From 4a19b292e25f1b4edb2d9a42ff1a64993b68639f Mon Sep 17 00:00:00 2001 From: meetagrawal09 Date: Sat, 17 Feb 2024 20:33:50 +0530 Subject: [PATCH 1/3] fixed notes --- base/workflow/DESCRIPTION | 4 ++-- base/workflow/R/run.write.configs.R | 5 +++++ base/workflow/tests/Rcheck_reference.log | 16 ++-------------- 3 files changed, 9 insertions(+), 16 deletions(-) diff --git a/base/workflow/DESCRIPTION b/base/workflow/DESCRIPTION index 123dd17e3d7..efd8efabefd 100644 --- a/base/workflow/DESCRIPTION +++ b/base/workflow/DESCRIPTION @@ -1,7 +1,7 @@ Package: PEcAn.workflow Type: Package -Title: PEcAn functions used for ecological forecasts and - reanalysis +Title: PEcAn Functions Used for Ecological Forecasts and + Reanalysis Version: 1.7.2 Date: 2021-10-04 Authors@R: c(person("Mike", "Dietze", role = c("aut"), diff --git a/base/workflow/R/run.write.configs.R b/base/workflow/R/run.write.configs.R index 00b82bf80ef..f6b009836a4 100644 --- a/base/workflow/R/run.write.configs.R +++ b/base/workflow/R/run.write.configs.R @@ -82,6 +82,11 @@ run.write.configs <- function(settings, write = TRUE, ens.sample.method = "unifo scipen <- getOption("scipen") options(scipen = 12) + trait.samples <- NULL + sa.samples <- NULL + ensemble.samples <- NULL + runs.samples <- NULL + PEcAn.uncertainty::get.parameter.samples(settings, posterior.files, ens.sample.method) samples.file <- file.path(settings$outdir, "samples.Rdata") if (file.exists(samples.file)) { diff --git a/base/workflow/tests/Rcheck_reference.log b/base/workflow/tests/Rcheck_reference.log index db508a93b02..3d3e30ec6d6 100644 --- a/base/workflow/tests/Rcheck_reference.log +++ b/base/workflow/tests/Rcheck_reference.log @@ -48,11 +48,6 @@ Strong dependencies not in mainstream repositories: PEcAn.data.atmosphere, PEcAn.data.land, PEcAn.DB, PEcAn.logger, PEcAn.remote, PEcAn.settings, PEcAn.uncertainty, PEcAn.utils -The Title field should be in title case. Current version is: -‘PEcAn functions used for ecological forecasts and reanalysis’ -In title case that is: -‘PEcAn Functions Used for Ecological Forecasts and Reanalysis’ - The Date field is over a month old. * checking package namespace information ... OK * checking package dependencies ... OK @@ -93,14 +88,7 @@ Maintainer field differs from that derived from Authors@R * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK -* checking R code for possible problems ... NOTE -run.write.configs: no visible binding for global variable - ‘trait.samples’ -run.write.configs: no visible binding for global variable ‘sa.samples’ -run.write.configs: no visible binding for global variable - ‘ensemble.samples’ -Undefined global functions or variables: - ensemble.samples sa.samples trait.samples +* checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK @@ -119,4 +107,4 @@ Undefined global functions or variables: * checking for detritus in the temp directory ... OK * DONE -Status: 1 WARNING, 2 NOTEs +Status: 1 WARNING, 1 NOTEs From 92c33aa1efc926243a0b9d61afbbb78d9660c2f7 Mon Sep 17 00:00:00 2001 From: Meet Agrawal Date: Sat, 17 Feb 2024 22:38:05 +0530 Subject: [PATCH 2/3] Updated run.write.configs.R --- base/workflow/R/run.write.configs.R | 5 ----- 1 file changed, 5 deletions(-) diff --git a/base/workflow/R/run.write.configs.R b/base/workflow/R/run.write.configs.R index f6b009836a4..00b82bf80ef 100644 --- a/base/workflow/R/run.write.configs.R +++ b/base/workflow/R/run.write.configs.R @@ -82,11 +82,6 @@ run.write.configs <- function(settings, write = TRUE, ens.sample.method = "unifo scipen <- getOption("scipen") options(scipen = 12) - trait.samples <- NULL - sa.samples <- NULL - ensemble.samples <- NULL - runs.samples <- NULL - PEcAn.uncertainty::get.parameter.samples(settings, posterior.files, ens.sample.method) samples.file <- file.path(settings$outdir, "samples.Rdata") if (file.exists(samples.file)) { From 089f2c7ac66f1d673cd72289f38ea85858ac78be Mon Sep 17 00:00:00 2001 From: Meet Agrawal Date: Sun, 18 Feb 2024 12:00:31 +0530 Subject: [PATCH 3/3] commented un-used var --- base/workflow/R/run.write.configs.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/base/workflow/R/run.write.configs.R b/base/workflow/R/run.write.configs.R index 00b82bf80ef..22ed6f3b729 100644 --- a/base/workflow/R/run.write.configs.R +++ b/base/workflow/R/run.write.configs.R @@ -91,7 +91,7 @@ run.write.configs <- function(settings, write = TRUE, ens.sample.method = "unifo ensemble.samples <- samples$ensemble.samples sa.samples <- samples$sa.samples runs.samples <- samples$runs.samples - env.samples <- samples$env.samples + ## env.samples <- samples$env.samples } else { PEcAn.logger::logger.error(samples.file, "not found, this file is required by the run.write.configs function") }