dpc10ster
commented
5 years ago This is the output of the R CMD check on my machine, with the offending lines quoted:
==> Rcpp::compileAttributes()
- Updated R/RcppExports.R
==> devtools::check(args = c('--no-build-vignettes'))
Updating RJafroc documentation Writing NAMESPACE Loading RJafroc Writing NAMESPACE ── Building ─────────────────────────────────────────────────────────────────── RJafroc ── Setting env vars: ● CFLAGS : -Wall -pedantic -fdiagnostics-color=always ● CXXFLAGS : -Wall -pedantic -fdiagnostics-color=always ● CXX11FLAGS: -Wall -pedantic -fdiagnostics-color=always ────────────────────────────────────────────────────────────────────────────────────────── ✔ checking for file ‘/Users/Dev/RJafroc/DESCRIPTION’ ... ─ preparing ‘RJafroc’: (2.7s) ✔ checking DESCRIPTION meta-information ... ─ cleaning src ─ installing the package to build vignettes ✔ creating vignettes (48.1s) ─ cleaning src ─ checking for LF line-endings in source and make files and shell scripts (735ms) ─ checking for empty or unneeded directories ─ looking to see if a ‘data/datalist’ file should be added ─ building ‘RJafroc_1.1.1.9000.tar.gz’
── Checking ─────────────────────────────────────────────────────────────────── RJafroc ── Setting env vars: ● _R_CHECK_CRAN_INCOMING_USEASPELL: TRUE ● _R_CHECK_CRAN_INCOMINGREMOTE : FALSE ● _R_CHECK_CRANINCOMING : FALSE ● _R_CHECK_FORCESUGGESTS : FALSE ── R CMD check ─────────────────────────────────────────────────────────────────
- using log directory ‘/Users/Dev/RJafroc.Rcheck’
- using R version 3.6.0 (2019-04-26)
- using platform: x86_64-apple-darwin15.6.0 (64-bit)
- using session charset: UTF-8
- using options ‘--no-manual --no-build-vignettes --as-cran’
- checking for file ‘RJafroc/DESCRIPTION’ ... OK
- checking extension type ... Package
- this is package ‘RJafroc’ version ‘1.1.1.9000’
- package encoding: UTF-8
- checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' OK
- checking if this is a source package ... OK
- checking if there is a namespace ... OK
- checking for executable files ... OK
- checking for hidden files and directories ... OK
- checking for portable file names ... OK
- checking for sufficient/correct file permissions ... OK
- checking whether package ‘RJafroc’ can be installed ... OK
- checking installed package size ... OK
- checking package directory ... OK
- checking for future file timestamps ... OK
- checking ‘build’ directory ... OK
- checking DESCRIPTION meta-information ... OK
- checking top-level files ... OK
- checking for left-over files ... OK
- checking index information ... OK
- checking package subdirectories ... OK
- checking R files for non-ASCII characters ... OK
- checking R files for syntax errors ... OK
- checking whether the package can be loaded ... OK
- checking whether the package can be loaded with stated dependencies ... OK
- checking whether the package can be unloaded cleanly ... OK
- checking whether the namespace can be loaded with stated dependencies ... OK
- checking whether the namespace can be unloaded cleanly ... OK
- checking dependencies in R code ... OK
- checking S3 generic/method consistency ... OK
- checking replacement functions ... OK
- checking foreign function calls ... OK
- checking R code for possible problems ... OK
- checking Rd files ... OK
- checking Rd metadata ... OK
- checking Rd line widths ... OK
- checking Rd cross-references ... OK
- checking for missing documentation entries ... OK
- checking for code/documentation mismatches ... OK
- checking Rd \usage sections ... OK
- checking Rd contents ... OK
- checking for unstated dependencies in examples ... OK
- checking contents of ‘data’ directory ... OK
- checking data for non-ASCII characters ... OK
- checking data for ASCII and uncompressed saves ... OK
- checking line endings in C/C++/Fortran sources/headers ... OK
- checking pragmas in C/C++ headers and code ... OK
- checking compilation flags used ... OK
- checking compiled code ... OK
- checking installed files from ‘inst/doc’ ... OK
- checking files in ‘vignettes’ ... OK
- checking examples ... OK
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... Running ‘testthat.R’ [304s/307s] OK
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes in ‘inst/doc’ ... OK
- checking running R code from vignettes ... ‘Ch00V1DataFormat.Rmd’ using ‘UTF-8’ ... OK ‘Ch10V1QuickStartDBMH.Rmd’ using ‘UTF-8’ ... OK ‘Ch10V2QuickStartDBMHExcel.Rmd’ using ‘UTF-8’ ... OK ‘Ch11V1SampleSize.Rmd’ using ‘UTF-8’ ... OK ‘Ch11V2SampleSize.Rmd’ using ‘UTF-8’ ... OK ‘Ch11V3SampleSize.Rmd’ using ‘UTF-8’ ... OK ‘Ch11V4SampleSize.Rmd’ using ‘UTF-8’ ... OK ‘Ch11V5SampleSize.Rmd’ using ‘UTF-8’ ... OK ‘Ch20V1improperROCs.Rmd’ using ‘UTF-8’ ... OK ‘Ch20V2degenerateROCs.Rmd’ using ‘UTF-8’ ... OK ‘Ch20V3proprocROCs.Rmd’ using ‘UTF-8’ ... OK ‘Ch20V4metzEqn36.Rmd’ using ‘UTF-8’ ... OK ‘Ch20V5cbmPlots.Rmd’ using ‘UTF-8’ ... OK ‘Ch30V1RoiParadigm.Rmd’ using ‘UTF-8’ ... OK ‘Ch30V2RoiParadigmSt.Rmd’ using ‘UTF-8’ ... OK NONE
- checking re-building of vignette outputs ... SKIPPED
- DONE
Status: OK
── R CMD check results ───────────────────────────────── RJafroc 1.1.1.9000 ──── Duration: 7m 24.6s
0 errors ✔ | 0 warnings ✔ | 0 notes ✔
R CMD check succeeded
pwep
codecov[bot]
I have pushed my edits to the
testthatfolder. With about 560 tests, I believe it is time to move on to CRAN submission process and final testing. The main work remaining here is to bring the standard of the code in all test files to that intest-significance-testing.Rwhich I can do for the next submission.Can you review the
DESCRIPTIONfile? Particularly the authors. You have played a critical part in this project and I want to give you full credit. Also, please review thecran-comments.mdand summarize your fixes to the Solaris problem? And theREADME.md- I need to include your contributions here. All edits will be much appreciated. No rush, just give me a general idea.RJafrocpasses all tests on my OSX machine but did generate an unusual warning, which is not listed in the final summary as a warning; strange; the relevant lines are shown below in my next commentCan you run tests on your machines?
When you feel it is appropriate, I suggest another Skype call, as some things are best discussed that way.
I replaced
options(warn = 2)but closed that file (Compare3RocFits.R) with a final call withoptions(warn = 0)