cran-comments.md

In devSJR/PCRedux: Quantitative Polymerase Chain Reaction (qPCR) Data Mining and Machine Learning Toolkit

Note

• The previous version of the package was taken from CRAN because an e-mail address in the chiPPCR package had reached EOL. This caused the arching of the MBmca, the chipPCR and the PCRedux package. Both the MBmca and the chipPCR package are back on CRAN.
  • The package was Submitted some days ago. However, this submission needed the addition of \value{} and fixes to \dontrun{}.
• The package is feature complete, parts of it were published (peer-reviewed) and used by peers use it. Therefore we change to version 1.0+
• Fixes of this submission include in total
  • addition of the \value{} tag
  • Fixes to \dontrun{}
  • Grammar and spelling corrections
  • The PCRedux package now has a cran-comments.md file
  • The PCRedux package has been tested with rhub
  • In DESCRIPTION, all authors now have an ORCID
  • The documentation of the pcrfit_single() function was improved
  • RoxygenNote is now on version 7.1.1 (previously 5.0.1)
  • Citations in the vignettes were revised
  • We make sure that we do not change the user's options, par or working directory
  • NEWS updated

Test environments

• local R installation, R 4.0.3
• ubuntu 16.04 (on travis-ci), R 4.0.3
• win-builder (devel)

R CMD check results

0 errors | 0 warnings | 1 note

• This is a new release.

check_rhub(env_vars=c(R_COMPILE_AND_INSTALL_PACKAGES = "always"))

✔ checking for file ‘/home/tux/Work/paper/PCRedux_all/PCRedux/DESCRIPTION’ (394ms) ─ preparing ‘PCRedux’: (652ms) ✔ checking DESCRIPTION meta-information ─ installing the package to build vignettes ✔ creating vignettes (18.5s) ─ checking for LF line-endings in source and make files and shell scripts ─ checking for empty or unneeded directories Removed empty directory ‘PCRedux/inst/PCRedux-app’ ─ building ‘PCRedux_1.1.tar.gz’

─ Uploading package ─ Preparing build, see status at https://builder.r-hub.io/status/PCRedux_1.1.tar.gz-6a71115909ea448badfdaf9822a657cc https://builder.r-hub.io/status/PCRedux_1.1.tar.gz-1550daa457e44f58aa6ef3c8f64a55af https://builder.r-hub.io/status/PCRedux_1.1.tar.gz-d9da8c4f46a94d73b8434eb601412329 ─ Build started ─ Creating new user ─ Downloading and unpacking package file ─ Querying package dependencies ─ Installing package dependencies ─ Running R CMD check setting R_CHECK_FORCE_SUGGESTS to false setting R_COMPILE_AND_INSTALL_PACKAGES to never setting R_CHECK_THINGS_IN_CHECK_DIR to false setting R_REMOTES_STANDALONE to true setting R_REMOTES_NO_ERRORS_FROM_WARNINGS to true setting R_COMPILE_AND_INSTALL_PACKAGES to always ─ using log directory 'C:/Users/USERChvwNfyzxk/PCRedux.Rcheck' ─ using R Under development (unstable) (2021-02-15 r80013) ─ using platform: x86_64-w64-mingw32 (64-bit) ─ using session charset: ISO8859-1 ─ using option '--as-cran' ✔ checking for file 'PCRedux/DESCRIPTION' ─ checking extension type ... Package ─ this is package 'PCRedux' version '1.1' ─ package encoding: UTF-8 N checking CRAN incoming feasibility Maintainer: 'Stefan Roediger [e-mail]'

New submission Package was archived on CRAN

CRAN repository db overrides: X-CRAN-Comment: Archived on 2020-12-16 as requires archived package 'chipPCR'. ✔ checking package namespace information ✔ checking package dependencies ✔ checking if this is a source package ✔ checking if there is a namespace ✔ checking for executable files ✔ checking for hidden files and directories ✔ checking for portable file names ✔ checking whether package 'PCRedux' can be installed ✔ checking installed package size ✔ checking package directory ✔ checking for future file timestamps ✔ checking 'build' directory ✔ checking DESCRIPTION meta-information ✔ checking top-level files ✔ checking for left-over files ✔ checking index information ✔ checking package subdirectories ✔ checking R files for non-ASCII characters ✔ checking R files for syntax errors ✔ checking whether the package can be loaded ✔ checking whether the package can be loaded with stated dependencies ✔ checking whether the package can be unloaded cleanly ✔ checking whether the namespace can be loaded with stated dependencies ✔ checking whether the namespace can be unloaded cleanly ✔ checking loading without being on the library search path ✔ checking use of S3 registration ✔ checking dependencies in R code ✔ checking S3 generic/method consistency ✔ checking replacement functions ✔ checking foreign function calls ✔ checking R code for possible problems ✔ checking Rd files ✔ checking Rd metadata ✔ checking Rd line widths ✔ checking Rd cross-references ✔ checking for missing documentation entries ✔ checking for code/documentation mismatches ✔ checking Rd \usage sections ✔ checking Rd contents ✔ checking for unstated dependencies in examples ✔ checking contents of 'data' directory ✔ checking data for non-ASCII characters ✔ checking data for ASCII and uncompressed saves N checking sizes of PDF files under 'inst/doc' Unable to find GhostScript executable to run checks on size reduction ✔ checking installed files from 'inst/doc' ✔ checking files in 'vignettes' ✔ checking examples ✔ checking examples with --run-donttest ✔ checking for unstated dependencies in 'tests' ─ checking tests ✔ Running 'spelling.R' ✔ Running 'testthat.R' ✔ checking for unstated dependencies in vignettes ✔ checking package vignettes in 'inst/doc' ✔ checking re-building of vignette outputs ✔ checking PDF version of manual ✔ checking for non-standard things in the check directory ✔ checking for detritus in the temp directory

─ Done with R CMD check ─ Cleaning up files and user

── PCRedux 1.1: NOTE

Build ID: PCRedux_1.1.tar.gz-6a71115909ea448badfdaf9822a657cc Platform: Windows Server 2008 R2 SP1, R-devel, 32/64 bit Submitted: 6m 50s ago Build time: 6m 31.1s

❯ checking CRAN incoming feasibility ... NOTE Maintainer: 'Stefan Roediger [e-mail]'

New submission Package was archived on CRAN

CRAN repository db overrides: X-CRAN-Comment: Archived on 2020-12-16 as requires archived package 'chipPCR'.

❯ checking sizes of PDF files under 'inst/doc' ... NOTE Unable to find GhostScript executable to run checks on size reduction

0 errors ✔ | 0 warnings ✔ | 2 notes ✖

── PCRedux 1.1: CREATED

Build ID: PCRedux_1.1.tar.gz-1550daa457e44f58aa6ef3c8f64a55af Platform: Ubuntu Linux 20.04.1 LTS, R-release, GCC Submitted: 6m 50s ago

── PCRedux 1.1: CREATED

Build ID: PCRedux_1.1.tar.gz-d9da8c4f46a94d73b8434eb601412329 Platform: Fedora Linux, R-devel, clang, gfortran Submitted: 6m 50s ago

devSJR/PCRedux documentation built on Aug. 3, 2022, 1:34 p.m.