cpp11
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r-lib
tests fail
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
@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'
@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
@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
@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
@nunotexbsd as I commented in the PR, can you install the github version from main?
In order to use FreeBSD ports framework cran helpers, I did download cpp11-main.zip, uncompress and apply https://github.com/r-lib/cpp11/pull/439/commits/9ebcf417d5ff771f50a9131c5382b757c0cbeb04 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.
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 ERRORMaybe 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()
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.
@nunotexbsd sorry, for a github repo the command is devtools::check(), unless you 1st build the tar file and then check the tar
@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 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