tests fail #419

nunotexbsd · 2024-12-06T09:19:33Z

Trying to find if a missing dependency is causing testunit to fail.
Tested on 0.5.0 and 0.5.1.

Any clues?

Thanks

> sessionInfo()
R version 4.4.2 (2024-10-31)
Platform: amd64-portbld-freebsd15.0
Running under: FreeBSD 15amd64-main 15.0-CURRENT FreeBSD 15.0-CURRENT 1500028 amd64

Matrix products: default
LAPACK: /usr/local/lib/R/lib/libRlapack.so;  LAPACK version 3.12.0

locale:
[1] C.UTF-8/C.UTF-8/C.UTF-8/C/C.UTF-8/C.UTF-8

time zone: Europe/Lisbon
tzcode source: system (FreeBSD)

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

loaded via a namespace (and not attached):
[1] compiler_4.4.2

<snip>
* checking examples ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ...
  'FAQ.Rmd' using 'UTF-8'... failed
  'converting.Rmd' using 'UTF-8'... OK
  'cpp11.Rmd' using 'UTF-8'... failed
  'internals.Rmd' using 'UTF-8'... OK
  'motivations.Rmd' using 'UTF-8'... failed
 ERROR
Errors in running code in vignettes:
when running code in 'FAQ.Rmd'
  ...

> add_some <- function(x, amount = 1) {
+     add_some_(x, amount)
+ }

> add_some(1)

  When sourcing 'FAQ.R':
Error: could not find function "add_some_"
Execution halted
when running code in 'cpp11.Rmd'
  ...
> 600/(0.005 - 0.002)
[1] 2e+05

> mod <- lm(mpg ~ wt, data = mtcars)

> mpe(mod)

  When sourcing 'cpp11.R':
Error: could not find function "mpe"
Execution halted
when running code in 'motivations.Rmd'
  ...
[1] 2 4 6

> x
[1] 1 2 3

> z <- times_two_rcpp(x)

  When sourcing 'motivations.R':
Error: could not find function "times_two_rcpp"
Execution halted

* checking re-building of vignette outputs ... SKIPPED
* DONE
Status: 1 ERROR, 1 NOTE
*** Error code 1

Full log:
00check.log

The text was updated successfully, but these errors were encountered:

pachadotdev · 2024-12-17T07:39:54Z

@nunotexbsd the full log says Rcpp is missing, and hence the times_two_rcpp cannot be compiled

you need to install these mentioned in the log

Packages suggested but not available for checking:
  'covr', 'ggplot2', 'lobstr', 'rmarkdown', 'scales', 'Rcpp'

nunotexbsd · 2024-12-17T11:07:16Z

@pachadotdev
Hello,

I think I have all dependencies covered in port.
Do you mind take a look?

Thanks!

TEST_DEPENDS=   R-cran-covr>0:devel/R-cran-covr \
                R-cran-decor>0:devel/R-cran-decor \
                R-cran-ggplot2>0:graphics/R-cran-ggplot2 \
                R-cran-knitr>0:print/R-cran-knitr \
                R-cran-mockery>0:devel/R-cran-mockery \
                R-cran-progress>0:devel/R-cran-progress \
                R-cran-Rcpp>0:devel/R-cran-Rcpp \
                R-cran-rmarkdown>0:textproc/R-cran-rmarkdown \
                R-cran-scales>0:graphics/R-cran-scales \
                R-cran-testthat>0:devel/R-cran-testthat
pre-test:
# R-cran-bench package does not exist yet
        @${LOCALBASE}/bin/Rscript -e 'install.packages("bench", \
                repos = "https://cloud.r-project.org")'
# R-cran-lobstr package does not exist yet
        @${LOCALBASE}/bin/Rscript -e 'install.packages("lobstr", \
                repos = "https://cloud.r-project.org")'

Short error log:

<snip>
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... OK
  Running 'testthat.R'
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... ERROR
Errors in running code in vignettes:
when running code in 'FAQ.Rmd'
  ...

> add_some <- function(x, amount = 1) {
+     add_some_(x, amount)
+ }

> add_some(1)

  When sourcing 'FAQ.R':
Error: could not find function "add_some_"
Execution halted
when running code in 'cpp11.Rmd'
  ...
> 600/(0.005 - 0.002)
[1] 2e+05

> mod <- lm(mpg ~ wt, data = mtcars)

> mpe(mod)

  When sourcing 'cpp11.R':
Error: could not find function "mpe"
Execution halted
when running code in 'motivations.Rmd'
  ...
[1] 2 4 6

> x
[1] 1 2 3

> z <- times_two_rcpp(x)

  When sourcing 'motivations.R':
Error: could not find function "times_two_rcpp"
Execution halted

  'FAQ.Rmd' using 'UTF-8'... failed
  'converting.Rmd' using 'UTF-8'... OK
  'cpp11.Rmd' using 'UTF-8'... failed
  'internals.Rmd' using 'UTF-8'... OK
  'motivations.Rmd' using 'UTF-8'... failed
* checking re-building of vignette outputs ... SKIPPED
* DONE
Status: 1 ERROR

Full log:
00check.log

pachadotdev · 2025-01-03T08:35:03Z

@nunotexbsd I was finally able to replicate the error you have!

I added that in an unrelated PR but now I will add that tiny change by separate https://github.com/r-lib/cpp11/pull/427/files#diff-a66dc48b52fad8fe92354878da72e04c4b0bfb9d4fea933afcfa3020ac61b0ebR15

nunotexbsd · 2025-01-03T11:58:48Z

@pachadotdev That's good news!

Didn't found a way to apply the shorter patch:
https://github.com/r-lib/cpp11/pull/427/files#diff-a66dc48b52fad8fe92354878da72e04c4b0bfb9d4fea933afcfa3020ac61b0ebR15 on 0.5.1 tarball from R-cran.

But I will stay tuned and wait for merge so I can test it.

Thanks

pachadotdev · 2025-01-03T12:43:36Z

@nunotexbsd as I commented in the PR, can you install the github version from main?

nunotexbsd · 2025-01-03T18:18:42Z

In order to use FreeBSD ports framework cran helpers, I did download cpp11-main.zip, uncompress and apply 9ebcf41 to it, create a new tarball and use it in ports.

Build is ok, but when running test:

* using log directory '/wrkdirs/usr/ports/devel/R-cran-cpp11/work/cpp11.Rcheck'
* using R version 4.4.2 (2024-10-31)
* using platform: amd64-portbld-freebsd15.0
* R was compiled by
    FreeBSD clang version 19.1.5 (https://github.com/llvm/llvm-project.git llvmorg-19.1.5-0-gab4b5a2db582)
    GNU Fortran (FreeBSD Ports Collection) 13.3.0
* running under: FreeBSD 15amd64-main 15.0-CURRENT FreeBSD 15.0-CURRENT 1500029 amd64
* using session charset: ASCII
* using options '--no-manual --no-build-vignettes'
* checking for file 'cpp11/DESCRIPTION' ... ERROR
Required fields missing or empty:
  'Author' 'Maintainer'
* DONE
Status: 1 ERROR

Maybe I missed something here.

pachadotdev · 2025-01-04T03:28:02Z

In order to use FreeBSD ports framework cran helpers, I did download cpp11-main.zip, uncompress and apply 9ebcf41 to it, create a new tarball and use it in ports.

Build is ok, but when running test:

* using log directory '/wrkdirs/usr/ports/devel/R-cran-cpp11/work/cpp11.Rcheck'
* using R version 4.4.2 (2024-10-31)
* using platform: amd64-portbld-freebsd15.0
* R was compiled by
    FreeBSD clang version 19.1.5 (https://github.com/llvm/llvm-project.git llvmorg-19.1.5-0-gab4b5a2db582)
    GNU Fortran (FreeBSD Ports Collection) 13.3.0
* running under: FreeBSD 15amd64-main 15.0-CURRENT FreeBSD 15.0-CURRENT 1500029 amd64
* using session charset: ASCII
* using options '--no-manual --no-build-vignettes'
* checking for file 'cpp11/DESCRIPTION' ... ERROR
Required fields missing or empty:
  'Author' 'Maintainer'
* DONE
Status: 1 ERROR

Maybe I missed something here.

how about

R
remotes::install_github("r-lib/cpp11")

or

git clone https://github.com/r-lib/cpp11.git
cd cpp11
R
devtools::install()

nunotexbsd · 2025-01-04T12:50:21Z

OK, I'm building required depends so I can do both methods outside poudriere.

git clone https://github.com/r-lib/cpp11.git
cd cpp11
R
devtools::install()

# R CMD check cpp11test

* using log directory ‘/home/nunotex/Work/cpp11/cpp11test.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: amd64-portbld-freebsd15.0
* R was compiled by
    FreeBSD clang version 19.1.5 (https://github.com/llvm/llvm-project.git llvmorg-19.1.5-0-gab4b5a2db582)
    GNU Fortran (FreeBSD Ports Collection) 13.3.0
* running under: FreeBSD leg.home 15.0-CURRENT FreeBSD 15.0-CURRENT #21 main-n274426-98e34e8e2557: Mon Dec 23 23:52:26 WET 2024     [email protected]:/usr/obj/usr/src/amd64.amd64/sys/GENERIC-NODEBUG amd64
* using session charset: UTF-8
* checking for file ‘cpp11test/DESCRIPTION’ ... ERROR
Required fields missing or empty:
  ‘Author’ ‘Maintainer’
* DONE

Status: 1 ERROR
See
  ‘/home/nunotex/Work/cpp11/cpp11test.Rcheck/00check.log’
for details.

pachadotdev · 2025-01-05T09:32:56Z

@nunotexbsd sorry, for a github repo the command is devtools::check(), unless you 1st build the tar file and then check the tar

nunotexbsd · 2025-01-05T12:17:55Z

@pachadotdev after installing missing deps with > install.packages("PkgName"):

> devtools::check()

<snip>
✔  checking Rd \usage sections ...
✔  checking Rd contents ...
✔  checking for unstated dependencies in examples ...
✔  checking line endings in C/C++/Fortran sources/headers ...
✔  checking pragmas in C/C++ headers and code ...
    WARNING
   ‘qpdf’ is needed for checks on size reduction of PDFs
✔  checking installed files from ‘inst/doc’ ...
✔  checking files in ‘vignettes’ ...
✔  checking examples (2.1s)
✔  checking for unstated dependencies in ‘tests’ ...
─  checking tests ...
    [13s/13s] OKthat.R’
   * checking for unstated dependencies in vignettes ... OK
   * checking package vignettes ... OK
   * checking re-building of vignette outputs ... [35s/35s] OK
   * checking for non-standard things in the check directory ... OK
   * checking for detritus in the temp directory ... OK
   * DONE

   Status: 1 WARNING
   See
     ‘/tmp/RtmpU7vTmY/file1232845813d99/cpp11.Rcheck/00check.log’
   for details.

── R CMD check results ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── cpp11 0.5.1.9000 ────
Duration: 59.7s

❯ checking pragmas in C/C++ headers and code ... OK
   WARNING
  ‘qpdf’ is needed for checks on size reduction of PDFs

0 errors ✔ | 1 warning ✖ | 0 notes ✔

pachadotdev · 2025-01-06T06:45:19Z

@pachadotdev after installing missing deps with > install.packages("PkgName"):

> devtools::check()

<snip>
✔  checking Rd \usage sections ...
✔  checking Rd contents ...
✔  checking for unstated dependencies in examples ...
✔  checking line endings in C/C++/Fortran sources/headers ...
✔  checking pragmas in C/C++ headers and code ...
    WARNING
   ‘qpdf’ is needed for checks on size reduction of PDFs
✔  checking installed files from ‘inst/doc’ ...
✔  checking files in ‘vignettes’ ...
✔  checking examples (2.1s)
✔  checking for unstated dependencies in ‘tests’ ...
─  checking tests ...
    [13s/13s] OKthat.R’
   * checking for unstated dependencies in vignettes ... OK
   * checking package vignettes ... OK
   * checking re-building of vignette outputs ... [35s/35s] OK
   * checking for non-standard things in the check directory ... OK
   * checking for detritus in the temp directory ... OK
   * DONE

   Status: 1 WARNING
   See
     ‘/tmp/RtmpU7vTmY/file1232845813d99/cpp11.Rcheck/00check.log’
   for details.

── R CMD check results ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── cpp11 0.5.1.9000 ────
Duration: 59.7s

❯ checking pragmas in C/C++ headers and code ... OK
   WARNING
  ‘qpdf’ is needed for checks on size reduction of PDFs

0 errors ✔ | 1 warning ✖ | 0 notes ✔

@nunotexbsd you are all set! the warning is something about the manual, which you can fix with a command equivalent to apt install qpdf and it only reduces the size of the pdf documentation

pachadotdev mentioned this issue Jan 3, 2025

fix sum rcpp error on Unix systems (cpp11test) #439

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tests fail #419

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tests fail #419

tests fail #419

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