From 5eeb186ec4a3e344963511b149d4805b7f3b6d11 Mon Sep 17 00:00:00 2001 From: Gregory Jefferis Date: Thu, 6 Jun 2024 00:10:09 +0100 Subject: [PATCH 1/7] suggest rdrop2 and add remote * has been archived on cran due to dependency issues --- DESCRIPTION | 9 +++++---- R/utilities-gdrive.R | 2 ++ 2 files changed, 7 insertions(+), 4 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index f4360dc..bbfc81c 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -31,7 +31,8 @@ Suggests: fastcluster, reticulate, doParallel, - qs + qs, + rdrop2 VignetteBuilder: knitr Depends: R (>= 3.1), @@ -58,7 +59,6 @@ Imports: jpeg, png, googledrive, - rdrop2, jsonlite, plyr, catmaid, @@ -83,8 +83,9 @@ Remotes: natverse/nat.nblast, natverse/nat, natverse/nat.flybrains, - schlegelp/nat.hdf5 + schlegelp/nat.hdf5, + karthik/rdrop2 Language: en-GB -RoxygenNote: 7.2.1 +RoxygenNote: 7.3.1 URL: https://github.com/flyconnectome/hemibrainr, https://flyconnectome.github.io/hemibrainr BugReports: https://github.com/flyconnectome/hemibrainr/issues diff --git a/R/utilities-gdrive.R b/R/utilities-gdrive.R index e67e541..11a9e1b 100644 --- a/R/utilities-gdrive.R +++ b/R/utilities-gdrive.R @@ -286,6 +286,8 @@ remote_upload <- function(file, verbose = verbose) } }else if(remote=="dropbox"){ + if(!requireNamespace('rdrop2', quietly = T)) + stop("Please install suggested package rdrop2 to use Dropbox") rdrop2::drop_upload(file = file, path = path, mode = "overwrite", From 5841d1ed0b82d4f86e67fe56c1339f0c0c23999a Mon Sep 17 00:00:00 2001 From: Gregory Jefferis Date: Thu, 6 Jun 2024 00:13:27 +0100 Subject: [PATCH 2/7] add remote for bitsqueezr * was already in suggests --- DESCRIPTION | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index bbfc81c..e449d35 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -84,7 +84,8 @@ Remotes: natverse/nat, natverse/nat.flybrains, schlegelp/nat.hdf5, - karthik/rdrop2 + karthik/rdrop2, + dbaston/bitsqueezr Language: en-GB RoxygenNote: 7.3.1 URL: https://github.com/flyconnectome/hemibrainr, https://flyconnectome.github.io/hemibrainr From 341081909fd50984d3710550aca448fb8cab6dfc Mon Sep 17 00:00:00 2001 From: Gregory Jefferis Date: Tue, 18 Jun 2024 13:34:38 +0200 Subject: [PATCH 3/7] don't run google auth in startup --- R/zzz.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/zzz.R b/R/zzz.R index a64aad1..95b6a0f 100644 --- a/R/zzz.R +++ b/R/zzz.R @@ -33,7 +33,7 @@ } # Set googlesheets API key - try(hemibrainr_google_login()) + # try(hemibrainr_google_login()) # Set Google sheets of interest hemibrainr_matching_gsheet = ifelse(!is.null(getOption("hemibrainr_matching_gsheet")),getOption("hemibrainr_matching_gsheet"),"1OSlDtnR3B1LiB5cwI5x5Ql6LkZd8JOS5bBr-HTi0pOw") From c00016a91f3724c1e13322cd80e95d930b9b51b3 Mon Sep 17 00:00:00 2001 From: Gregory Jefferis Date: Tue, 18 Jun 2024 14:04:40 +0200 Subject: [PATCH 4/7] roxygenize --- man/flywire_neurons.Rd | 1 + 1 file changed, 1 insertion(+) diff --git a/man/flywire_neurons.Rd b/man/flywire_neurons.Rd index 7d43ab1..e05ba3f 100644 --- a/man/flywire_neurons.Rd +++ b/man/flywire_neurons.Rd @@ -10,6 +10,7 @@ flywire_neurons( x = NULL, WithConnectors = FALSE, local = FALSE, + version = NULL, brain = c("FlyWire", "JRCFIB2018Fraw", "JRCFIB2018F", "FAFB", "FAFB14", "JFRC2", "JFRC2013", "JRC2018F", "FCWB"), mirror = FALSE, From 1eb880a1b6441ff919ee043783cc9b185aac721a Mon Sep 17 00:00:00 2001 From: Gregory Jefferis Date: Tue, 18 Jun 2024 15:15:28 +0200 Subject: [PATCH 5/7] missing imports --- NAMESPACE | 4 ++++ R/hemibrainr-package.R | 4 ++++ 2 files changed, 8 insertions(+) diff --git a/NAMESPACE b/NAMESPACE index 167f7b8..bdac4cf 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -264,6 +264,10 @@ importFrom(rgl,spheres3d) importFrom(rlang,.data) importFrom(stats,ave) importFrom(stats,dist) +importFrom(stats,na.omit) +importFrom(stats,offset) importFrom(stats,sd) importFrom(utils,download.file) importFrom(utils,installed.packages) +importFrom(utils,setTxtProgressBar) +importFrom(utils,txtProgressBar) diff --git a/R/hemibrainr-package.R b/R/hemibrainr-package.R index bffbb54..684669d 100644 --- a/R/hemibrainr-package.R +++ b/R/hemibrainr-package.R @@ -5,5 +5,9 @@ # The following block is used by usethis to automatically manage # roxygen namespace tags. Modify with care! ## usethis namespace: start +#' @importFrom stats na.omit +#' @importFrom stats offset +#' @importFrom utils setTxtProgressBar +#' @importFrom utils txtProgressBar ## usethis namespace: end NULL From 78cdcf30711ddc7f5eb29266cebcfdd5077c1cf7 Mon Sep 17 00:00:00 2001 From: Gregory Jefferis Date: Tue, 18 Jun 2024 15:20:13 +0200 Subject: [PATCH 6/7] more import fixes --- DESCRIPTION | 6 +++++- R/hemibrain_synapses.R | 2 +- 2 files changed, 6 insertions(+), 2 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index e449d35..a1d0de3 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -32,7 +32,11 @@ Suggests: reticulate, doParallel, qs, - rdrop2 + rdrop2, + arrow, + doSNOW, + ggplot2, + gridExtra VignetteBuilder: knitr Depends: R (>= 3.1), diff --git a/R/hemibrain_synapses.R b/R/hemibrain_synapses.R index b4de88d..da950cb 100644 --- a/R/hemibrain_synapses.R +++ b/R/hemibrain_synapses.R @@ -569,7 +569,7 @@ hemibrain_ntplot.neuronlist <- function(x, do.call(gridExtra::grid.arrange, c(plist, ncol=nCol)) }else{ syns.nt = lapply(x, function(y) y$connectors) - syns.nt = do.call(pluyr::rbind.fill, syns.nt) + syns.nt = do.call(plyr::rbind.fill, syns.nt) syns.nt$id = "collapse" hemibrain_ntplot.data.frame(syns.nt) } From dd729c30032ae1383aed091f595feeebee1e110e Mon Sep 17 00:00:00 2001 From: Gregory Jefferis Date: Tue, 25 Jun 2024 12:18:03 +0100 Subject: [PATCH 7/7] switch to v2 r install as macosx failing --- .github/workflows/R-CMD-check.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 1a2bc11..0c25d9b 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -45,7 +45,7 @@ jobs: steps: - uses: actions/checkout@v2 - - uses: r-lib/actions/setup-r@v1 + - uses: r-lib/actions/setup-r@v2 with: r-version: ${{ matrix.config.r }}