barracuda156
commented
3 months ago The rest passes fine.
* using log directory ‘/opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_R_R-mvgam/R-mvgam/work/mvgam/mvgam.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: powerpc-apple-darwin10.0.0d2 (32-bit)
* R was compiled by
gcc-mp-13 (MacPorts gcc13 13.3.0_0+stdlib_flag) 13.3.0
GNU Fortran (MacPorts gcc13 13.3.0_0+stdlib_flag) 13.3.0
* running under: OS X Snow Leopard 10.6
* using session charset: UTF-8
* using options ‘--no-manual --no-build-vignettes’
* checking for file ‘mvgam/DESCRIPTION’ ... OK
* this is package ‘mvgam’ version ‘1.1.2’
* 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 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 ‘mvgam’ can be installed ... OK
* used C++ compiler: ‘g++-mp-13 (MacPorts gcc13 13.3.0_0+stdlib_flag) 13.3.0’
* used SDK: ‘NA’‘NA’‘NA’‘NA’‘NA’‘NA’
* checking installed package size ... NOTE
installed size is 5.3Mb
sub-directories of 1Mb or more:
R 1.8Mb
doc 2.4Mb
* checking package directory ... 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 code 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 whether startup messages can be suppressed ... 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 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking use of PKG_*FLAGS in Makefiles ... 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 ... 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 ‘data_in_mvgam.Rmd’
...
Number of Fisher Scoring iterations: 6
> summary(gam(y ~ series + s(time, by = series), data = simdat$data_train,
+ family = poisson()))
When sourcing ‘data_in_mvgam.R’:
Error: could not find function "gam"
Execution halted
when running code in ‘nmixtures.Rmd’
...
> plot(mod, type = "smooths", trend_effects = TRUE)
> plot_predictions(mod, condition = "species", type = "detection") +
+ ylab("Pr(detection)") + ylim(c(0, 1)) + theme_classic() +
+ theme(leg .... [TRUNCATED]
When sourcing ‘nmixtures.R’:
Error: could not find function "plot_predictions"
Execution halted
‘data_in_mvgam.Rmd’ using ‘UTF-8’... failed
‘forecast_evaluation.Rmd’ using ‘UTF-8’... OK
‘mvgam_overview.Rmd’ using ‘UTF-8’... OK
‘nmixtures.Rmd’ using ‘UTF-8’... failed
‘shared_states.Rmd’ using ‘UTF-8’... OK
‘time_varying_effects.Rmd’ using ‘UTF-8’... OK
‘trend_formulas.Rmd’ using ‘UTF-8’... OK
* checking re-building of vignette outputs ... SKIPPED
* DONE
Status: 1 ERROR, 1 NOTE
nicholasjclark
No failures with tests, but many of them are skipped, why is that? The only dependency which I have incomplete is
R-cmdstanr(package itself is installed, but CmdStan is not, so it won't be properly usable).