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RGLab / FAUST

Full annotation using shape-constrained trees
GNU General Public License v3.0
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Missing 'faustIntro' vignette #2

Closed brentocarrigan closed 5 years ago

brentocarrigan commented 5 years ago

Hi Evan,

scamp and FAUST installed successfully from source, including options to install vignette - however vignette still not found. What would you suggest?

Initial trial of vignette

> library(faust)
> vignette('faustIntro')
Warning message:
vignette ‘faustIntro’ not found

Trial re-install faust needs force = TRUE option

> devtools::install_github("RGLab/FAUST", build = TRUE, build_opts = c("--no-resave-data", "--no-manual"))
Skipping install of 'faust' from a github remote, the SHA1 (a02f71a0) has not changed since last install.
  Use `force = TRUE` to force installation

With force = TRUE

> devtools::install_github("RGLab/FAUST", build = TRUE, build_opts = c("--no-resave-data", "--no-manual"), force = TRUE)
Downloading GitHub repo RGLab/FAUST@master
These packages have more recent versions available.
Which would you like to update?

1: All                            
2: CRAN packages only             
3: None                           
4: ggplot2 (3.2.0 -> 3.2.1) [CRAN]

Enter one or more numbers, or an empty line to skip updates:
> 3
✔  checking for file ‘/private/var/folders/kp/dwz7y9gx6n37wt0f12yp8x2s8cbn2c/T/Rtmp9SNAhb/remotes25b093441ba/RGLab-FAUST-a02f71a/DESCRIPTION’ ...
─  preparing ‘faust’: (2.4s)
✔  checking DESCRIPTION meta-information ...
─  cleaning src
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  building ‘faust_0.0.2.901.tar.gz’
   Warning: invalid uid value replaced by that for user 'nobody'

* installing *source* package ‘faust’ ...
** using staged installation
** libs

## clang++ output omitted

** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (faust)

Re-trial of vignette

> vignette('faustIntro')
Warning message:
vignette ‘faustIntro’ not found

What do you think?

> sessionInfo()
R version 3.6.0 (2019-04-26)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.6

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

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

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

other attached packages:
 [1] faust_0.0.2.901           tidyr_0.8.3               dplyr_0.8.3              
 [4] knitr_1.23                cowplot_1.0.0             ggplot2_3.2.0            
 [7] scamp_0.2.36              ggdendro_0.1-20           flowWorkspace_3.32.0     
[10] ncdfFlow_2.30.1           BH_1.69.0-1               RcppArmadillo_0.9.600.4.0
[13] flowCore_1.50.0           flowWorkspaceData_2.20.0 

loaded via a namespace (and not attached):
 [1] matrixStats_0.54.0  fs_1.3.1            usethis_1.5.1       devtools_2.1.0      RColorBrewer_1.1-2 
 [6] rprojroot_1.3-2     Rgraphviz_2.28.0    tools_3.6.0         backports_1.1.4     R6_2.4.0           
[11] KernSmooth_2.23-15  lazyeval_0.2.2      BiocGenerics_0.30.0 colorspace_1.4-1    withr_2.1.2        
[16] tidyselect_0.2.5    gridExtra_2.3       prettyunits_1.0.2   processx_3.4.1      curl_4.0           
[21] compiler_3.6.0      graph_1.62.0        cli_1.1.0           Biobase_2.44.0      desc_1.2.0         
[26] scales_1.0.0        DEoptimR_1.0-8      hexbin_1.27.3       mvtnorm_1.0-11      robustbase_0.93-5  
[31] ggridges_0.5.1      callr_3.3.1         stringr_1.4.0       digest_0.6.20       rmarkdown_1.14     
[36] rrcov_1.4-7         pkgconfig_2.0.2     htmltools_0.3.6     sessioninfo_1.1.1   rlang_0.4.0        
[41] rstudioapi_0.10     magrittr_1.5        Rcpp_1.0.2          munsell_0.5.0       viridis_0.5.1      
[46] stringi_1.4.3       whisker_0.3-2       yaml_2.2.0          MASS_7.3-51.4       zlibbioc_1.30.0    
[51] pkgbuild_1.0.3      plyr_1.8.4          grid_3.6.0          parallel_3.6.0      crayon_1.3.4       
[56] lattice_0.20-38     ps_1.3.0            pillar_1.4.2        corpcor_1.6.9       stats4_3.6.0       
[61] pkgload_1.0.2       glue_1.3.1          evaluate_0.14       latticeExtra_0.6-28 data.table_1.12.2  
[66] remotes_2.1.0       BiocManager_1.30.4  RcppParallel_4.4.3  testthat_2.2.1      gtable_0.3.0       
[71] purrr_0.3.2         assertthat_0.2.1    xfun_0.8            IDPmisc_1.1.19      pcaPP_1.9-73       
[76] viridisLite_0.3.0   tibble_2.1.3        memoise_1.1.0       flowViz_1.48.0      cluster_2.1.0
juyeongkim commented 5 years ago

@brentocarrigan,

There was a change in remotes package. Try to re-install the package via:

remotes::install_github("RGLab/FAUST", force = TRUE, build_vignettes = TRUE)

https://github.com/bryandmartin/corncob/issues/47#issuecomment-515440073 https://github.com/r-lib/remotes/blob/master/NEWS.md#remotes-210

evangreene commented 5 years ago

@juyeongkim: Thanks for the link!

@brentocarrigan: please let me know if the remotes installation works for you. If it does, I will update the recommended installation per @juyeongkim's suggestion.

brentocarrigan commented 5 years ago

Hi both, thank you - yes, using

remotes::install_github("RGLab/FAUST", force = TRUE, build_vignettes = TRUE)

has fixed it for me!

hamid-bolouri commented 5 years ago

Hi; After hitting the same issue, I just tried

remotes::install_github("RGLab/FAUST", force = TRUE, build_vignettes = TRUE)

but get an error:

Error: Failed to install 'faust' from GitHub: System command error, exit status: 1, stderr empty

Any thoughts?

(Note: sessionInfo() doesn't show this, but I am running RStudio remotely on a GCloud instance.)

Thanks

Hamid

traceback() 7: stop(remote_install_error(remotes[[i]], e)) 6: value[3L] 5: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 4: tryCatchList(expr, classes, parentenv, handlers) 3: tryCatch(res[[i]] <- install_remote(remotes[[i]], ...), error = function(e) { stop(remote_install_error(remotes[[i]], e)) }) 2: install_remotes(remotes, auth_token = auth_token, host = host, dependencies = dependencies, upgrade = upgrade, force = force, quiet = quiet, build = build, build_opts = build_opts, build_manual = build_manual, build_vignettes = build_vignettes, repos = repos, type = type, ...) 1: remotes::install_github("RGLab/FAUST", force = TRUE, build_vignettes = TRUE)

sessionInfo() R version 3.6.0 (2019-04-26) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Debian GNU/Linux 9 (stretch)

Matrix products: default BLAS: /usr/lib/libblas/libblas.so.3.7.0 LAPACK: /usr/lib/lapack/liblapack.so.3.7.0

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages: [1] faust_0.0.2.901 usethis_1.5.0 devtools_2.0.2 BiocManager_1.30.4

loaded via a namespace (and not attached): [1] Biobase_2.44.0 viridis_0.5.1 pkgload_1.0.2 tidyr_0.8.3 viridisLite_0.3.0 RcppParallel_4.4.3
[7] assertthat_0.2.1 stats4_3.6.0 latticeExtra_0.6-28 flowWorkspace_3.32.0 robustbase_0.93-5 remotes_2.1.0
[13] sessioninfo_1.1.1 pillar_1.4.2 backports_1.1.4 lattice_0.20-38 glue_1.3.1 digest_0.6.20
[19] RColorBrewer_1.1-2 colorspace_1.4-1 cowplot_1.0.0 plyr_1.8.4 pcaPP_1.9-73 pkgconfig_2.0.2
[25] zlibbioc_1.30.0 purrr_0.3.2 flowCore_1.50.0 corpcor_1.6.9 mvtnorm_1.0-11 scales_1.0.0
[31] processx_3.4.0 whisker_0.3-2 tibble_2.1.3 ggplot2_3.2.0 withr_2.1.2 flowViz_1.48.0
[37] BiocGenerics_0.30.0 hexbin_1.27.3 lazyeval_0.2.2 cli_1.1.0 magrittr_1.5 crayon_1.3.4
[43] IDPmisc_1.1.19 memoise_1.1.0 ps_1.3.0 fs_1.3.1 MASS_7.3-51.3 pkgbuild_1.0.3
[49] graph_1.62.0 tools_3.6.0 data.table_1.12.2 ncdfFlow_2.30.1 prettyunits_1.0.2 scamp_0.2.36
[55] matrixStats_0.54.0 stringr_1.4.0 munsell_0.5.0 cluster_2.0.8 callr_3.2.0 compiler_3.6.0
[61] rlang_0.4.0 grid_3.6.0 ggridges_0.5.1 rstudioapi_0.10 testthat_2.1.1 gtable_0.3.0
[67] curl_4.0 rrcov_1.4-7 R6_2.4.0 gridExtra_2.3 dplyr_0.8.3 rprojroot_1.3-2
[73] KernSmooth_2.23-15 desc_1.2.0 Rgraphviz_2.28.0 stringi_1.4.3 parallel_3.6.0 Rcpp_1.0.2
[79] DEoptimR_1.0-8 tidyselect_0.2.5