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.....
Related
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?
I am trying to run a flexdashboard with a couple plotly graphs, but I receive the error:
Error in switch(options$dev, pdf = ".pdf", jpeg = ".jpeg", ".png") :
EXPR must be a length 1 vector Calls: <Anonymous> ... fun ->
withVisible -> knit_print -> html_screenshot
The example code I am running is a set of ggplotly example code.
Session info:
R version 3.3.1 (2016-06-21)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C LC_TIME=English_United States.1252
attached base packages:
[1] grid stats graphics grDevices utils datasets methods base
other attached packages:
[1] maps_3.2.0 bindrcpp_0.2 highcharter_0.5.0 quantmod_0.4-12 TTR_0.23-3
[6] xts_0.10-0 zoo_1.8-0 formattable_0.2.0.1 officer_0.2.1 flextable_0.4.2
[11] gridExtra_2.3 knitr_1.17 kableExtra_0.7.0 dplyr_0.7.4 lubridate_1.6.0
[16] rstudioapi_0.7 RODBC_1.3-15 plotly_4.7.1 ggplot2_2.2.1
loaded via a namespace (and not attached):
[1] httr_1.3.1 tidyr_0.7.2 jsonlite_1.5 viridisLite_0.2.0 R.utils_2.6.0
[6] shiny_1.0.5 assertthat_0.2.0 yaml_2.1.16 gdtools_0.1.6 backports_1.1.1
[11] lattice_0.20-35 glue_1.1.1 rlist_0.4.6.1 uuid_0.1-2 digest_0.6.12
[16] rvest_0.3.2 colorspace_1.3-2 htmltools_0.3.6 httpuv_1.3.5 R.oo_1.21.0
[21] plyr_1.8.4 psych_1.7.8 pkgconfig_2.0.1 broom_0.4.2 flexdashboard_0.5.1
[26] purrr_0.2.3 xtable_1.8-2 scales_0.5.0 tibble_1.3.4 lazyeval_0.2.0
[31] mnormt_1.5-5 magrittr_1.5 mime_0.5 evaluate_0.10.1 R.methodsS3_1.7.1
[36] nlme_3.1-131 xml2_1.1.1 foreign_0.8-69 tools_3.3.1 data.table_1.10.4
[41] hms_0.3 stringr_1.2.0 munsell_0.4.3 zip_1.0.0 rlang_0.1.2
[46] htmlwidgets_1.0 crosstalk_1.0.0 igraph_1.1.2 base64enc_0.1-3 labeling_0.3
[51] rmarkdown_1.6 gtable_0.2.0 curl_3.0 reshape2_1.4.2 R6_2.2.2
[56] bindr_0.1 rprojroot_1.2 readr_1.1.1 stringi_1.1.5 parallel_3.3.1
[61] Rcpp_0.12.12 tidyselect_0.2.0
A similar error resulted in the case of this question on github, but I am not using shiny nor do I set a working directory in the code. Any ideas?
Overview
From All apps with htmlwidgets failing to render on Mac after #150, Yihui identified this error with version 1.17 of the knitr package.
This is the same version you currently have installed (see 'other attached packages' section in sessionInfo()). To squash the error message, please run the following code in r to update the knitr package to version 1.19:
# install package from CRAN
install.packages( pkgs = 'knitr' )
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!
I have problem with the function ggparagraph() from ggpubr package. Its content is not drawing. If I use the function:
example(ggparagraph)
The plot is drawing without any problem, but the "ggparagraph area" (below plot) is empty. The same problem is if I use custom scripts, where the ggparagraph is applied.
R does not print any error message. Where can be the problem?
My session info is:
sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 15063)
Matrix products: default
locale:
1 LC_COLLATE=Slovak_Slovakia.1250 LC_CTYPE=Slovak_Slovakia.1250
[3] LC_MONETARY=Slovak_Slovakia.1250 LC_NUMERIC=C
[5] LC_TIME=Slovak_Slovakia.1250
attached base packages:
1 stats graphics grDevices utils datasets methods base
other attached packages:
1 ggpubr_0.1.4 magrittr_1.5 gridExtra_2.2.1 dplyr_0.7.2
[5] purrr_0.2.3 readr_1.1.1 tidyr_0.6.3 tibble_1.3.3
[9] ggplot2_2.2.1 tidyverse_1.1.1
loaded via a namespace (and not attached):
1 Rcpp_0.12.12 cellranger_1.1.0 compiler_3.4.1 plyr_1.8.4
[5] bindr_0.1 forcats_0.2.0 tools_3.4.1 jsonlite_1.5
[9] lubridate_1.6.0 nlme_3.1-131 gtable_0.2.0 lattice_0.20-35
[13] pkgconfig_2.0.1 rlang_0.1.2 psych_1.7.5 parallel_3.4.1
[17] haven_1.1.0 bindrcpp_0.2 xml2_1.1.1 stringr_1.2.0
[21] httr_1.2.1 hms_0.3 cowplot_0.8.0 grid_3.4.1
[25] glue_1.1.1 R6_2.2.2 readxl_1.0.0 foreign_0.8-69
[29] reshape2_1.4.2 modelr_0.1.1 scales_0.4.1 rvest_0.3.2
[33] assertthat_0.2.0 mnormt_1.5-5 colorspace_1.3-2 labeling_0.3
[37] stringi_1.1.5 lazyeval_0.2.0 munsell_0.4.3 broom_0.4.2
Finally, I don't find where is the problem, but if I install this package from github (instead of CRAN), all paragraphs are rendered correctly.
My Shiny apps had been running fine until last week.
I am trying to run the apps today and getting errors in most of them :
Below is the error and my sessionInfo.
I am using Shinydashboard and other shiny libraries to render an app.
Error in withReactiveDomain(shinysession, { :
No handler registered for for type file1:shiny.file
sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.1 (Yosemite)
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] parallel stats4 grid stats graphics grDevices utils datasets methods base
other attached packages:
[1] locfit_1.5-9.1 ggbiplot_0.55 scales_0.4.0
[4] chimera_1.14.0 Homo.sapiens_1.3.1 org.Hs.eg.db_3.3.0
[7] GO.db_3.3.0 OrganismDbi_1.14.1 TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
[10] GenomicFeatures_1.24.5 BSgenome.Hsapiens.UCSC.hg19_1.4.0 BSgenome_1.40.1
[13] rtracklayer_1.32.2 AnnotationDbi_1.34.4 GenomicAlignments_1.8.4
[16] Rsamtools_1.24.0 Biostrings_2.40.2 XVector_0.12.1
[19] BiocInstaller_1.22.3 gTrack_0.1.0 gUtils_0.2.0
[22] data.table_1.9.6 stringr_1.1.0 devtools_1.12.0
[25] reshape_0.8.5 DESeq2_1.12.4 SummarizedExperiment_1.2.3
[28] Biobase_2.32.0 GenomicRanges_1.24.3 GenomeInfoDb_1.8.7
[31] IRanges_2.6.1 S4Vectors_0.10.3 BiocGenerics_0.18.0
[34] xlsx_0.5.7 xlsxjars_0.6.1 rJava_0.9-8
[37] shinydashboard_0.5.3 DT_0.2 shiny_0.14.1
[40] ggplot2_2.1.0 sva_3.20.0 genefilter_1.54.2
[43] mgcv_1.8-15 nlme_3.1-128 matrixStats_0.51.0
[46] pvclust_2.0-0 gplots_3.0.1 reshape2_1.4.1
[49] plyr_1.8.4 ComplexHeatmap_1.11.7
loaded via a namespace (and not attached):
[1] colorspace_1.2-7 rjson_0.2.15 class_7.3-14 modeltools_0.2-21 mclust_5.2
[6] circlize_0.3.9 GlobalOptions_0.0.10 flexmix_2.3-13 mvtnorm_1.0-5 splines_3.3.1
[11] robustbase_0.92-6 geneplotter_1.50.0 Formula_1.2-1 jsonlite_1.1 annotate_1.50.1
[16] cluster_2.0.5 kernlab_0.9-25 graph_1.50.0 httr_1.2.1 Matrix_1.2-7.1
[21] acepack_1.3-3.3 htmltools_0.3.5 tools_3.3.1 gtable_0.2.0 Rcpp_0.12.7
[26] trimcluster_0.1-2 gdata_2.17.0 fpc_2.1-10 mime_0.5 gtools_3.5.0
[31] XML_3.98-1.4 dendextend_1.3.0 DEoptimR_1.0-6 zlibbioc_1.18.0 MASS_7.3-45
[36] RBGL_1.48.1 RColorBrewer_1.1-2 yaml_2.1.13 curl_2.1 memoise_1.0.0
[41] gridExtra_2.2.1 biomaRt_2.28.0 rpart_4.1-10 latticeExtra_0.6-28 stringi_1.1.2
[46] RSQLite_1.0.0 caTools_1.17.1 BiocParallel_1.6.6 shape_1.4.2 chron_2.3-47
[51] prabclus_2.2-6 bitops_1.0-6 lattice_0.20-34 htmlwidgets_0.7 labeling_0.3
[56] magrittr_1.5 R6_2.2.0 Hmisc_3.17-4 DBI_0.5-1 whisker_0.3-2
[61] foreign_0.8-67 withr_1.0.2 survival_2.39-5 RCurl_1.95-4.8 nnet_7.3-12
[66] KernSmooth_2.23-15 GetoptLong_0.1.5 git2r_0.15.0 digest_0.6.10 diptest_0.75-7
[71] xtable_1.8-2 httpuv_1.3.3 munsell_0.4.3
Any idea,what this could be?
Thanks,
Ron
Shiny version 0.14.2 was published last week (along with new versions of R and RStudio). Maybe this broke something in your code. One way to protect against this is to use something like packrat package that locks in a certain version of an R package so that your code is not changed by a new package. You can then test your code against an upgrade and troubleshoot before using that new version.
Restarting R studio worked.There was no need to update any packages.