diff --git a/modules/data.remote/R/NLCD.R b/modules/data.remote/R/NLCD.R index 32517eff2ae..6bda926c5a5 100644 --- a/modules/data.remote/R/NLCD.R +++ b/modules/data.remote/R/NLCD.R @@ -23,10 +23,9 @@ download.NLCD <- function(outdir, year = 2011, con = NULL) { ## before downloading, check if the file already exists on this host if (!is.null(con)) { - - chk <- dbfile.check(type = "Input", id = input.id, con = con) + chk <- PEcAn.DB::dbfile.check(type = "Input", id = input.id, con = con) if (nrow(chk) > 0) { - machines <- db.query(paste("SELECT * from machines where id in (", + machines <- PEcAn.DB::db.query(paste("SELECT * from machines where id in (", paste(chk$machine_id, sep = ","), ")"), con) if (PEcAn.remote::fqdn() %in% machines$hostname) { ## record already exists on this host @@ -49,7 +48,7 @@ download.NLCD <- function(outdir, year = 2011, con = NULL) { prefix <- table(sapply(strsplit(dir(data_dir), ".", fixed = TRUE), function(x) { x[1] })) prefix <- names(which.max(prefix)) site.id <- 1000000676 - return(dbfile.insert(data_dir, in.prefix = prefix, type = "Input", input.id, con, + return(PEcAn.DB::dbfile.insert(data_dir, in.prefix = prefix, type = "Input", input.id, con, reuse = TRUE)) } return(data_dir) @@ -78,9 +77,9 @@ extract_NLCD <- function(buffer, coords, data_dir = NULL, con = NULL, year = 201 } else { print(paste("Year not yet supported: ", year)) } - chk <- dbfile.check(type = "Input", id = input.id, con = con) + chk <- PEcAn.DB::dbfile.check(type = "Input", id = input.id, con = con) if (nrow(chk) > 0) { - machines <- db.query(paste("SELECT * from machines where id in (", + machines <- PEcAn.DB::db.query(paste("SELECT * from machines where id in (", paste(chk$machine_id, sep = ","), ")"), con) if (PEcAn.remote::fqdn() %in% machines$hostname) { ## record already exists on this host diff --git a/modules/data.remote/R/call_MODIS.R b/modules/data.remote/R/call_MODIS.R index 61e41a6f845..b4791cd004e 100755 --- a/modules/data.remote/R/call_MODIS.R +++ b/modules/data.remote/R/call_MODIS.R @@ -283,7 +283,7 @@ call_MODIS <- function(var, product, fname <- paste(site_info$site_id[i], "/", product, "_", band, "_", start_date, "-", end_date, "_unfiltered.csv", sep = "") } fname <- file.path(outdir, fname) - write.csv(site, fname, row.names = FALSE) + utils::write.csv(site, fname, row.names = FALSE) } } diff --git a/modules/data.remote/R/download.thredds.R b/modules/data.remote/R/download.thredds.R index 04fc4b99923..d4a5ca4c728 100755 --- a/modules/data.remote/R/download.thredds.R +++ b/modules/data.remote/R/download.thredds.R @@ -69,7 +69,7 @@ download.thredds.AGB <- function(outdir = NULL, site_ids, run_parallel = FALSE, # option to save output dataset to directory for user. if (!(is.null(outdir))) { - write.csv(output, file = paste0(outdir, "THREDDS_", sub("^([^.]*).*", "\\1",basename(files[1])), "_site_", site, ".csv"), row.names = FALSE) + utils::write.csv(output, file = paste0(outdir, "THREDDS_", sub("^([^.]*).*", "\\1",basename(files[1])), "_site_", site, ".csv"), row.names = FALSE) } return(output) @@ -86,8 +86,8 @@ download.thredds.AGB <- function(outdir = NULL, site_ids, run_parallel = FALSE, PEcAn.logger::logger.info(paste0("Running in parallel with: ", ncores)) cl = parallel::makeCluster(ncores) doParallel::registerDoParallel(cl) - data = foreach(i = seq_along(mylat), .combine = rbind) %dopar% get_data(i) - stopCluster(cl) + data = foreach::foreach(i = seq_along(mylat), .combine = rbind) %dopar% get_data(i) + parallel::stopCluster(cl) } else { # setup sequential run diff --git a/modules/data.remote/tests/Rcheck_reference.log b/modules/data.remote/tests/Rcheck_reference.log index 182f76f6d12..814dfe66e10 100644 --- a/modules/data.remote/tests/Rcheck_reference.log +++ b/modules/data.remote/tests/Rcheck_reference.log @@ -1,55 +1,12 @@ -* using log directory ‘/home/tanishq010/pecan/modules/PEcAn.data.remote.Rcheck’ -* using R version 4.2.1 (2022-06-23) +* using log directory ‘/tmp/Rtmpr2UgRH/PEcAn.data.remote.Rcheck’ +* using R version 4.1.3 (2022-03-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 -* using options ‘--no-tests --no-manual --as-cran’ +* using options ‘--no-manual --as-cran’ * checking for file ‘PEcAn.data.remote/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘PEcAn.data.remote’ version ‘1.7.2.9000’ * package encoding: UTF-8 -* checking CRAN incoming feasibility ... WARNING -Maintainer: ‘Bailey Morrison ’ - -New submission - -Version contains large components (1.7.2.9000) - -License components with restrictions and base license permitting such: - BSD_3_clause + file LICENSE -File 'LICENSE': - University of Illinois/NCSA Open Source License - - Copyright (c) 2012, University of Illinois, NCSA. All rights reserved. - - Permission is hereby granted, free of charge, to any person obtaining - a copy of this software and associated documentation files (the - "Software"), to deal with the Software without restriction, including - without limitation the rights to use, copy, modify, merge, publish, - distribute, sublicense, and/or sell copies of the Software, and to - permit persons to whom the Software is furnished to do so, subject to - the following conditions: - - - Redistributions of source code must retain the above copyright - notice, this list of conditions and the following disclaimers. - - Redistributions in binary form must reproduce the above copyright - notice, this list of conditions and the following disclaimers in the - documentation and/or other materials provided with the distribution. - - Neither the names of University of Illinois, NCSA, nor the names - of its contributors may be used to endorse or promote products - derived from this Software without specific prior written permission. - - THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, - EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF - MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. - IN NO EVENT SHALL THE CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR - ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF - CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION - WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS WITH THE SOFTWARE. - -Strong dependencies not in mainstream repositories: - PEcAn.DB, PEcAn.utils, PEcAn.logger, PEcAn.remote - -The Date field is over a month old. * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK @@ -63,11 +20,7 @@ The Date field is over a month old. * checking installed package size ... OK * checking package directory ... OK * checking for future file timestamps ... OK -* checking DESCRIPTION meta-information ... NOTE -Author field differs from that derived from Authors@R - Author: ‘Mike Dietze, Bailey Morrison’ - Authors@R: ‘Mike Dietze [aut], Bailey Morrison [aut, cre], University of Illinois, NCSA [cph]’ - +* checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK @@ -80,47 +33,22 @@ Author field differs from that derived from Authors@R * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK -* checking use of S3 registration ... OK * checking dependencies in R code ... WARNING 'library' or 'require' calls in package code: ‘PEcAn.DB’ ‘doParallel’ ‘raster’ ‘rgdal’ Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. -Namespace in Imports field not imported from: ‘stringr’ - All declared Imports should be used. +Missing or unexported objects: + ‘PEcAn.utils::download_file’ ‘PEcAn.utils::need_packages’ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE -call_MODIS: no visible global function definition for ‘write.csv’ download.LandTrendr.AGB: no visible binding for global variable ‘k’ -download.NLCD: no visible global function definition for ‘dbfile.check’ -download.NLCD: no visible global function definition for ‘db.query’ -download.NLCD: no visible global function definition for - ‘dbfile.insert’ -download.thredds.AGB : get_data: no visible global function definition - for ‘write.csv’ -download.thredds.AGB: no visible global function definition for - ‘foreach’ -download.thredds.AGB: no visible global function definition for - ‘stopCluster’ -extract_NLCD: no visible global function definition for ‘dbfile.check’ -extract_NLCD: no visible global function definition for ‘db.query’ -extract_NLCD: no visible global function definition for ‘raster’ -extract_NLCD: no visible global function definition for ‘SpatialPoints’ -extract_NLCD: no visible global function definition for ‘CRS’ -extract_NLCD: no visible global function definition for ‘spTransform’ -extract_NLCD: no visible global function definition for ‘crs’ -extract_NLCD: no visible global function definition for ‘extract’ grid2netcdf: no visible binding for global variable ‘years’ grid2netcdf: no visible binding for global variable ‘yieldarray’ Undefined global functions or variables: - CRS SpatialPoints crs db.query dbfile.check dbfile.insert - download.file extract foreach k raster spTransform stopCluster - write.csv -Consider adding - importFrom("utils", "download.file", "write.csv") -to your NAMESPACE file. + k years yieldarray * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK @@ -146,4 +74,9 @@ Extensions’ manual. * checking for detritus in the temp directory ... OK * DONE -Status: 3 WARNINGs, 2 NOTEs +Status: 2 WARNINGs, 1 NOTE +See + ‘/tmp/Rtmpr2UgRH/PEcAn.data.remote.Rcheck/00check.log’ +for details. + +