0.3.5

.Rbuildignore

@@ -4,3 +4,6 @@
 ^README\.Rmd$
 ^\.github$
 ^codecov\.yml$
+^cran-comments\.md$
+^revdep$
+^CRAN-SUBMISSION$

CRAN-SUBMISSION

@@ -0,0 +1,3 @@
+Version: 0.3.4
+Date: 2024-07-28 00:17:35 UTC
+SHA: fe7b689d67185647ced81f0ffe43174c58b9867f

DESCRIPTION

@@ -1,10 +1,11 @@
 Package: SCFMonitor
-Title: Clear monitor and graphing software processing Gaussian .log file
-Version: 0.3.3.1000
+Title: Clear Monitor and Graphing Software Processing Gaussian .log File
+Version: 0.3.5
 Authors@R: 
     person("Pengjun", "Guo", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0009-0007-2717-0519"))
-Description: SCFMonitor enables Gaussian the quantum chemistry calculation software users to easily read the Gaussian .log files and monitor the SCF convergence and geometry optimization process with little effort and clear, beautiful and clean outputs. It can generate graphs using tidyverse to let users check SCF convergence and geometry optimization process real time. The software supports processing .log files remotely using with rbase::url(). This software is a suitcase for saving time and energy for the researchers, supporting multiple versions of Gaussian.
+Description: Self-Consistent Field(SCF) calculation method is one of the most important steps in the calculation methods of quantum chemistry. Ehrenreich, H., & Cohen, M. H. (1959). <doi:10.1103/PhysRev.115.786> However, the most prevailing software in this area, 'Gaussian''s SCF convergence process is hard to monitor, especially while the job is still running, causing researchers difficulty in knowing whether the oscillation has started or not, wasting time and energy on useless configurations or abandoning the jobs that can actually work. M.J. Frisch, G.W. Trucks, H.B. Schlegel et al. (2016). <https://gaussian.com> 'SCFMonitor' enables 'Gaussian' quantum chemistry calculation software users to easily read the 'Gaussian' .log files and monitor the SCF convergence and geometry optimization process with little effort and clear, beautiful, and clean outputs. It can generate graphs using 'tidyverse' to let users check SCF convergence and geometry optimization processes in real-time. The software supports processing .log files remotely using with rbase::url(). This software is a suitcase for saving time and energy for the researchers, supporting multiple versions of 'Gaussian'.
+Maintainer: Pengjun Guo <[email protected]>
 License: MIT + file LICENSE
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)

NEWS.md

@@ -1,3 +1,7 @@
-# SCFMonitor (development version)
+# SCFMonitor 0.3.5
 
-* Initial CRAN submission.
+This is a resubmission. In this version I have:
+
+* Changed the documentation of the functions in which return value is not in presence.
+
+* Add citation in the DESCRIPTION.

R/DirectingOptiRounds.R

@@ -3,7 +3,7 @@
 #' This function is a internal function that directs the optimization round of a SCF convergence round. This helps SCFMonitor devide the SCF rounds to different sections that each refers to an optimization cycle.
 #' @param Pending A integer refering to the row of the directed SCF convergence cycle is in.
 #' @param index A tibble including all the row number
-#' @return A integer directing the Optimization round of that SCF convergence round is in.
+#' @returns A integer directing the Optimization round of that SCF convergence round is in.
 #' @export
 #' @examples
 #' library(tibble)

R/FormOptiSCFConvergenceRoundTibble.R

@@ -2,7 +2,7 @@
 #'
 #' This function outputs a tibble showing each the number of SCF rounds applied in each optimization cycle and outputs it as a tibble.
 #' @param directory A string vector describing the directory of the Gaussian log file.
-#' @return A tibble countain two columns, describing each optimization rounds and the number of SCF rounds it undergoes until convergence.
+#' @returns A tibble countain two columns, describing each optimization rounds and the number of SCF rounds it undergoes until convergence.
 #' @importFrom readr read_file
 #' @importFrom stringr str_split str_detect str_trim
 #' @importFrom tidyselect starts_with

R/MultipleRoundOptiSCFIntegratedMonitor.R

@@ -3,6 +3,7 @@
 #' This function reads a log file automatically and shows the SCF convergence process of it by generating line plots
 #' @param directory A string vector describing the directory of the Gaussian log file.
 #' @param top_rounds A numeric vector deciding which SCF convergence process will be shown in the diagram. etc. input 5 for the newest 5 rounds of optimization. Enter -1 for showing all the processes.
+#' @returns No return value, called for side effects
 #' @export
 #' @examples
 #'

R/MultipleRoundOptiSCFplotting.R

@@ -5,6 +5,7 @@
 #' @param SCFconver A numeric vector showing the SCF convergence requirement read from the gaussian .log file.
 #' @param BOT A numeric vector describing the starting optimization round for plotting
 #' @param TOP A numeric vector describing the ending optimization round for plotting
+#' @returns No return value, called for side effects
 #' @importFrom tidyr pivot_longer
 #' @importFrom dplyr mutate filter
 #' @importFrom stringr str_replace

R/OptiConvergenceMonitor.R

@@ -2,6 +2,7 @@
 #'
 #' This function reads a log file automatically and shows the optimization convergence process of it by generating line plots
 #' @param directory A string vector describing the directory of the Gaussian log file.
+#' @returns No return value, called for side effects
 #' @importFrom readr read_file
 #' @importFrom stringr str_split str_detect str_trim str_replace str_sub
 #' @importFrom tidyselect starts_with

R/OptiSCFConvergenceRoundMonitor.R

@@ -2,6 +2,7 @@
 #'
 #' This function reads a log file automatically and generate a plot showing the steps it takes to reach SCF convergence for each optimization process.
 #' @param directory A string vector describing the directory of the Gaussian log file.
+#' @returns No return value, called for side effects
 #' @importFrom ggplot2 ggplot aes geom_line geom_smooth theme_minimal
 #' @export
 #' @examples

R/OptiSCFMonitorAsList.R

@@ -2,7 +2,7 @@
 #'
 #' This function reads a Gaussian .log file and outputs a list of tibbles, each of which is the SCF Data of a optimization step.
 #' @param directory A string vector describing the directory of the Gaussian log file.
-#' @return A list of lists. First lists is a list of tibble, each element in the list refers to a tibble recording the SCF Data of a optimization step. The second list only have one element that is a numeric vector refering to the SCF convergence requirement read from log file.
+#' @returns A list of lists. First lists is a list of tibble, each element in the list refers to a tibble recording the SCF Data of a optimization step. The second list only have one element that is a numeric vector refering to the SCF convergence requirement read from log file.
 #' @importFrom readr read_file
 #' @importFrom stringr str_split str_detect str_trim str_replace str_extract
 #' @importFrom tidyselect starts_with

R/OptiSCFMonitorAsWholeTibble.R

@@ -2,7 +2,7 @@
 #'
 #' This function outputs a tibble containing the data of each rounds of SCF calculation labeled with the optimization round it's in (if it's a optimization job, otherwise it will be only 1)
 #' @param directory A string vector describing the directory of the Gaussian log file.
-#' @return A list containing two elements. The first one is a tibble containing the SCF data of every rounds labeled with the optimization steps they are in. The second element is a numeric vector that refers to the SCF convergence standard.
+#' @returns A list containing two elements. The first one is a tibble containing the SCF data of every rounds labeled with the optimization steps they are in. The second element is a numeric vector that refers to the SCF convergence standard.
 #' @importFrom readr read_file
 #' @importFrom stringr str_split str_detect str_extract str_replace str_trim
 #' @importFrom utils head

R/SCFMonitorExample.R

@@ -1,7 +1,7 @@
 #' Acquire Path to SCFMonitor Example data
 #'
 #' Makes the TestData.log, a log file generated by Gaussian 16 for testing the package, easy to access.
-#' @return A string vector showing the path to
+#' @returns A string vector showing the path to
 #' @export
 #' @examples
 #' FormOptiSCFConvergenceRoundTibble(SCFMonitorExample())

R/SingleRoundOptiSCFIntegratedMonitor.R

@@ -3,6 +3,7 @@
 #' This function reads a log file automatically and shows the SCF convergence process of a single round of optimization by generating line plots
 #' @param directory A string vector describing the directory of the Gaussian log file.
 #' @param optiround A numeric vector deciding which SCF convergence process will be shown in the diagram. etc. input 5 for the 5th round of optimization. If it's not an optimization job than enter 1 for acquiring the only one.
+#' @returns No return value, called for side effects
 #' @export
 #' @examples
 #'

R/SingleSCFplotting.R

@@ -3,6 +3,7 @@
 #' An internal function plots the generated single-round SCF convergence tibble
 #' @param SCFData The tibble generated by SingleRoundOptiSCFIntegratedMonitor() describing the SCF convergence process for single round of optimization(or other Gaussian job types).
 #' @param SCFconver A numeric vector showing the SCF convergence requirement read from the gaussian .log file.
+#' @returns No return value, called for side effects
 #' @importFrom tidyr pivot_longer
 #' @importFrom dplyr mutate
 #' @importFrom stringr str_replace

README.Rmd

@@ -30,8 +30,8 @@ SCF monitor works for the `.log` files of the jobs that is still under calculati
 You can install the development version of SCFMonitor from [GitHub](https://github.com/) with:
 
 ``` r
-# install.packages("devtools")
-devtools::install_github("AzuleneG/SCFMonitor")
+install.packages("SCFMonitor")
+library(SCFMonitor)
 ```
 
 ## Function and Example

README.md

@@ -31,8 +31,8 @@ You can install the development version of SCFMonitor from
 [GitHub](https://github.com/) with:
 
 ``` r
-# install.packages("devtools")
-devtools::install_github("AzuleneG/SCFMonitor")
+install.packages("SCFMonitor")
+library(SCFMonitor)
 ```
 
 ## Function and Example

cran-comments.md

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+## R CMD check results
+
+0 errors | 0 warnings | 0 note
+
+* This is a new release.

revdep/.gitignore

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+checks
+library
+checks.noindex
+library.noindex
+cloud.noindex
+data.sqlite
+*.html

revdep/README.md

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+# Platform
+
+|field    |value                                    |
+|:--------|:----------------------------------------|
+|version  |R version 4.4.1 (2024-06-14)             |
+|os       |macOS Sonoma 14.2.1                      |
+|system   |aarch64, darwin20                        |
+|ui       |RStudio                                  |
+|language |(EN)                                     |
+|collate  |en_US.UTF-8                              |
+|ctype    |en_US.UTF-8                              |
+|tz       |America/Los_Angeles                      |
+|date     |2024-07-27                               |
+|rstudio  |2024.04.2+764 Chocolate Cosmos (desktop) |
+|pandoc   |NA                                       |
+
+# Dependencies
+
+|package    |old |new        |Δ  |
+|:----------|:---|:----------|:--|
+|SCFMonitor |NA  |0.3.3.1000 |*  |
+|colorspace |NA  |2.1-1      |*  |
+
+# Revdeps
+

revdep/cran.md

@@ -0,0 +1,7 @@
+## revdepcheck results
+
+We checked 0 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package.
+
+ * We saw 0 new problems
+ * We failed to check 0 packages
+

revdep/failures.md

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+*Wow, no problems at all. :)*

revdep/problems.md

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+*Wow, no problems at all. :)*