From 78d421dc463dbfb993e372073c8de406d1f45da7 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 16 Nov 2022 14:51:17 +0100 Subject: Update DESCRIPTION and NEWS, check and test --- log/check.log | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'log/check.log') diff --git a/log/check.log b/log/check.log index 3fea2ec6..7aa4610c 100644 --- a/log/check.log +++ b/log/check.log @@ -41,7 +41,7 @@ Maintainer: ‘Johannes Ranke ’ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK -* checking R code for possible problems ... [14s/14s] OK +* checking R code for possible problems ... [18s/18s] OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK @@ -57,7 +57,7 @@ Maintainer: ‘Johannes Ranke ’ * checking data for ASCII and uncompressed saves ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK -* checking examples ... [15s/15s] OK +* checking examples ... [20s/20s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... SKIPPED * checking for unstated dependencies in vignettes ... OK -- cgit v1.2.1 From 5364f037a72863ef5ba81e14ba4417f68fd389f9 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 18 Nov 2022 19:14:47 +0100 Subject: Make mixed model test data permanent to ensure reproducibility To ensure that tests on different platforms work on the same data, the mixed modelling test data previosly generated in tests/testthat/setup_script.R were generated once using the script in inst/dataset/generation/ds_mixed.R, and are now distributed with the package. --- log/check.log | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'log/check.log') diff --git a/log/check.log b/log/check.log index 7aa4610c..31fc31eb 100644 --- a/log/check.log +++ b/log/check.log @@ -5,7 +5,7 @@ * using options ‘--no-tests --as-cran’ * checking for file ‘mkin/DESCRIPTION’ ... OK * checking extension type ... Package -* this is package ‘mkin’ version ‘1.2.0’ +* this is package ‘mkin’ version ‘1.2.1’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... Note_to_CRAN_maintainers Maintainer: ‘Johannes Ranke ’ @@ -41,7 +41,7 @@ Maintainer: ‘Johannes Ranke ’ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK -* checking R code for possible problems ... [18s/18s] OK +* checking R code for possible problems ... [17s/17s] OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK -- cgit v1.2.1 From 74e44dfed5af6e6fd421abe82d3e3f190771f85a Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 1 Dec 2022 11:20:00 +0100 Subject: Possibility to manually specify no_random_effects in mhmkin --- log/check.log | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) (limited to 'log/check.log') diff --git a/log/check.log b/log/check.log index 31fc31eb..42365918 100644 --- a/log/check.log +++ b/log/check.log @@ -5,7 +5,7 @@ * using options ‘--no-tests --as-cran’ * checking for file ‘mkin/DESCRIPTION’ ... OK * checking extension type ... Package -* this is package ‘mkin’ version ‘1.2.1’ +* this is package ‘mkin’ version ‘1.2.2’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... Note_to_CRAN_maintainers Maintainer: ‘Johannes Ranke ’ @@ -18,7 +18,7 @@ Maintainer: ‘Johannes Ranke ’ * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking serialization versions ... OK -* checking whether package ‘mkin’ can be installed ... OK +* checking whether package ‘mkin’ can be installed ... [11s/11s] OK * checking installed package size ... OK * checking package directory ... OK * checking for future file timestamps ... OK @@ -41,7 +41,7 @@ Maintainer: ‘Johannes Ranke ’ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK -* checking R code for possible problems ... [17s/17s] OK +* checking R code for possible problems ... [19s/19s] OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK @@ -57,7 +57,7 @@ Maintainer: ‘Johannes Ranke ’ * checking data for ASCII and uncompressed saves ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK -* checking examples ... [20s/20s] OK +* checking examples ... [24s/24s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... SKIPPED * checking for unstated dependencies in vignettes ... OK -- cgit v1.2.1 From 886c9ef013124aa954d960c655b349b5340ff154 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 19 Dec 2022 12:31:56 +0100 Subject: Rename template folder, create format Instead of rmarkdown::pdf_document, mkin::hierarchical_kinetics is used as a document format in the template. In this way, the template file can be freed from some R code and yaml options that the average user does not have to be aware of. --- log/check.log | 21 ++++++++++++++++----- 1 file changed, 16 insertions(+), 5 deletions(-) (limited to 'log/check.log') diff --git a/log/check.log b/log/check.log index 42365918..aec61e33 100644 --- a/log/check.log +++ b/log/check.log @@ -1,5 +1,5 @@ * using log directory ‘/home/jranke/git/mkin/mkin.Rcheck’ -* using R version 4.2.2 (2022-10-31) +* using R version 4.2.2 Patched (2022-11-10 r83330) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using options ‘--no-tests --as-cran’ @@ -18,7 +18,7 @@ Maintainer: ‘Johannes Ranke ’ * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking serialization versions ... OK -* checking whether package ‘mkin’ can be installed ... [11s/11s] OK +* checking whether package ‘mkin’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking for future file timestamps ... OK @@ -41,7 +41,14 @@ Maintainer: ‘Johannes Ranke ’ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK -* checking R code for possible problems ... [19s/19s] OK +* checking R code for possible problems ... NOTE +parplot.multistart.saem.mmkin: no visible global function definition + for ‘quantile’ +Undefined global functions or variables: + quantile +Consider adding + importFrom("stats", "quantile") +to your NAMESPACE file. * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK @@ -57,7 +64,7 @@ Maintainer: ‘Johannes Ranke ’ * checking data for ASCII and uncompressed saves ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK -* checking examples ... [24s/24s] OK +* checking examples ... [11s/11s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... SKIPPED * checking for unstated dependencies in vignettes ... OK @@ -69,5 +76,9 @@ Maintainer: ‘Johannes Ranke ’ * checking for detritus in the temp directory ... OK * DONE -Status: OK +Status: 1 NOTE +See + ‘/home/jranke/git/mkin/mkin.Rcheck/00check.log’ +for details. + -- cgit v1.2.1 From 24eb77216700cf8b2f2bde3abad84c1f83f9e32a Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 9 Jan 2023 06:22:04 +0100 Subject: Prebuilt PDF vignettes, summary_listing --- log/check.log | 34 ++++++++++++++++++++++------------ 1 file changed, 22 insertions(+), 12 deletions(-) (limited to 'log/check.log') diff --git a/log/check.log b/log/check.log index aec61e33..a81475d9 100644 --- a/log/check.log +++ b/log/check.log @@ -7,11 +7,28 @@ * checking extension type ... Package * this is package ‘mkin’ version ‘1.2.2’ * package encoding: UTF-8 -* checking CRAN incoming feasibility ... Note_to_CRAN_maintainers +* checking CRAN incoming feasibility ... NOTE Maintainer: ‘Johannes Ranke ’ + +Size of tarball: 6636884 bytes * checking package namespace information ... OK * checking package dependencies ... OK -* checking if this is a source package ... OK +* checking if this is a source package ... NOTE +Found the following apparent object files/libraries: + vignettes/2022_wp_1/cyan_dlls/dfop_path_1.so + vignettes/2022_wp_1/cyan_dlls/dfop_path_2.so + vignettes/2022_wp_1/cyan_dlls/fomc_path_1.so + vignettes/2022_wp_1/cyan_dlls/fomc_path_2.so + vignettes/2022_wp_1/cyan_dlls/hs_path_1.so + vignettes/2022_wp_1/cyan_dlls/sfo_path_1.so + vignettes/2022_wp_1/cyan_dlls/sforb_path_1.so + vignettes/2022_wp_1/cyan_dlls/sforb_path_2.so + vignettes/2022_wp_1/dmta_dlls/m_dfop_path.so + vignettes/2022_wp_1/dmta_dlls/m_fomc_path.so + vignettes/2022_wp_1/dmta_dlls/m_hs_path.so + vignettes/2022_wp_1/dmta_dlls/m_sfo_path.so + vignettes/2022_wp_1/dmta_dlls/m_sforb_path.so +Object files/libraries should not be included in a source package. * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK @@ -41,14 +58,7 @@ Maintainer: ‘Johannes Ranke ’ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK -* checking R code for possible problems ... NOTE -parplot.multistart.saem.mmkin: no visible global function definition - for ‘quantile’ -Undefined global functions or variables: - quantile -Consider adding - importFrom("stats", "quantile") -to your NAMESPACE file. +* checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK @@ -64,7 +74,7 @@ to your NAMESPACE file. * checking data for ASCII and uncompressed saves ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK -* checking examples ... [11s/11s] OK +* checking examples ... [10s/10s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... SKIPPED * checking for unstated dependencies in vignettes ... OK @@ -76,7 +86,7 @@ to your NAMESPACE file. * checking for detritus in the temp directory ... OK * DONE -Status: 1 NOTE +Status: 2 NOTEs See ‘/home/jranke/git/mkin/mkin.Rcheck/00check.log’ for details. -- cgit v1.2.1