Version 1.4 Submission

22.11.2024

Test environments

Local R installation, R 4.4.0
Ubuntu 24.04 (on GitHub Actions), R 4.4.0
Win-builder (devel)

Submission comments

Added addStructure and setSuperpose functions to load and overlap multiple structures in the same stage.
Updated internal logic with R 4.3.0's stricter && and || evaluations to prevent errors with multi-element vectors.

Round 3

Test environments

local R installation, R 4.0.4
ubuntu 16.04 (on travis-ci), R 4.0.4
win-builder (devel)

Submission comments

Provided \value to remaining functions

Reviewer comments

Please add \value to .Rd files regarding exported methods and explain the functions results in the documentation. Please write about the structure of the output (class) and also what the output means. (If a function does not return a value, please document that too, e.g. \value{No return value, called for side effects} or similar) Missing Rd-tags: addRepresentation.Rd: \value setFocus.Rd: \value setQuality.Rd: \value setRock.Rd: \value setSpin.Rd: \value stageParameters.Rd: \value zoomMove.Rd: \value

Round 2

26.05.21

Test environments

local R installation, R 4.0.4
ubuntu 16.04 (on travis-ci), R 4.0.4
win-builder (devel)

Submission comments

Reduced the length of the title
Provided \value to applicable methods
Added single quotes if applicable in description
Added link to htmlwidgets and NGL website in description

Reviewer comments

Please reduce the length of the tile to less than 65 characters .
Please add \value to .Rd files regarding exported methods and explain the functions results in the documentation. Please write about the structure of the output (class) and also what the output means. (If a function does not return a value, please document that too, e.g. \value{No return value, called for side effects} or similar) Missing Rd-tags in up to 23 .Rd files, e.g.: addRepresentation.Rd: \value addSelection.Rd: \value NGLVieweR_example.Rd: \value NGLVieweR-shiny.Rd: \value NGLVieweR.Rd: \value removeSelection.Rd: \value ...
Please always write package names, software names and API (application programming interface) names in single quotes in title and description. e.g: --> 'NGLvieweR'
Please provide a link to the used webservices to the description field of your DESCRIPTION file in the form 'http:...' or 'https:...' with angle brackets for auto-linking and no space after 'http:' and 'https:'.

Round 1

25.05.2021

Test environments

local R installation, R 4.0.4
ubuntu 16.04 (on travis-ci), R 4.0.4
win-builder (devel)

Submission comments

'LazyData' is specified without a 'data' directory

Error fixed by removing LazyData from DESCRIPTION

R CMD check results

0 errors | 0 warnings | 3 notes

This is a new release.
Possibly mis-spelled words in DESCRIPTION: Databank (2:30) NGL (3:13) NGLvieweR (9:5) PDB (2:40, 9:76) databank (9:66) js (3:17)

These are abbreviations.

Found the following (possibly) invalid URLs: URL: https://niels-van-der-velden.shinyapps.io/shinyNGLVieweR/ From: inst/doc/NGLVieweR.html README.md Status: Error Message: libcurl error code 35: schannel: next InitializeSecurityContext failed: SEC_E_ILLEGAL_MESSAGE (0x80090326) - This error usually occurs when a fatal SSL/TLS alert is received (e.g. handshake failed).

I checked the URL and the website loads fine.