I didn't find any results on my internet calls. How to fix this error is caused?
library(ggplot2)
ggplot(data = mtcars, aes(x=disp , y=wt)) +
geom_point(stat = "identity")
result;
Error: Can't find stat called "identity"
My sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.1 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1
locale:
[1] LC_CTYPE=tr_TR.UTF-8 LC_NUMERIC=C
[3] LC_TIME=tr_TR.UTF-8 LC_COLLATE=tr_TR.UTF-8
[5] LC_MONETARY=tr_TR.UTF-8 LC_MESSAGES=tr_TR.UTF-8
[7] LC_PAPER=tr_TR.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=tr_TR.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] ggplot2_3.1.0 shiny_1.2.0
loaded via a namespace (and not attached):
[1] Rcpp_1.0.0 pillar_1.3.0 compiler_3.5.1
[4] cellranger_1.1.0 RColorBrewer_1.1-2 later_0.7.5
[7] plyr_1.8.4 bindr_0.1.1 forcats_0.3.0
[10] tools_3.5.1 digest_0.6.18 viridisLite_0.3.0
[13] jsonlite_1.5 tibble_1.4.2 gtable_0.2.0
[16] pkgconfig_2.0.2 rlang_0.3.0.1 ggplotgui_1.0.0
[19] rstudioapi_0.8 yaml_2.2.0 haven_1.1.2
[22] bindrcpp_0.2.2 withr_2.1.2 stringr_1.3.1
[25] httr_1.3.1 dplyr_0.7.8 htmlwidgets_1.3
[28] hms_0.4.2 grid_3.5.1 tidyselect_0.2.5
[31] data.table_1.11.8 glue_1.3.0 R6_2.3.0
[34] plotly_4.8.0 readxl_1.1.0 readr_1.1.1
[37] tidyr_0.8.2 purrr_0.2.5 magrittr_1.5
[40] scales_1.0.0 promises_1.0.1 htmltools_0.3.6
[43] assertthat_0.2.0 xtable_1.8-3 mime_0.6
[46] colorspace_1.3-2 httpuv_1.4.5 stringi_1.2.4
[49] lazyeval_0.2.1 munsell_0.5.0 crayon_1.3.4
Related
I got error editable from DT package
Error in if (editable) params$editable = editable :
argument is not interpretable as logical
In addition: Warning message:
In if (editable) params$editable = editable :
the condition has length > 1 and only the first element will be used
library(DT)
DT::datatable(head(iris), editable = list(
target = 'row', disable = list(columns = c(1, 3, 4)))
)
This is my R sessionInfo()
> sessionInfo()
R version 3.5.3 (2019-03-11)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux
Matrix products: default
BLAS: /usr/lib64/libblas.so.3.4.2
LAPACK: /usr/lib64/liblapack.so.3.4.2
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] DT_0.5 readr_1.3.1 tidyr_0.8.3 tibble_2.1.1
[5] tidyverse_1.2.1 fs_1.2.7 RColorBrewer_1.1-2 rvg_0.2.0
[9] magrittr_1.5 officer_0.3.3 esquisse_0.3.0.940 scales_1.0.0
[13] colourpicker_1.0 shinyjqui_0.3.2 plotly_4.9.0 ggplot2_3.1.1
[17] forcats_0.4.0 arsenal_3.0.0 waiter_0.0.1 shinydashboardPlus_0.7.0
[21] future_1.12.0 data.table_1.12.2 shinyFiles_0.7.2 stringi_1.4.3
[25] shinyjs_1.0 shinyWidgets_0.4.8 purrr_0.3.2 rintrojs_0.2.0
[29] shinyBS_0.61 shinyalert_1.0 shinydashboard_0.7.1 stringr_1.4.0
[33] lubridate_1.7.4 dplyr_0.8.0.1 haven_2.1.0 shiny_1.3.1
loaded via a namespace (and not attached):
[1] nlme_3.1-137 httr_1.4.0 tools_3.5.3 backports_1.1.4 R6_2.4.0 lazyeval_0.2.2
[7] colorspace_1.4-1 withr_2.1.2 tidyselect_0.2.5 compiler_3.5.3 cli_1.1.0 rvest_0.3.3
[13] xml2_1.2.0 digest_0.6.18 rmarkdown_1.12 base64enc_0.1-3 pkgconfig_2.0.2 htmltools_0.3.6
[19] htmlwidgets_1.3 rlang_0.3.4 readxl_1.3.1 rstudioapi_0.10 generics_0.0.2 jsonlite_1.6
[25] crosstalk_1.0.0 zip_2.0.1 Rcpp_1.0.1 munsell_0.5.0 gdtools_0.1.8 yaml_2.2.0
[31] plyr_1.8.4 grid_3.5.3 parallel_3.5.3 listenv_0.7.0 promises_1.0.1 crayon_1.3.4
[37] miniUI_0.1.1.1 lattice_0.20-38 hms_0.4.2 knitr_1.22 pillar_1.3.1 uuid_0.1-2
[43] codetools_0.2-16 glue_1.3.1 packrat_0.5.0 evaluate_0.13 modelr_0.1.4 httpuv_1.5.1
[49] testthat_2.0.1 cellranger_1.1.0 gtable_0.3.0 assertthat_0.2.1 xfun_0.6 mime_0.6
[55] xtable_1.8-4 broom_0.5.2 later_0.8.0 rsconnect_0.8.13 viridisLite_0.3.0 tinytex_0.12
[61] globals_0.12.4 ellipsis_0.1.0
I am trying to use foreach and doParallel to optimize the computation of some image processing. I have ParamIter which is the parameter to iterate over. ImageProcessing is my custom function to process the images and save the data that has been processed.
library(methods)
library(fftwtools)
library(EBImage)
library(tidyverse)
library(foreach)
library(doParallel)
registerDoParallel(20)
foreach(ParamIter = unique(AllImages$ParamIter)) %dopar% {
AllImagesTemp = AllImages[AllImages$ParamIter == ParamIter,]
ImageProcessing(Image = AllImagesTemp,
Plate = unique(AllImagesTemp$Plate),
TimePoint = unique(AllImagesTemp$TimePoint),
Marker = unique(AllImagesTemp$Marker),
Replicate = unique(AllImagesTemp$Replicate),
Well = unique(AllImagesTemp$ID),
Position = unique(AllImagesTemp$Position),
SaveDir = WellDir,
SaveParam = ParamIter,
ThrEmptyImage = .04)
}
Everything works perfectly locally on a machine with Ubuntu 18.04 and a session as per below:
> sessionInfo()
R version 3.5.3 (2019-03-11)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.2 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=de_DE.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=de_DE.UTF-8
[6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=de_DE.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] bindrcpp_0.2.2 fftwtools_0.9-8 doParallel_1.0.14 iterators_1.0.10 foreach_1.4.4 forcats_0.3.0 stringr_1.4.0 dplyr_0.7.7
[9] purrr_0.3.1 readr_1.1.1 tidyr_0.8.2 tibble_2.0.1 ggplot2_3.1.0 tidyverse_1.2.1 EBImage_4.24.0
loaded via a namespace (and not attached):
[1] tidyselect_0.2.5 locfit_1.5-9.1 haven_1.1.2 lattice_0.20-38 colorspace_1.4-0 htmltools_0.3.6 yaml_2.2.0
[8] rlang_0.3.1 pillar_1.3.1 withr_2.1.2 glue_1.3.0 BiocGenerics_0.28.0 modelr_0.1.2 readxl_1.1.0
[15] jpeg_0.1-8 bindr_0.1.1 plyr_1.8.4 munsell_0.5.0 gtable_0.2.0 cellranger_1.1.0 rvest_0.3.2
[22] htmlwidgets_1.3 codetools_0.2-16 broom_0.5.0 Rcpp_1.0.0 backports_1.1.3 scales_1.0.0 jsonlite_1.6
[29] abind_1.4-5 hms_0.4.2 png_0.1-7 digest_0.6.18 stringi_1.3.1 tiff_0.1-5 grid_3.5.3
[36] cli_1.0.1 tools_3.5.3 bitops_1.0-6 magrittr_1.5 RCurl_1.95-4.11 lazyeval_0.2.1 crayon_1.3.4
[43] pkgconfig_2.0.2 xml2_1.2.0 lubridate_1.7.4 assertthat_0.2.0 httr_1.4.0 rstudioapi_0.9.0 R6_2.3.0
[50] nlme_3.1-137 compiler_3.5.3
However if I am trying to do this on my local cluster it doesn't work and provides me with this error:
Error in { :
task 1 failed - "a call to callNextMethod() appears in a call to ‘.Method’, but the call does not seem to come from either a generic function or another 'callNextMethod'"
Calls: %dopar% -> <Anonymous>
Execution halted
My session on the centos cluster looks like:
R version 3.4.1 (2017-06-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS: /cm/shared/apps/R/64/3.4.1/lib64/R/lib/libRblas.so
LAPACK: /cm/shared/apps/R/64/3.4.1/lib64/R/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] 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
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] doParallel_1.0.14 iterators_1.0.10 foreach_1.4.4 forcats_0.3.0
[5] stringr_1.3.1 dplyr_0.7.8 purrr_0.3.0 readr_1.3.1
[9] tidyr_0.8.2 tibble_2.0.1 ggplot2_3.1.0 tidyverse_1.2.1
[13] EBImage_4.20.1 fftwtools_0.9-8
loaded via a namespace (and not attached):
[1] tidyselect_0.2.5 locfit_1.5-9.1 haven_2.0.0
[4] lattice_0.20-35 colorspace_1.4-0 generics_0.0.2
[7] htmltools_0.3.6 rlang_0.3.1 pillar_1.3.1
[10] withr_2.1.2 glue_1.3.0 BiocGenerics_0.24.0
[13] modelr_0.1.2 readxl_1.2.0 bindrcpp_0.2.2
[16] jpeg_0.1-8 bindr_0.1.1 plyr_1.8.4
[19] munsell_0.5.0 gtable_0.2.0 cellranger_1.1.0
[22] rvest_0.3.2 htmlwidgets_1.3 codetools_0.2-15
[25] broom_0.5.1 Rcpp_1.0.0 scales_1.0.0
[28] backports_1.1.3 jsonlite_1.6 abind_1.4-5
[31] hms_0.4.2 png_0.1-7 digest_0.6.18
[34] stringi_1.2.4 tiff_0.1-5 grid_3.4.1
[37] cli_1.0.1 bitops_1.0-6 tools_3.4.1
[40] magrittr_1.5 RCurl_1.95-4.10 lazyeval_0.2.1
[43] crayon_1.3.4 pkgconfig_2.0.2 xml2_1.2.0
[46] lubridate_1.7.4 assertthat_0.2.0 httr_1.4.0
[49] rstudioapi_0.9.0 R6_2.3.0 nlme_3.1-131
[52] compiler_3.4.1
I do not understand the error and what it is pointing me towards. Does someone have an idea of how I could solve this problem?
Upgrading to a newer version of R is not a possibility on my local cluster.
Cheers,
Mathieu
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.....
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
Has anyone experienced having their plot labels cropped in knitted PDF's in Linux? This does not happen in my Windows machine.
Here is a minimal r-markdown example to replicate this problem.
---
output:
pdf_document:
keep_tex: true
---
---
{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
---
---
{r pressure, echo=FALSE}
plot(pressure)
---
Here is the output.
I have submitted this as a bug report here.
sessionInfo()
R version 3.4.4 (2018-03-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: elementary OS 0.4.1 Loki
Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.6.0
LAPACK: /usr/lib/lapack/liblapack.so.3.6.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats grDevices utils datasets graphics methods base
loaded via a namespace (and not attached):
[1] tseries_0.10-44 httr_1.3.1 tufte_0.3
[4] tidyr_0.8.0 jsonlite_1.5 uroot_2.0-9
[7] modelr_0.1.1 assertthat_0.2.0 TTR_0.23-3
[10] selectr_0.4-1 cellranger_1.1.0 yaml_2.1.18
[13] progress_1.2.0 pillar_1.2.2 backports_1.1.2
[16] lattice_0.20-35 glue_1.2.0 quadprog_1.5-5
[19] digest_0.6.15 rvest_0.3.2 colorspace_1.3-2
[22] htmltools_0.3.6 plyr_1.8.4 psych_1.8.3.3
[25] timeDate_3043.102 pkgconfig_2.0.1 broom_0.4.4
[28] haven_1.1.1 purrr_0.2.4 scales_0.5.0.9000
[31] git2r_0.21.0 tibble_1.4.2 ggplot2_2.2.1.9000
[34] withr_2.1.2 urca_1.3-0 nnet_7.3-12
[37] ansistrings_1.0.0.9000 lazyeval_0.2.1 cli_1.0.0.9002
[40] quantmod_0.4-13 mnormt_1.5-5 magrittr_1.5
[43] crayon_1.3.4 readxl_1.1.0 memoise_1.1.0
[46] evaluate_0.10.1 nlme_3.1-131.1 forcats_0.3.0
[49] xts_0.10-2 xml2_1.2.0 foreign_0.8-69
[52] rsconnect_0.8.8 tools_3.4.4 prettyunits_1.0.2
[55] hms_0.4.2 stringr_1.3.0 munsell_0.4.3
[58] bindrcpp_0.2.2 compiler_3.4.4 rlang_0.2.0.9001
[61] grid_3.4.4 rstudioapi_0.7 labeling_0.3
[64] rmarkdown_1.9 gtable_0.2.0 fracdiff_1.4-2
[67] curl_3.2 reshape2_1.4.3 R6_2.2.2
[70] zoo_1.8-1 lubridate_1.7.4 knitr_1.20
[73] dplyr_0.7.4 utf8_1.1.3 bindr_0.1.1
[76] rprojroot_1.3-2 readr_1.1.1 stringi_1.1.7
[79] parallel_3.4.4 Rcpp_0.12.16 lmtest_0.9-36