Installing MXnet on MAC for R - r

I see that this question has been asked before, however none of the solutions seem to work for me.
I am trying to install mxnet on MacOS Mojave ver 10.14.3 for R. But I just can't get it to work.
I followed the installation instructions on the mxnet website and tried to build from source but to no success. Here's the error I get:
Error: package or namespace load failed for ‘mxnet’:
.onLoad failed in loadNamespace() for 'mxnet', details:
call: dyn.load(file, DLLpath = DLLpath, ...)
error: unable to load shared object '/Library/Frameworks/R.framework/Versions/3.5/Resources/library/mxnet/libs/libmxnet.so':
dlopen(/Library/Frameworks/R.framework/Versions/3.5/Resources/library/mxnet/libs/libmxnet.so, 10): Library not loaded: /usr/local/opt/openblas/lib/libopenblasp-r0.3.1.dylib
Referenced from: /Library/Frameworks/R.framework/Versions/3.5/Resources/library/mxnet/libs/libmxnet.so
Reason: image not found
I tried adding the soft link for openBlas using:
ln -sf /usr/local/opt/openblas/lib/libopenblasp-r0.3.* /usr/local/opt/openblas/lib/libopenblasp-r0.3.1.dylib
but it didn't work. When I run sessioninfo() in R, this is the output I get:
> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS 10.14.3
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_IE.UTF-8/en_IE.UTF-8/en_IE.UTF-8/C/en_IE.UTF-8/en_IE.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods
[7] base
other attached packages:
[1] usethis_1.4.0 devtools_2.0.1
loaded via a namespace (and not attached):
[1] Rcpp_1.0.0 tidyr_0.8.1 prettyunits_1.0.2
[4] ps_1.1.0 visNetwork_2.0.5 assertthat_0.2.0
[7] rprojroot_1.3-2 digest_0.6.18 R6_2.3.0
[10] plyr_1.8.4 backports_1.1.2 ggplot2_3.0.0
[13] pillar_1.3.1 rlang_0.3.1 lazyeval_0.2.1
[16] rstudioapi_0.8 callr_3.0.0 DiagrammeR_1.0.0
[19] desc_1.2.0 downloader_0.4 readr_1.3.1
[22] stringr_1.3.1 htmlwidgets_1.3 igraph_1.2.2
[25] munsell_0.5.0 compiler_3.5.1 influenceR_0.1.0
[28] rgexf_0.15.3 pkgconfig_2.0.2 base64enc_0.1-3
[31] pkgbuild_1.0.2 htmltools_0.3.6 tidyselect_0.2.4
[34] tibble_2.0.1 gridExtra_2.3 XML_3.98-1.16
[37] viridisLite_0.3.0 crayon_1.3.4 dplyr_0.7.6
[40] withr_2.1.2 grid_3.5.1 jsonlite_1.6
[43] gtable_0.2.0 magrittr_1.5 scales_1.0.0
[46] cli_1.0.1 stringi_1.2.4 fs_1.2.6
[49] remotes_2.0.2 viridis_0.5.1 testthat_2.0.1
[52] bindrcpp_0.2.2 brew_1.0-6 RColorBrewer_1.1-2
[55] tools_3.5.1 glue_1.3.0 purrr_0.2.5
[58] hms_0.4.2 Rook_1.1-1 processx_3.2.0
[61] pkgload_1.0.2 yaml_2.2.0 colorspace_1.3-2
[64] sessioninfo_1.1.1 memoise_1.1.0 bindr_0.1.1
Any suggestions as to how I'd fix this?

Related

Initializing renv causes RStudio to collapse

I recently installed both R and RStudio on a new computer, and wanted to create an RProject. I used to use the package renv before and it worked pretty well so far.
However, when I tried to initialize the renv library it first created all the necessary folders within the Rproject, but then suddenly gives th following error:
Fehler in data[[1]] . Indizierung ausserhalb der Grenzen
Afterwards it says: Fataler Fehler: unable to initialize the JIT
And finally produces a fatal error and collapses.
I already un- and reinstalled both R and RStudio twice, but without success.
Any ideas?
R version 3.6.3 (2020-02-29)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)
Matrix products: default
locale:
[1] LC_COLLATE=German_Switzerland.1252 LC_CTYPE=German_Switzerland.1252 LC_MONETARY=German_Switzerland.1252
[4] LC_NUMERIC=C LC_TIME=German_Switzerland.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] Rcpp_1.0.5 plyr_1.8.6 compiler_3.6.3 pillar_1.4.3 later_1.0.0 shinyjs_1.1
[7] tools_3.6.3 digest_0.6.25 viridisLite_0.3.0 jsonlite_1.7.0 lifecycle_0.1.0 tibble_2.1.3
[13] gtable_0.3.0 pkgconfig_2.0.3 rlang_0.4.7 shiny_1.4.0 DBI_1.1.0 rstudioapi_0.11
[19] crosstalk_1.0.0 RPostgreSQL_0.6-2 yaml_2.2.1 xfun_0.12 fastmap_1.0.1 stringr_1.4.0
[25] httr_1.4.1 dplyr_0.8.4 vctrs_0.2.3 htmlwidgets_1.5.1 DT_0.12 tidyselect_1.0.0
[31] leaflet_2.0.3 grid_3.6.3 data.table_1.12.8 glue_1.3.1 R6_2.4.1 plotly_4.9.2
[37] reshape2_1.4.3 tidyr_1.0.2 purrr_0.3.3 ggplot2_3.2.1 magrittr_1.5 shinycssloaders_0.3
[43] scales_1.1.0 promises_1.1.0 htmltools_0.5.0 assertthat_0.2.1 mime_0.9 xtable_1.8-4
[49] colorspace_1.4-1 httpuv_1.5.2 config_0.3 tinytex_0.20 stringi_1.4.6 lazyeval_0.2.2
[55] munsell_0.5.0 crayon_1.3.4 ```

R is throwing errors for semPlot and semPath

Update: This problem seems to be unique to Mac
The installation of semPlot seems to go fine, but when I call the library, it throws an error about package 'glasso' not found. When I try to use semPath, it says the function is not found.
Have restarted RStudio countless times. R is up to date as is my computer (MacOS Mojave version 10.14.6).
I tried the solution in an earlier post about restarting RStudio and then installing again and installing XML as well and that did not work either. I included the dependencies argument to make sure it was completely installed although I don't think that has anything to do with it. Code is below including the session info.
install.packages("semPlot", dependencies = TRUE)
library(semPlot)
semPaths(aa.cfa.fitted)
sessionInfo()
Output is as follows:
> install.packages("semPlot", dependencies = TRUE)
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/semPlot_1.1.2.tgz'
Content type 'application/x-gzip' length 344192 bytes (336 KB)
==================================================
downloaded 336 KB
The downloaded binary packages are in
/var/folders/9b/fg1p3n5j3_d8wvtpwz1_tvx00000gn/T//RtmpyOIMa0/downloaded_packages
> library(semPlot)
Error: package or namespace load failed for ‘semPlot’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
there is no package called ‘glasso’
> semPaths(aa.cfa.fitted)
Error in semPaths(aa.cfa.fitted) : could not find function "semPaths"
> sessionInfo()
R version 3.6.1 (2019-07-05)
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
Random number generation:
RNG: Mersenne-Twister
Normal: Inversion
Sample: Rounding
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
other attached packages:
[1] GPArotation_2014.11-1 nFactors_2.3.3.1
[3] lattice_0.20-38 boot_1.3-23
[5] MASS_7.3-51.4 psych_1.8.12
[7] lavaan_0.6-5
loaded via a namespace (and not attached):
[1] splines_3.6.1 carData_3.0-2 Formula_1.2-3
[4] BDgraph_2.61 stats4_3.6.1 latticeExtra_0.6-28
[7] lisrelToR_0.1.4 pbivnorm_0.6.0 pillar_1.4.2
[10] backports_1.1.4 digest_0.6.21 RColorBrewer_1.1-2
[13] checkmate_1.9.4 minqa_1.2.4 colorspace_1.4-1
[16] htmltools_0.3.6 Matrix_1.2-17 plyr_1.8.4
[19] XML_3.98-1.20 pkgconfig_2.0.3 xtable_1.8-4
[22] corpcor_1.6.9 scales_1.0.0 jpeg_0.1-8
[25] openxlsx_4.1.0.1 fdrtool_1.2.15 lme4_1.1-21
[28] arm_1.10-1 tibble_2.1.3 htmlTable_1.13.2
[31] rockchalk_1.8.144 ggplot2_3.2.1 nnet_7.3-12
[34] lazyeval_0.2.2 mnormt_1.5-5 magrittr_1.5
[37] survival_2.44-1.1 crayon_1.3.4 kutils_1.69
[40] nlme_3.1-141 foreign_0.8-72 truncnorm_1.0-8
[43] regsem_1.3.9 data.table_1.12.2 tools_3.6.1
[46] stringr_1.4.0 munsell_0.5.0 cluster_2.1.0
[49] zip_2.0.4 compiler_3.6.1 sem_3.1-9
[52] rlang_0.4.0 grid_3.6.1 nloptr_1.2.1
[55] rstudioapi_0.10 htmlwidgets_1.3 igraph_1.2.4.1
[58] Rsolnp_1.16 base64enc_0.1-3 mi_1.0
[61] gtable_0.3.0 abind_1.4-5 reshape2_1.4.3
[64] gridExtra_2.3 knitr_1.25 Hmisc_4.2-0
[67] stringi_1.4.3 matrixcalc_1.0-3 parallel_3.6.1
[70] Rcpp_1.0.2 rpart_4.1-15 acepack_1.4.1
[73] png_0.1-7 xfun_0.10 coda_0.19-3
What about installing glasso first?
install.packages("glasso")
install.packages("semPlot")
I assume that this should solve it (no MacOS around to test, sorry).

R : problem in installing package 'Frostarella/DSUR.noof'

I am trying to install DSUR.noof package from GitHub and followed the instructions accordingly
install.packages("devtools")
library(devtools)
install_github("Frostarella/DSUR.noof")
When I try to run the last command(install_github("Frostarella/DSUR.noof") I am getting the below error in Rstudio
Error: 'setInternet2' is defunct.
what could went wrong ? can some one help me
> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)
Matrix products: default
locale:
[1] LC_COLLATE=English_Sweden.1252
[2] LC_CTYPE=English_Sweden.1252
[3] LC_MONETARY=English_Sweden.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_Sweden.1252
attached base packages:
[1] stats graphics grDevices utils datasets
[6] methods base
other attached packages:
[1] usethis_1.4.0 devtools_2.0.1 ggplot2_3.1.0
loaded via a namespace (and not attached):
[1] Rcpp_0.12.18 pillar_1.3.0 compiler_3.5.1
[4] plyr_1.8.4 bindr_0.1.1 remotes_2.0.2
[7] prettyunits_1.0.2 tools_3.5.1 digest_0.6.15
[10] pkgbuild_1.0.2 pkgload_1.0.2 memoise_1.1.0
[13] tibble_1.4.2 gtable_0.2.0 pkgconfig_2.0.1
[16] rlang_0.2.1 cli_1.0.0 rstudioapi_0.7
[19] yaml_2.2.0 bindrcpp_0.2.2 withr_2.1.2
[22] dplyr_0.7.6 fs_1.2.6 desc_1.2.0
[25] rprojroot_1.3-2 grid_3.5.1 tidyselect_0.2.4
[28] glue_1.3.0 R6_2.2.2 processx_3.2.1
[31] sessioninfo_1.1.1 purrr_0.2.5 callr_3.1.1
[34] magrittr_1.5 backports_1.1.2 scales_1.0.0
[37] ps_1.3.0 assertthat_0.2.0 colorspace_1.4-0
[40] labeling_0.3 lazyeval_0.2.1 munsell_0.5.0
[43] crayon_1.3.4
I was running on Anaconda Rstudio before, then installed CRAN R problem solved.....

render / build_site not working when a chunk contains ggplot images

When I try to render an rmarkdown file with a ggplot image, all the chunks work that do not contain a ggplot image and it fails without an error when it tries to run said chunk.
The output I get in my terminal is
Killed
It runs fine on my local machine with the latest version of R and all the packages updated.
Below is the environment I am using in docker to try to run the same thing (when it fails).
R version 3.4.1 (2017-06-30)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: Amazon Linux AMI 2017.09
Matrix products: default
BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so
locale:
[1] C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] bindrcpp_0.2.2 blogdown_0.10 rmarkdown_1.11 here_0.1
[5] PRROC_1.3.1 DT_0.5 forcats_0.3.0
stringr_1.3.1
[9] dplyr_0.7.8 purrr_0.2.5 readr_1.3.1
tidyr_0.8.2
[13] tibble_2.0.1 ggplot2_3.1.0 tidyverse_1.2.1
data.table_1.12.0
loaded via a namespace (and not attached):
[1] Rcpp_1.0.0 lubridate_1.7.4 lattice_0.20-35
assertthat_0.2.0
[5] rprojroot_1.3-2 digest_0.6.18 mime_0.6 R6_2.3.0
[9] cellranger_1.1.0 plyr_1.8.4 backports_1.1.3 evaluate_0.12
[13] httr_1.4.0 pillar_1.3.1 rlang_0.3.1
lazyeval_0.2.1
[17] readxl_1.2.0 rstudioapi_0.9.0 Matrix_1.2-10
reticulate_1.10
[21] htmlwidgets_1.3 munsell_0.5.0 shiny_1.2.0 broom_0.5.1
[25] compiler_3.4.1 httpuv_1.4.5.1 modelr_0.1.2 xfun_0.4
[29] pkgconfig_2.0.2 htmltools_0.3.6 tidyselect_0.2.5 crayon_1.3.4
[33] withr_2.1.2 later_0.7.5 grid_3.4.1 nlme_3.1-131
[37] jsonlite_1.6 xtable_1.8-3 gtable_0.2.0 magrittr_1.5
[41] scales_1.0.0 cli_1.0.1 stringi_1.2.4
promises_1.0.1
[45] xml2_1.2.0 generics_0.0.2 tools_3.4.1 glue_1.3.0
[49] hms_0.4.2 crosstalk_1.0.0 yaml_2.2.0
colorspace_1.4-0
[53] rvest_0.3.2 knitr_1.21 bindr_0.1.1 haven_2.0.0

Why is my resource_map function in R asking for a quasiquoted argument?

I am trying to run (in R) this off-the-shelf example from the Resource Map function help page:
library(bupaR)
library(eventdataR)
data(patients)
resource_map(patients)
and somehow it is returning this error:
Error: UQ() can only be used within a quasiquoted argument
Can someone help me understand and propose a fix as well? Is it something with my R/Rstudio, because this example comes straight from the "resource_map" help page.
Here is the sessioninfo:
R version 3.4.3 (2017-11-30) Platform: x86_64-apple-darwin15.6.0
(64-bit) Running under: macOS High Sierra 10.13.3
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
other attached packages: [1] bindrcpp_0.2 xesreadR_0.2.2
processmonitR_0.1.0 processmapR_0.2.1 eventdataR_0.1.2
petrinetR_0.1.0 [7] edeaR_0.7.2 bupaR_0.3.2
loaded via a namespace (and not attached): [1] Rook_1.1-1
purrr_0.2.4 ggthemes_3.4.0 colorspace_1.3-2
viridisLite_0.3.0 miniUI_0.1.1 [7] htmltools_0.3.6
yaml_2.1.17 plotly_4.7.1 XML_3.98-1.10
rlang_0.2.0 pillar_1.2.1 [13] glue_1.2.0
RColorBrewer_1.1-2 bindr_0.1 plyr_1.8.4
stringr_1.3.0 munsell_0.4.3 [19] gtable_0.2.0
visNetwork_2.0.3 htmlwidgets_1.0 forcats_0.3.0
httpuv_1.3.6.2 DiagrammeR_0.9.2 [25] Rcpp_0.12.15
xtable_1.8-2 readr_1.1.1 scales_0.5.0
jsonlite_1.5 rgexf_0.15.3 [31] mime_0.5
gridExtra_2.3 brew_1.0-6 ggplot2_2.2.1 hms_0.4.1
digest_0.6.15 [37] stringi_1.1.6 dplyr_0.7.4
shiny_1.0.5 grid_3.4.3 influenceR_0.1.0
tools_3.4.3 [43] magrittr_1.5 lazyeval_0.2.1
tibble_1.4.2 tidyr_0.8.0 pkgconfig_2.0.1 xml2_1.2.0
[49] data.table_1.10.4-3 downloader_0.4 lubridate_1.7.3
httr_1.3.1 assertthat_0.2.0 rstudioapi_0.7 [55]
viridis_0.5.0 R6_2.2.2 igraph_1.1.2
shinyTime_0.2.1 compiler_3.4.3
Thanks!

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