opencv crashing R session? - r
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).
Related
Could not open url 'http://cran.rstudio.com/bin/windows/contrib/4.2/PACKAGES'
When I install new version of Rstudio (the latest version: 2022.02.3-492),
many packages that were previously installed do not work.
enter image description here
Also, install.packages does not work due to "cannot open URL 'http://cran.rstudio.com/bin/windows/contrib/4.2/PACKAGES'"
First, I checked getOption("repos") and it prints
CRAN
"http://cran.rstudio.com/"
attr(,"RStudio")
[1] TRUE
Next, checked sessionInfo(), and it prints
R version 4.2.0 (2022-04-22 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19043)
Matrix products: default
locale:
[1] LC_COLLATE=Korean_Korea.utf8 LC_CTYPE=Korean_Korea.utf8
[3] LC_MONETARY=Korean_Korea.utf8 LC_NUMERIC=C
[5] LC_TIME=Korean_Korea.utf8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_4.2.0 tools_4.2.0
Finally, checked my firewall blocker and allowed an application of RStudio R session.
However, none of them works.
It is making me crasy. How can I fix the problem?
In RStudio Go to Tools -> Global Options and in the Packages tab uncheck the box "use secure download method for HTTP". Packages menu screenshot
R project "unexpected string constant" error when program start
When I turn on my R project, this strange error occurred.
Error: 1:41: unexpected string constant
4:
5: if(capabilities("
^
I reinstalled it twice, but the same problem happened. The same problem occurred when installing the lower-version(3.3.1).
Due to this error, I can not make any R markdown document.
This is my session information.
sessionInfo()
R version 3.6.2 (2019-12-12)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.5
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/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_3.6.2 tools_3.6.2
I'm really want to know how to deal with this strange error. Thank you!
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 ...
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
Synchronizing R system settings from Terminal, GUI and RStudio
My problem on my MacOS is that I can use R from GUI (aka console, downloaded from CRAN), Terminal or from RStudio but I cannot have them function in the same way. Specific example is I can use rJava on Terminal and RStudio but not on GUI. Similar stuff happens for Rmarkdown pdf outputs. I usually get errors from GUI but everything is fine on Terminal or RStudio. How do I update R GUI settings to the same as Terminal's? ps. For instance R CMD javareconf command handled the Terminal R but not R GUI. edit: It is not actually something that requires a minimal working example but let's try library(rJava) after installing it. R Called from Terminal (same with RStudio) No problems. sessionInfo() R version 3.5.0 (2018-04-23) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS High Sierra 10.13.5 Matrix products: default BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib locale: [1] C/UTF-8/C/C/C/C attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] compiler_3.5.0 R GUI sessionInfo() R version 3.5.0 (2018-04-23) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS High Sierra 10.13.5 Matrix products: default BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.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_3.5.0 tools_3.5.0 Some differences between Sys.getenv() are GUI has the following extra LD_LIBRARY_PATH :#JAVA_LD# DYLD_LIBRARY_PATH /Library/Java/JavaVirtualMachines/jdk-10.0.1.jdk/Contents/Home/lib/server Brief update: I was able to correct Rmarkdown situation by using this link and reading help by writing ?Startup on R console. Changed the Renviron file on my R.home()/etc/. But still no rJava.
For R Markdown problem, I managed to handle it by adding a ~/.Renviron file and defining PATH parameter with the value I got from Terminal's Sys.getenv() parameters. The only thing that worked for rJava for High Sierra is the following answer (changed the version to 3.5 though) https://stackoverflow.com/a/47685001/3608936