diff --git a/.github/workflows/lint.yaml b/.github/workflows/lint.yaml deleted file mode 100644 index 6912ca9..0000000 --- a/.github/workflows/lint.yaml +++ /dev/null @@ -1,9 +0,0 @@ -on: - push: - branches: [main, master] - -name: lint - -jobs: - lint: - uses: hugheylab/actions/.github/workflows/lint.yaml@main diff --git a/DESCRIPTION b/DESCRIPTION index 0340f8e..074bdf9 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: seeker Type: Package Title: Simplified Fetching and Processing of Microarray and RNA-Seq Data -Version: 1.1.3 +Version: 1.1.4 Authors@R: c( person('Jake', 'Hughey', , 'jakejhughey@gmail.com', role = c('aut', 'cre')), person('Josh', 'Schoenbachler', , 'josh.schoenbachler@gmail.com', role = 'aut')) @@ -51,7 +51,7 @@ Imports: withr (>= 2.4.2), yaml (>= 2.2.1) Suggests: - ArrayExpress (>= 1.50.0), + ArrayExpress (>= 1.62.0), Biobase, doParallel (>= 1.0.17), knitr, diff --git a/NEWS.md b/NEWS.md index a8e9325..d4b6032 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,7 @@ +# seeker 1.1.4 +* Fixed processing of ArrayExpress data (thanks to @jacorvar). +* Removed deprecated argument from `biomaRt::listEnsemblArchives()`. + # seeker 1.1.3 * Updated test for fetching metadata again. * `fetchMetadata()` now orders its result. diff --git a/R/array_utils.R b/R/array_utils.R index a28b1c6..5646a78 100644 --- a/R/array_utils.R +++ b/R/array_utils.R @@ -158,7 +158,7 @@ getNaiveEsetAe = function(study, outputDir, rawDir) { # if (metadataOnly) return(list(eset = eset)) if ((platform %in% getPlatforms('cdf')$ae_accession) && hasRaw) { - mage = ArrayExpress::getAE(study, path = outputDir, type = 'raw') + mage = ArrayExpress::getAE(study, path = outputDir, type = 'full') eset = ArrayExpress::ae2bioc(mage) rmaOk = TRUE } else { @@ -174,8 +174,8 @@ getNaiveEsetAe = function(study, outputDir, rawDir) { if (!dir.exists(rawDir)) dir.create(rawDir) - . = file.rename(file.path(outputDir, mage$rawFiles), - file.path(rawDir, mage$rawFiles)) + . = file.rename(file.path(outputDir, basename(mage$rawFiles)), + file.path(rawDir, basename(mage$rawFiles))) return(list(eset = eset, rmaOk = rmaOk))} diff --git a/R/tximport.R b/R/tximport.R index d5ed524..30153e5 100644 --- a/R/tximport.R +++ b/R/tximport.R @@ -29,7 +29,7 @@ getTx2gene = function( withr::local_options(timeout = 600) if (is.null(version)) { # let's be strict - arch = setDT(biomaRt::listEnsemblArchives(https = TRUE)) + arch = setDT(biomaRt::listEnsemblArchives()) version = as.integer(arch[arch$current_release == '*']$version)} if (!is.null(outputDir)) { diff --git a/cran-comments.md b/cran-comments.md index 2f0dff5..d75820c 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -8,17 +8,28 @@ ### R-hub -R-hub builds are giving errors because "Bioconductor does not yet build and check packages for R version 4.4". +`devtools::check_rhub()`: -See results for [Windows](https://builder.r-hub.io/status/seeker_1.1.3.tar.gz-7dd2f5c93e324fceb89b5451f55325ec), [Ubuntu](https://builder.r-hub.io/status/seeker_1.1.3.tar.gz-e086fb7a85834001b34f4a6111838921), and [Fedora](https://builder.r-hub.io/status/seeker_1.1.3.tar.gz-c75d4dfc8fd74825b4fbac365d27c862). + 0 errors ✓ | 0 warnings ✓ | 2 notes ✓ + +❯ checking for non-standard things in the check directory ... NOTE + Found the following files/directories: + ''NULL'' + +❯ checking for detritus in the temp directory ... NOTE + Found the following files/directories: + 'lastMiKTeXException' + +See results for [Windows](https://builder.r-hub.io/status/seeker_1.1.4.tar.gz-1fd21b320f264289820666012a924a8a), [Ubuntu](https://builder.r-hub.io/status/seeker_1.1.4.tar.gz-dd2ecaaf51d24135a360cee4e0b8a858), and [Fedora](https://builder.r-hub.io/status/seeker_1.1.4.tar.gz-6cfb237d17794ae5bd6fa302781fb7b0). ### GitHub Actions 0 errors ✓ | 0 warnings ✓ | 0 notes ✓ -See results for Mac, Windows, and Ubuntu [here](https://github.com/hugheylab/seeker/actions/runs/5062969952). +See results for Mac, Windows, and Ubuntu [here](). ## Changes from current CRAN release -* Updated test for fetching metadata, this time to make it less sensitive to arbitrary changes on the remote resource. -* `fetchMetadata()` now orders its result. +* Fixed processing of ArrayExpress data (thanks to @jacorvar). +* Removed deprecated argument from `biomaRt::listEnsemblArchives()`. +* Updated test standards. diff --git a/inst/extdata/platform_cdf.csv b/inst/extdata/platform_cdf.csv index 06391d2..3eb3d9c 100644 --- a/inst/extdata/platform_cdf.csv +++ b/inst/extdata/platform_cdf.csv @@ -14,5 +14,6 @@ pd.mouse430.2,mouse4302mm,A-AFFY-45 pd.u133.x3p,u133x3phs,A-AFFY-54 pd.rat230.2,rat2302rn,A-AFFY-43 pd.hg.u133a,hgu133ahs,A-AFFY-33 +pd.hg.u133.plus.2,hgu133plus2hs,A-AFFY-44 pd.mogene.1.0.st.v1,mogene10stmm,A-AFFY-130 pd.mogene.2.0.st,mogene20stmm,A-GEOD-16570 diff --git a/tests/testthat/data/GPL6887.qs b/tests/testthat/data/GPL6887.qs index e3eb0b6..1e62d00 100644 Binary files a/tests/testthat/data/GPL6887.qs and b/tests/testthat/data/GPL6887.qs differ diff --git a/tests/testthat/data/GPL7202.qs b/tests/testthat/data/GPL7202.qs index 566e4e2..f64b4d1 100644 Binary files a/tests/testthat/data/GPL7202.qs and b/tests/testthat/data/GPL7202.qs differ diff --git a/tests/testthat/data/GSE147674_eset.qs b/tests/testthat/data/GSE147674_eset.qs index b66da3f..0b8c3b0 100644 Binary files a/tests/testthat/data/GSE147674_eset.qs and b/tests/testthat/data/GSE147674_eset.qs differ diff --git a/tests/testthat/data/GSE167458_eset.qs b/tests/testthat/data/GSE167458_eset.qs index b324ae8..e250667 100644 Binary files a/tests/testthat/data/GSE167458_eset.qs and b/tests/testthat/data/GSE167458_eset.qs differ diff --git a/tests/testthat/data/GSE50143_eset.qs b/tests/testthat/data/GSE50143_eset.qs index e1e1bfb..d8a8ef7 100644 Binary files a/tests/testthat/data/GSE50143_eset.qs and b/tests/testthat/data/GSE50143_eset.qs differ diff --git a/tests/testthat/data/map_pkg_ver.qs b/tests/testthat/data/map_pkg_ver.qs index 5a2e8d1..fcab9ae 100644 Binary files a/tests/testthat/data/map_pkg_ver.qs and b/tests/testthat/data/map_pkg_ver.qs differ diff --git a/tests/testthat/data/multiqc_output.qs b/tests/testthat/data/multiqc_output.qs index 46b39dd..59e000a 100644 Binary files a/tests/testthat/data/multiqc_output.qs and b/tests/testthat/data/multiqc_output.qs differ diff --git a/tests/testthat/data/seeker_output_full.qs b/tests/testthat/data/seeker_output_full.qs index 3e642c2..ffb1b04 100644 Binary files a/tests/testthat/data/seeker_output_full.qs and b/tests/testthat/data/seeker_output_full.qs differ