dmphillippo / multinma

Network meta-analysis of individual and aggregate data in Stan
https://dmphillippo.github.io/multinma
33 stars 15 forks source link

The following directory looks like a leftover from 'knitr': ‘figure’. Please remove from your package. #39

Open barracuda156 opened 3 months ago

barracuda156 commented 3 months ago

There is a warning during tests:

--->  Testing R-multinma
Warning: R-multinma is configured to build no architecture-specific files, but installed Mach-O files built for the following archs:
ppc:
  /opt/local/Library/Frameworks/R.framework/Versions/4.4/Resources/library/multinma/libs/multinma.so

Executing:  cd "/opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_R_R-multinma/R-multinma/work/multinma-0.7.0" && /opt/local/bin/R CMD check ./multinma_0.7.0.tar.gz --no-manual --no-build-vignettes 
* using log directory ‘/opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_R_R-multinma/R-multinma/work/multinma-0.7.0/multinma.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: powerpc-apple-darwin10.0.0d2 (32-bit)
* R was compiled by
    gcc-mp-13 (MacPorts gcc13 13.2.0_4+stdlib_flag) 13.2.0
    GNU Fortran (MacPorts gcc13 13.2.0_4+stdlib_flag) 13.2.0
* running under: OS X Snow Leopard 10.6
* using session charset: UTF-8
* using options ‘--no-manual --no-build-vignettes’
* checking for file ‘multinma/DESCRIPTION’ ... OK
* this is package ‘multinma’ version ‘0.7.0’
* 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 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 ‘multinma’ can be installed ... OK
* used C++ compiler: ‘g++-mp-13 (MacPorts gcc13 13.2.0_4+stdlib_flag) 13.2.0’
* used SDK: ‘NA’‘NA’‘NA’‘NA’‘NA’‘NA’
* checking C++ specification ... OK
  Not all R platforms support C++17
* checking installed package size ... NOTE
  installed size is 11.4Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    libs   9.4Mb
* checking package 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 line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... OK
* checking files in ‘vignettes’ ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
  ‘example_atrial_fibrillation.html’
  ‘example_atrial_fibrillation.html.asis’ ‘example_bcg_vaccine.html’
  ‘example_bcg_vaccine.html.asis’ ‘example_blocker.html’
  ‘example_blocker.html.asis’ ‘example_diabetes.html’
  ‘example_diabetes.html.asis’ ‘example_dietary_fat.html’
  ‘example_dietary_fat.html.asis’ ‘example_hta_psoriasis.html’
  ‘example_hta_psoriasis.html.asis’ ‘example_ndmm.html’
  ‘example_ndmm.html.asis’ ‘example_parkinsons.html’
  ‘example_parkinsons.html.asis’ ‘example_plaque_psoriasis.html’
  ‘example_plaque_psoriasis.html.asis’ ‘example_smoking.html’
  ‘example_smoking.html.asis’ ‘example_statins.html’
  ‘example_statins.html.asis’ ‘example_thrombolytics.html’
  ‘example_thrombolytics.html.asis’ ‘example_transfusion.html’
  ‘example_transfusion.html.asis’ ‘vignette_overview.Rmd’
The following directory looks like a leftover from 'knitr':
  ‘figure’
Please remove from your package.
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... WARNING
Directory 'inst/doc' does not exist.
Package vignettes without corresponding single PDF/HTML:
  ‘vignette_overview.Rmd’
  ‘example_atrial_fibrillation.html.asis’
  ‘example_bcg_vaccine.html.asis’
  ‘example_blocker.html.asis’
  ‘example_diabetes.html.asis’
  ‘example_dietary_fat.html.asis’
  ‘example_hta_psoriasis.html.asis’
  ‘example_ndmm.html.asis’
  ‘example_parkinsons.html.asis’
  ‘example_plaque_psoriasis.html.asis’
  ‘example_smoking.html.asis’
  ‘example_statins.html.asis’
  ‘example_thrombolytics.html.asis’
  ‘example_transfusion.html.asis’
* checking running R code from vignettes ...
  ‘vignette_overview.Rmd’ using ‘UTF-8’... OK
  ‘example_atrial_fibrillation.html.asis’ using ‘UTF-8’... OK
  ‘example_bcg_vaccine.html.asis’ using ‘UTF-8’... OK
  ‘example_blocker.html.asis’ using ‘UTF-8’... OK
  ‘example_diabetes.html.asis’ using ‘UTF-8’... OK
  ‘example_dietary_fat.html.asis’ using ‘UTF-8’... OK
  ‘example_hta_psoriasis.html.asis’ using ‘UTF-8’... OK
  ‘example_ndmm.html.asis’ using ‘UTF-8’... OK
  ‘example_parkinsons.html.asis’ using ‘UTF-8’... OK
  ‘example_plaque_psoriasis.html.asis’ using ‘UTF-8’... OK
  ‘example_smoking.html.asis’ using ‘UTF-8’... OK
  ‘example_statins.html.asis’ using ‘UTF-8’... OK
  ‘example_thrombolytics.html.asis’ using ‘UTF-8’... OK
  ‘example_transfusion.html.asis’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... SKIPPED
* DONE

Status: 2 WARNINGs, 2 NOTEs
dmphillippo commented 3 months ago

Hi @barracuda156, I'm not seeing any issues from my end, either locally / GitHub / CRAN. Are you sure you have all the suggested dependencies installed? You will need the R.rsp package to build the vignettes properly; these are precompiled due to CRAN limitations on compile time, so the R.rsp .asis mechanism is used to set these up.