[R-pkg-devel] FW: [CRAN-pretest-archived] CRAN submission bwt 1.1.0

[Hugh Parsonage]

Hi,

There are a few problems with the submission. Probably more than can
be resolved by people on the mailing list. Speaking generally, a
WARNING in a CRAN check is something that *must* be fixed, rather than
something which you can just acknowledge. The two warnings that you
mentioned are that you probably have (in your DESCRIPTION file)

License: GNU General Public License v3.0

when you should have

License: GPL-3

The second warning is about undocumented code objects. You can choose
not to export them, but if you do export them as you currently are,
you will need to document them.

I notice that there are other problems too: consult the links in the
auto-generated email from CRAN, see the 00check file. You should fix
every problem until there are no ERRORS, WARNINGS, or NOTEs.


Best.

On 31 May 2018 at 00:03, khoong Wei Hao <khoongweihao using hotmail.com> wrote:
> Hi Everyone,
>
> I encountered an issue during my submission of my package (see original message below).
>
> I ran checks and tests with testthat::test_dir("tests/") and devtoos::check(), and all seemed fine except some issues with undocumented objects which I did note in the .Rd file, and the documentation appeared in the console as I ran the package. The following is my R console output:
>
>> devtools::check()
> Updating bwt documentation
> Loading bwt
> First time using roxygen2. Upgrading automatically...
> Warning: The existing 'NAMESPACE' file was not generated by roxygen2, and will not be overwritten.
> Setting env vars ----------------------------------------------------------------------------------------------------
> CFLAGS  : -Wall -pedantic
> CXXFLAGS: -Wall -pedantic
> Building bwt --------------------------------------------------------------------------------------------------------
> "C:/PROGRA~1/R/R-33~1.2/bin/x64/R" --no-site-file --no-environ --no-save --no-restore --quiet CMD build  \
>   "C:\Users\khoongwh\Documents\bwt" --no-resave-data --no-manual
>
> * checking for file 'C:\Users\khoongwh\Documents\bwt/DESCRIPTION' ... OK
> * preparing 'bwt':
> * checking DESCRIPTION meta-information ... OK
> * checking for LF line-endings in source and make files
> * checking for empty or unneeded directories Removed empty directory 'bwt/man'
> Removed empty directory 'bwt/tests/testthat'
> * building 'bwt_1.1.0.tar.gz'
>
> Setting env vars ----------------------------------------------------------------------------------------------------
> _R_CHECK_CRAN_INCOMING_ : FALSE
> _R_CHECK_FORCE_SUGGESTS_: FALSE
> Checking bwt --------------------------------------------------------------------------------------------------------
> "C:/PROGRA~1/R/R-33~1.2/bin/x64/R" --no-site-file --no-environ --no-save --no-restore --quiet CMD check  \
>   "C:\Users\khoongwh\AppData\Local\Temp\RtmpKmUMRO/bwt_1.1.0.tar.gz" --as-cran --timings --no-manual
>
> * using log directory 'C:/Users/khoongwh/AppData/Local/Temp/RtmpKmUMRO/bwt.Rcheck'
> * using R version 3.3.2 (2016-10-31)
> * using platform: x86_64-w64-mingw32 (64-bit)
> * using session charset: ISO8859-1
> * using options '--no-manual --as-cran'
> * checking for file 'bwt/DESCRIPTION' ... OK
> * checking extension type ... Package
> * this is package 'bwt' version '1.1.0'
> * package encoding: UTF-8
> * checking package namespace information ... OK
> * checking package dependencies ... OK
> * checking if this is a source package ... OK
> * checking if there is a namespace ... OK
> * checking for .dll and .exe files ... OK
> * checking for hidden files and directories ... OK
> * checking for portable file names ... OK
> * checking whether package 'bwt' can be installed ... OK
> * checking package directory ... OK
> * checking DESCRIPTION meta-information ... WARNING Non-standard license specification:
>   GNU General Public License v3.0
> Standardizable: FALSE
> * 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 loading without being on the library search path ... 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 for missing documentation entries ... WARNING Undocumented code objects:
>   'bwt' 'ibwt'
> All user-level objects in a package should have documentation entries.
> See chapter 'Writing R documentation files' in the 'Writing R Extensions' manual.
> * checking examples ... NONE
> * checking for unstated dependencies in 'tests' ... OK
> * checking tests ...
>   Running 'testthat.R'
> Warning message:
> running command '"C:/PROGRA~1/R/R-33~1.2/bin/x64/R" CMD BATCH --vanilla  "testthat.R" "testthat.Rout"' had status 1  ERROR Running the tests in 'tests/testthat.R' failed.
> Last 13 lines of output:
>
>   Type 'demo()' for some demos, 'help()' for on-line help, or
>   'help.start()' for an HTML browser interface to help.
>   Type 'q()' to quit R.
>
>   > library(testthat)
>   Warning message:
>   package 'testthat' was built under R version 3.3.3
>   > library(bwt)
>   >
>   > test_check("bwt")
>   Error: No tests found for bwt
>   Execution halted
> * DONE
>
> Status: 1 ERROR, 2 WARNINGs
> See
>   'C:/Users/khoongwh/AppData/Local/Temp/RtmpKmUMRO/bwt.Rcheck/00check.log'
> for details.
>
> R CMD check results
> 1 error  | 2 warnings | 0 notes
> checking tests ... ERROR
> Running the tests in 'tests/testthat.R' failed.
> Last 13 lines of output:
>
>   Type 'demo()' for some demos, 'help()' for on-line help, or
>   'help.start()' for an HTML browser interface to help.
>   Type 'q()' to quit R.
>
>   > library(testthat)
>   Warning message:
>   package 'testthat' was built under R version 3.3.3
>   > library(bwt)
>   >
>   > test_check("bwt")
>   Error: No tests found for bwt
>   Execution halted
>
> checking DESCRIPTION meta-information ... WARNING Non-standard license specification:
>   GNU General Public License v3.0
> Standardizable: FALSE
>
> checking for missing documentation entries ... WARNING Undocumented code objects:
>   'bwt' 'ibwt'
> All user-level objects in a package should have documentation entries.
> See chapter 'Writing R documentation files' in the 'Writing R Extensions' manual.
>
> May I know how can I proceed? I am kind of lost a this pint in time, even after looking up CRAN's documentations.. If it helps, attached in this email is my .tar.gz file which I have submitted earlier.
>
> Thank you and I apologize for any inconvenience that I may have caused..
>
> Warmest Regards,
>
> Wei Hao Khoong (Mr)
>
> -----Original Message-----
> From: Uwe.Ligges using R-Project.org <Uwe.Ligges using R-Project.org>
> Sent: Wednesday, 30 May 2018 12:11 AM
> To: khoongweihao using hotmail.com
> Cc: CRAN-submissions using R-project.org
> Subject: [CRAN-pretest-archived] CRAN submission bwt 1.1.0
>
> Dear maintainer,
>
> package bwt_1.1.0.tar.gz does not pass the incoming checks automatically, please see the following pre-tests:
>
>
> Status: 3 WARNINGs, 3 NOTEs
> Debian: <https://win-builder.r-project.org/incoming_pretest/bwt_1.1.0_20180529_101440/Debian/00check.log>
> Status: 3 WARNINGs, 3 NOTEs
>
>
>
> Please fix all problems and resubmit a fixed version via the webform.
> If you are not sure how to fix the problems shown, please ask for help on the R-package-devel mailing list:
> <https://stat.ethz.ch/mailman/listinfo/r-package-devel>
> If you are fairly certain the rejection is a false positive, please reply-all to this message and explain.
>
> More details are given in the directory:
> <https://win-builder.r-project.org/incoming_pretest/bwt_1.1.0_20180529_101440/>
> The files will be removed after roughly 7 days.
>
> No strong reverse dependencies to be checked.
>
> Best regards,
> CRAN teams' auto-check service
>
> ______________________________________________
> R-package-devel using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>