 2022-07-05 [1] CRAN (R 4.4.0) | |
| GenomeInfoDb * 1.40.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0) | |
| GenomeInfoDbData 1.2.12 2024-05-03 [1] Bioconductor | |
| GenomicAlignments 1.40.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0) | |
| GenomicRanges * 1.56.0 2024-05-01 [1] Bioconductor 3.19 (R 4.4.0) | |
| glue 1.7.0 2024-01-09 [1] CRAN (R 4.4.0) | |
| hms 1.1.3 2023-03-21 [1] CRAN (R 4.4.0) | |
| htmltools 0.5.8.1 2024-04-04 [1] CRAN (R 4.4.0) | |
| htmlwidgets 1.6.4 2023-12-06 [1] CRAN (R 4.4.0) | |
| httpuv 1.6.15 2024-03-26 [1] CRAN (R 4.4.0) | |
| httr 1.4.7 2023-08-15 [1] CRAN (R 4.4.0) | |
| IRanges * 2.38.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0) | |
| jsonlite 1.8.8 2023-12-04 [1] CRAN (R 4.4.0) | |
| later 1.3.2 2023-12-06 [1] CRAN (R 4.4.0) | |
| lattice 0.22-6 2024-03-20 [1] CRAN (R 4.4.0) | |
| lifecycle 1.0.4 2023-11-07 [1] CRAN (R 4.4.0) | |
| lubridate 1.9.3 2023-09-27 [1] CRAN (R 4.4.0) | |
| magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.4.0) | |
| Matrix 1.7-0 2024-03-22 [1] CRAN (R 4.4.0) | |
| MatrixGenerics * 1.16.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0) | |
| matrixStats * 1.3.0 2024-04-11 [1] CRAN (R 4.4.0) | |
| memoise 2.0.1 2021-11-26 [1] CRAN (R 4.4.0) | |
| mime 0.12 2021-09-28 [1] CRAN (R 4.4.0) | |
| miniUI 0.1.1.1 2018-05-18 [1] CRAN (R 4.4.0) | |
| pillar 1.9.0 2023-03-22 [1] CRAN (R 4.4.0) | |
| pkgbuild 1.4.4 2024-03-17 [1] CRAN (R 4.4.0) | |
| pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.4.0) | |
| pkgload 1.3.4 2024-01-16 [1] CRAN (R 4.4.0) | |
| profvis 0.3.8 2023-05-02 [1] CRAN (R 4.4.0) | |
| promises 1.3.0 2024-04-05 [1] CRAN (R 4.4.0) | |
| prompt 1.0.2.9000 2024-05-03 [1] Github (gaborcsardi/prompt@17bd0e1) | |
| purrr 1.0.2 2023-08-10 [1] CRAN (R 4.4.0) | |
| R.cache 0.16.0 2022-07-21 [1] CRAN (R 4.4.0) | |
| R.methodsS3 1.8.2 2022-06-13 [1] CRAN (R 4.4.0) | |
| R.oo 1.26.0 2024-01-24 [1] CRAN (R 4.4.0) | |
| R.utils 2.12.3 2023-11-18 [1] CRAN (R 4.4.0) | |
| R6 2.5.1 2021-08-19 [1] CRAN (R 4.4.0) | |
| Rcpp 1.0.12 2024-01-09 [1] CRAN (R 4.4.0) | |
| RCurl 1.98-1.14 2024-01-09 [1] CRAN (R 4.4.0) | |
| recount3 * 1.14.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0) | |
| remotes 2.5.0 2024-03-17 [1] CRAN (R 4.4.0) | |
| restfulr 0.0.15 2022-06-16 [1] CRAN (R 4.4.0) | |
| rjson 0.2.21 2022-01-09 [1] CRAN (R 4.4.0) | |
| rlang 1.1.3 2024-01-10 [1] CRAN (R 4.4.0) | |
| Rsamtools 2.20.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0) | |
| RSQLite 2.3.6 2024-03-31 [1] CRAN (R 4.4.0) | |
| rsthemes 0.4.0 2024-05-03 [1] Github (gadenbuie/rsthemes@34a55a4) | |
| rstudioapi 0.16.0 2024-03-24 [1] CRAN (R 4.4.0) | |
| rtracklayer 1.64.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0) | |
| S4Arrays 1.4.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0) | |
| S4Vectors * 0.42.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0) | |
| sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.4.0) | |
| shiny 1.8.1.1 2024-04-02 [1] CRAN (R 4.4.0) | |
| SparseArray 1.4.3 2024-05-07 [1] Bioconductor 3.19 (R 4.4.0) | |
| stringi 1.8.4 2024-05-06 [1] CRAN (R 4.4.0) | |
| stringr 1.5.1 2023-11-14 [1] CRAN (R 4.4.0) | |
| styler 1.10.3 2024-04-07 [1] CRAN (R 4.4.0) | |
| SummarizedExperiment * 1.34.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0) | |
| suncalc 0.5.1 2022-09-29 [1] CRAN (R 4.4.0) | |
| testthat * 3.2.1.1 2024-04-14 [1] CRAN (R 4.4.0) | |
| tibble 3.2.1 2023-03-20 [1] CRAN (R 4.4.0) | |
| tidyselect 1.2.1 2024-03-11 [1] CRAN (R 4.4.0) | |
| timechange 0.3.0 2024-01-18 [1] CRAN (R 4.4.0) | |
| UCSC.utils 1.0.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0) | |
| urlchecker 1.0.1 2021-11-30 [1] CRAN (R 4.4.0) | |
| usethis * 2.2.3 2024-02-19 [1] CRAN (R 4.4.0) | |
| utf8 1.2.4 2023-10-22 [1] CRAN (R 4.4.0) | |
| vctrs 0.6.5 2023-12-01 [1] CRAN (R 4.4.0) | |
| withr 3.0.0 2024-01-16 [1] CRAN (R 4.4.0) | |
| XML 3.99-0.16.1 2024-01-22 [1] CRAN (R 4.4.0) | |
| xtable 1.8-4 2019-04-21 [1] CRAN (R 4.4.0) | |
| XVector 0.44.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0) | |
| yaml 2.3.8 2023-12-11 [1] CRAN (R 4.4.0) | |
| zlibbioc 1.50.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0) | |
| [1] /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library | |
| ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── | |
| > curl::curl_version() | |
| $version | |
| [1] "8.6.0" | |
| $ssl_version | |
| [1] "(SecureTransport) LibreSSL/3.3.6" | |
| $libz_version | |
| [1] "1.2.12" | |
| $libssh_version | |
| [1] NA | |
| $libidn_version | |
| [1] NA | |
| $host | |
| [1] "x86_64-apple-darwin23.0" | |
| $protocols | |
| [1] "dict" "file" "ftp" "ftps" "gopher" "gophers" "http" "https" "imap" "imaps" "ldap" "ldaps" "mqtt" "pop3" | |
| [15] "pop3s" "rtsp" "smb" "smbs" "smtp" "smtps" "telnet" "tftp" | |
| $ipv6 | |
| [1] TRUE | |
| $http2 | |
| [1] TRUE | |
| $idn | |
| [1] FALSE | |
| ``` |
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