Re-initialize with packrat::init() - r

I have no idea how to make this problem reproducible, but here is a description of the problem nevertheless. I upgraded to R v 3.4.0 yesterday (sessionInfo() is below) and one of my RStudio projects couldn't update packages in packrat. After messing around with various "fixes" without success, I decided to delete packrat (packrat directory, project dir's .RStudio file) in the end. Unfortunately, I can't seem to re-initialize packrat in this project now. The following is the R output from
> packrat::init()
Initializing packrat project in directory:
- "~/my-project-path"
Error in isNamespaceLoaded(pkg) :
attempt to use zero-length variable name
In addition: Warning message:
In FUN(X[[i]], ...) : Package '' not available in repository or locally
> sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: OS X El Capitan 10.11.6
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_3.4.0 magrittr_1.5 tools_3.4.0 yaml_2.1.14 stringi_1.1.5
[6] knitr_1.15.1 stringr_1.2.0 packrat_0.4.8-1 evaluate_0.10
Any help is very much appreciated. I thought about re-cloning the repo from github, but that would involve copy a large amount of files over from various directories that aren't under revision control currently.
Thanks!

Related

Error in inla.call.builtin() : INLA installation error; no such file

I have recently updated INLA using the inla.update on my machine. Now everytime I try to run a function from the package, such as inla.mesh.2d I obtain the following error:
Error in inla.call.builtin() : INLA installation error; no such file
I tried uninstalling and reinstalling INLA package both in its testing and stable version but it still won't work.
I will paste below the output from sessionInfo():
R version 4.0.3 (2020-10-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 10.16
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
locale:
[1] it_IT.UTF-8/it_IT.UTF-8/it_IT.UTF-8/C/it_IT.UTF-8/it_IT.UTF-8
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] INLA_22.01.16 sp_1.4-5 foreach_1.5.1 Matrix_1.3-4
loaded via a namespace (and not attached):
[1] compiler_4.0.3 tools_4.0.3 tinytex_0.32 splines_4.0.3 codetools_0.2-18 grid_4.0.3
[7] iterators_1.0.13 xfun_0.23 lattice_0.20-44
Thank You!

The error you are getting may solve if you update your R to its latest version so INLA requirements are met. Restart, and it may resolve.
If this does not resolve the problem, installing directly from the R interface (vs RStudio) might fix the problem. This link explains how it is done and might be helpful if the first solution did not help.
https://groups.google.com/g/r-inla-discussion-group/c/f3LAE2VHZQw

opencv crashing R session?

I'm running some very simple code:
library(opencv)
ocv_video(ocv_face)
And the session immediately aborts.
Any ideas? (note: running R 4.0.2)
R version 4.0.2 (2020-06-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.5
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
locale:
[1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] opencv_0.1
loaded via a namespace (and not attached):
[1] compiler_4.0.2 magrittr_1.5 tools_4.0.2 Rcpp_1.0.4.6

Solution
For anyone else who arrives here, the solution is to run the same code from terminal. That is press cmd + space to bring up spotlight search, type terminal to open terminal. Type R to open the R interpreter, and use that instead of RStudio.
Cause of the crash
The reason it works from terminal but no RStudio is because from terminal, a prompt will appear asking you to give opencv permission to use your webcam, but this prompt will not appear in RStudio (it causes the crash).

Why I cannot get this string in RStudio?

I am trying to read a phylogeny (as text) into R using RStudio. I copied the text and put them in quotes. But now I cannot even assign it to a variable in R.
tree = "(((((((((((((Potentilla_intermedia:0.311566,Potentilla_recta:0.311566):0.802855,Potentilla_pensylvanica:1.114421):0.041676,(Potentilla_gracilis:1.110417,Potentilla_argentea:1.110417):0.04568):8.56704,(((Potentilla_norvegica:0.063773,Potentilla_supina:0.063773):0.051902,Potentilla_hippiana:0.115675):8.590754,Argentina_anserina:8.706429):1.016709):0.602701,Potentilla_bipinnatifida:10.325839):8.923901,(((Potentilla_anglica:1.366781,Potentilla_reptans:1.366781):5.302408,(Potentilla_simplex:0.031597,Potentilla_canadensis:0.031597):6.637592):0.621378,Duchesnea_indica:7.290567):11.959172):1.543066,Potentilla_sterilis:20.792806):11.333216,(((((Fragaria_chiloensis:2.648747,Fragaria_vesca:2.648747):1.022985,Fragaria_virginiana:3.671731):17.684618,(Dasiphora_fruticosa:11.647099,Potentilla_arguta:11.647099):9.709251):0.676268,Drymocallis_arguta:22.032617):0.405466,((Alchemilla_monticola:16.875311,Alchemilla_xanthochlora:16.875311):0.887368,Comarum_palustre:17.762679):4.675404):9.687939):6.026567,((((((((Rosa_setigera:3.378155,Rosa_blanda:3.378155):0.030747,Rosa_carolina:3.408902):0.025377,Rosa_arkansana:3.434279):1.991106,((Rosa_rubiginosa:2.358272,Rosa_spinosissima:2.358272):0.07664,Rosa_multiflora:2.434911):2.990474):0.128884,Rosa_woodsii:5.554269):0.86504,Rosa_acicularis:6.419309):6.730804,(((((Rosa_micrantha:0.188519,Rosa_canina:0.188519):0.012649,Rosa_tomentosa:0.201168):0.03073,Rubus_plicatifolius:0.231898):0.29401,Rosa_palustris:0.525908):2.38304,Rosa_rugosa:2.908948):10.241165):23.677485,((((Agrimonia_pubescens:0.020923,Agrimonia_gryposepala:0.020923):3.336778,Agrimonia_striata:3.357701):1.373162,(Agrimonia_rostellata:1.363567,Agrimonia_parviflora:1.363567):3.367296):20.869366,Sanguisorba_minor:25.600229):11.227369):1.324992):6.47604,((((Geum_laciniatum:1.819705,Geum_canadense:1.819705):3.890036,(Geum_aleppicum:5.612049,Geum_urbanum:5.612049):0.097692):2.792243,((Geum_macrophyllum:2.602326,Geum_triflorum:2.602326):2.49947,Geum_vernum:5.101796):3.400188):2.651319,Geum_rivale:11.153303):33.475326):1.449852,((((((((((((((((((((((Rubus_semisetosus:2.411266,Rubus_frondosus:2.411266):0.563329,Rubus_wisconsinensis:2.974595):0.095095,(Rubus_wheeleri:2.378801,Rubus_fulleri:2.378801):0.690888):0.0356,Rubus_glandicaulis:3.10529):0.272207,(Rubus_miscix:2.288585,Rubus_spectatus:2.288585):1.088911):0.685377,(Rubus_ithacanus:3.983737,Rubus_steelei:3.983737):0.079136):0.015284,Rubus_enslenii:4.078157):0.068184,Rubus_pensilvanicus:4.146341):0.314926,(Rubus_argutus:0.58418,Rubus_cuneifolius:0.58418):3.877087):0.02081,(((Rubus_regionalis:4.019817,Rubus_canadensis:4.019817):0.059086,Rubus_rosa:4.078903):0.160428,Rubus_recurvans:4.239331):0.242746):0.015005,(Rubus_allegheniensis:4.31499,Rubus_uvidus:4.31499):0.182092):0.019612,Rubus_vermontanus:4.516694):0.891371,(Rubus_hispidus:4.440803,Rubus_permixtus:4.440803):0.967262):1.32483,Rubus_vagus:6.732895):0.023439,Rubus_superioris:6.756333):0.020104,(((((((Rubus_trivialis:1.652243,Rubus_flagellaris:1.652243):0.36229,(Rubus_multifer:0.538518,Rubus_curtipes:0.538518):1.476014):0.807236,Rubus_stipulatus:2.821768):0.295305,Rubus_junceus:3.117074):0.198123,Rubus_missouricus:3.315197):0.971918,Rubus_elegantulus:4.287115):2.388002,Rubus_alumnus:6.675117):0.101321):0.025475,((Rubus_laciniatus:0.125186,Rubus_bifrons:0.125186):0.11903,Rubus_praecox:0.244216):6.557697):4.346196,Rubus_pubescens:11.148109):0.061953,Rubus_idaeus:11.210062):0.042458,((Rubus_phoenicolasius:11.083887,Rubus_occidentalis:11.083887):0.087068,Rubus_arcticus:11.170956):0.081565):7.121242,((Rubus_uniformis:8.388795,Rubus_parviflorus:8.388795):6.470355,Rubus_odoratus:14.85915):3.514612):14.711986,Rubus_meracus:33.085749):12.992732):16.915234,((Filipendula_rubra:19.826137,Filipendula_vulgaris:19.826137):0.073841,Filipendula_ulmaria:19.899978):43.093736):13.354116,(((((((((((((((((((((((((((((((((((Crataegus_dodgei:0.015733,Crataegus_dissona:0.015733):0.010796,Crataegus_michauxii:0.026529):0.010633,Crataegus_formosa:0.037162):0.011471,Crataegus_pedicellata:0.048633):0.014098,Crataegus_irrasa:0.062731):0.019132,Crataegus_florifera:0.081863):0.032863,Crataegus_lumaria:0.114726):0.465517,Crataegus_fulleriana:0.580243):0.006081,Crataegus_disperma:0.586324):0.099168,(Crataegus_jesupii:0.549784,Crataegus_lucorum:0.549784):0.135708):0.00584,Crataegus_fluviatilis:0.691331):0.380201,Crataegus_scabrida:1.071532):0.019968,Crataegus_calpodendron:1.0915):0.033869,Crataegus_succulenta:1.125369):0.262341,((Crataegus_holmesiana:0.712472,Crataegus_mollis:0.712472):0.144634,Crataegus_coccinioides:0.857106):0.530604):0.398534,Crataegus_marshallii:1.786245):0.228259,Crataegus_crus-galli:2.014503):0.161619,Crataegus_intricata:2.176122):0.016118,((Crataegus_macrosperma:0.790887,Crataegus_pruinosa:0.790887):0.122301,(Crataegus_chrysocarpa:0.193226,Crataegus_macracantha:0.193226):0.719962):1.279051):0.017649,Crataegus_submollis:2.209889):0.014998,Crataegus_phaenopyrum:2.224886):0.018512,Crataegus_uniflora:2.243399):0.438351,Crataegus_persimilis:2.68175):0.045017,Crataegus_punctata:2.726768):0.058153,Crataegus_laevigata:2.78492):0.065678,Crataegus_spathulata:2.850598):0.26874,Crataegus_viridis:3.119338):0.332928,Crataegus_douglasii:3.452267):0.094595,Crataegus_monogyna:3.546862):3.832148,((((((Malus_toringo:2.491744,Malus_pumila:2.491744):1.007309,Malus_baccata:3.499053):1.351718,Malus_coronaria:4.850771):1.621923,(Malus_angustifolia:0.049008,Malus_ioensis:0.049008):6.423685):0.035427,Cotoneaster_divaricatus:6.50812):0.736585,Chaenomeles_speciosa:7.244705):0.134305):1.72489,((Aronia_arbutifolia:0.094396,Aronia_melanocarpa:0.094396):8.89729,(Pyrus_communis:7.94625,Sorbus_aucuparia:7.94625):1.045436):0.112214):0.313393,((((Amelanchier_spicata:5.295684,Amelanchier_sanguinea:5.295684):0.053588,Amelanchier_alnifolia:5.349272):2.667629,((Amelanchier_arborea:0.249044,Amelanchier_bartramiana:0.249044):0.767662,Amelanchier_canadensis:1.016706):7.000194):0.24348,(Amelanchier_interior:7.807145,Amelanchier_laevis:7.807145):0.453236):1.156912):0.239145,Sorbus_decora:9.656438):1.019952,Sorbus_americana:10.67639):38.78046,((((((((((((Prunus_hortulana:3.586661,Prunus_persica:3.586661):0.523019,Prunus_mexicana:4.10968):0.275607,Prunus_munsoniana:4.385286):0.329537,(Prunus_armeniaca:1.156849,Prunus_tomentosa:1.156849):3.557974):0.032697,(Prunus_angustifolia:4.478999,Prunus_pumila:4.478999):0.268521):0.03745,Prunus_alleghaniensis:4.784971):1.404974,(Prunus_americana:2.365429,Prunus_nigra:2.365429):3.824516):0.37487,(Prunus_cerasus:2.734566,Prunus_pensylvanica:2.734566):3.830249):4.856241,((Prunus_padus:1.415647,Prunus_virginiana:1.415647):3.401352,Prunus_serotina:4.817):6.604057):29.162527,Sorbaria_sorbifolia:40.583584):2.924475,(Rhodotypos_scandens:36.33611,Physocarpus_opulifolius:36.33611):7.17195):2.718224,(((Spiraea_X_bumalda:10.834237,Spiraea_alba:10.834237):3.799914,Spiraea_tomentosa:14.634152):11.287431,Aruncus_dioicus:25.921583):20.304701):3.230567):26.89098);"
Note: it works on macOS R app, but not on terminal R or RStudio.
Can anyone run the above code? I am surprised that this does not work. There must be something basic about R that I am not know, even after using it for year...
Thanks!
R version 3.5.3 (2019-03-11)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.4
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_3.5.3 assertthat_0.2.1 cli_1.1.0 tools_3.5.3 withr_2.1.2 rstudioapi_0.9.0
[7] crayon_1.3.4 packrat_0.5.0 sessioninfo_1.1.1

I can't explain why it works differently in different console environments, and particularly why it does work in the MacOS R application (for me it doesn't work under an ESS shell in Ubuntu), but the link given above points to a comment in the Introduction to R:
Command lines entered at the console are limited^4 to about 4095 bytes (not characters)
If you put the code above in a file and source() it, it works fine. nchar(tree) is 6936.
The discussion in the link also points to the place where the limit is hardcoded in R, so if you were really desperate you could modify that value and recompile R ...

how to fix the error: Error in importIntoEnv(pkgenv, exports, nsenv, exports),cannot add bindings to a locked environment devtools-roxygen2?

After updating Rstudio and macOS, my package is no more loadable with devtools:
devtools::load_all(".")
Loading mgwrsar
Error in importIntoEnv(pkgenv, exports, nsenv, exports) :
cannot add bindings to a locked environment
I update the following packages: devtools, roxygen2 and rstudioapi, but it doesn't resolve this issue
I try to switch to hadley devtools version : install_github("hadley/devtools")
same issue.
My session info :
> sessionInfo()
R version 3.4.4 (2018-03-15)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS 10.14.1
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods
[7] base
loaded via a namespace (and not attached):
[1] compiler_3.4.4 tools_3.4.4 yaml_2.1.19

You can also get this error from calling library(package) from within the package itself.

Duckmayr's response helped me solve my issue for this same problem:
Do you assign anything to the global environment in your package?
I had saved a new R script in my package project as mypackage/R/myscript.R instead of mypackage/separate_testing_folder/myscript.R. Of course, nothing but actual code pertaining to definition of functions etc should be saved in any scripts within the R/ directory.

In my case, I was accidentally referencing the name of my package INSIDE of my DESCRIPTION. Woops, something like this - I fixed it like so.
Package: utilities
Depends:
dplyr, # and comma here
utilities # remove this

R-Rcpp package linking to nlopt library

In some ways this is a continuation of this older post, R packages with Rcpp and nloptr.
Mostly, this solution proved temporary, for several reasons, some minor, but mostly I am working to prefect this project for a cran submission and this remains the last hurdle.
That said, I attempted and failed to get this example running https://github.com/jyypma/nloptr/issues/39.
The error here is "..../sourceCpp_2.so Reason: image not found"
After, this I made a test package with nlopt installed into the 'inst' folder and 'makevars' and 'makevars.win' in the 'src' along with the test example from above.
This package is now on GitHub: https://github.com/shortyatz/Nlopt-and-Rcpp.
And gives me a similar error message to the one above.
Here is my session info:
R version 3.5.0 (2018-04-23)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.6
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] Rcpp_0.12.18
loaded via a namespace (and not attached):
[1] compiler_3.5.0 tools_3.5.0 RcppArmadillo_0.8.600.0.0 yaml_2.2.0

Resources