ProfVis ( or rstudio profile" in ubuntu returns /profiles/fileXXXXXXXXXXX.html not found

[nevilamos]

RStudio Edition : Server (free version) RStudio Version : 1.2.1335 OS Version : Ubuntu 18.04.2 LTS R Version : 3.6.0 (2019-04-26)

I am trying to profile a number of funntions running in rstudio server on aws.

when the function /profiling completes instead of the usual output I just see an window with

/profiles/filexxxxxxxxx.html not found.

how do I get thu correct profvis output?

toy example ( not the function I'm trying to profile

simulation <- function(p=1000, n=100){

• df <- list()
• for(i in 1:p){ # simulate p columns of data
• df[[paste0("Var", i)]] <- rnorm(n)
• }
• df <- as.data.frame(df)
• return(apply(df, 2, mean))
• } profvis(simulation()) Warning messages: 1: In (function (line, mem, time) : NAs introduced by coercion to integer range 2: In (function (line, mem, time) : NAs introduced by coercion to integer range 3: In (function (line, mem, time) : NAs introduced by coercion to integer range 4: In (function (line, mem, time) : NAs introduced by coercion to integer range 5: In (function (line, mem, time) : NAs introduced by coercion to integer range 6: In (function (line, mem, time) : NAs introduced by coercion to integer range 7: In dir.create(tempPath, recursive = TRUE) : '/home/rstudio/ShinyApps/FAME_FMR/.Rproj.user/2B0B60B/profiles-cache' already exists dir("/home/rstudio/ShinyApps/FAME_FMR/.Rproj.user/2B0B60B/profiles-cache") character(0) Warning message: In dir.create(tempPath, recursive = TRUE) : '/home/rstudio/ShinyApps/FAME_FMR/.Rproj.user/2B0B60B/profiles-cache' already exists

R version 3.6.0 (2019-04-26) 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/openblas/libblas.so.3 LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so

locale: [1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8 LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
[7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] parallel tools stats graphics grDevices utils datasets methods base

other attached packages: [1] profvis_0.3.6 Rfast_1.9.9 RcppZiggurat_0.1.5 Rcpp_1.0.1 data.table_1.12.8 filematrix_1.3 tabularaster_0.6.5 [8] reshape2_1.4.3 tiff_0.1-5 dplyr_0.8.0.1 doParallel_1.0.15 iterators_1.0.12 foreach_1.5.0 sf_0.9-5
[15] fasterize_1.0.2 raster_3.3-7 tidyr_0.8.3 Matrix.utils_0.9.8 Matrix_1.2-17 sp_1.4-2

loaded via a namespace (and not attached): [1] tidyselect_0.2.5 purrr_0.3.2 splines_3.6.0 lattice_0.20-38 spatstat.utils_1.17-0 htmltools_0.3.6
[7] yaml_2.2.0 mgcv_1.8-28 rlang_0.3.4 e1071_1.7-3 spatstat.data_1.4-3 pillar_1.3.1
[13] spatstat_1.64-1 glue_1.3.1 DBI_1.0.0 plyr_1.8.4 stringr_1.4.0 htmlwidgets_1.3
[19] codetools_0.2-16 class_7.3-15 KernSmooth_2.23-15 tensor_1.5 classInt_0.4-3 grr_0.9.5
[25] jsonlite_1.6 abind_1.4-5 deldir_0.1-28 digest_0.6.18 stringi_1.4.3 polyclip_1.10-0
[31] grid_3.6.0 magrittr_1.5 goftest_1.2-2 tibble_2.1.1 crayon_1.3.4 pkgconfig_2.0.2
[37] assertthat_0.2.1 rstudioapi_0.10 R6_2.4.0 rpart_4.1-15 units_0.6-7 nlme_3.1-139

[kevinushey]

Can you please fill out the bug report header?

System details

RStudio Edition : <!-- Desktop or Server -->
RStudio Version : 
OS Version      : 
R Version       : 

[nevilamos]

Added to original post - apologies for omitting it.

On Tue, 21 Jul 2020 at 03:07, Kevin Ushey notifications@github.com wrote:

Can you please fill out the bug report header? System details

RStudio Edition : RStudio Version : OS Version : R Version :

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/rstudio/profvis/issues/119#issuecomment-661198299, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALKPWC3RMAOWQWGCPOLHYSTR4R2UTANCNFSM4PCEE5EQ .

[giovannic]

Any news on this?

RStudio Edition : RStudio Server RStudio Version : Version 1.4.1103 OS Version : Ubuntu Bionic R Version : 4.0.3

I'm getting the same error running from a docker image: rocker/rstudio:4.0.3

test code:

profvis({for (i in seq(1e6)) {i^6}})

Error message:

/profiles/file[hash].html not found

Log:

[s6-init] making user provided files available at /var/run/s6/etc...exited 0.
[s6-init] ensuring user provided files have correct perms...exited 0.
[fix-attrs.d] applying ownership & permissions fixes...
[fix-attrs.d] done.
[cont-init.d] executing container initialization scripts...
[cont-init.d] userconf: executing...
[cont-init.d] userconf: exited 0.
[cont-init.d] done.
[services.d] starting services
[services.d] done.
26 Feb 2021 14:49:26 [rsession-rstudio] WARNING FileLock classes not yet initialized; please call 'FileLock::initialize()' and 'FileLock::cleanUp()' as appropriate; LOGGED FROM: static bool rstudio::core::FileLock::verifyInitialized() src/cpp/core/file_lock/FileLock.cpp:110

[svalvaro]

I have also ran into this, and I solved it by specifying the output of the profile file, like this:

profvis({func}, prof_output = getwd())

[DGrv]

I add this issue because I did have the rmarkdown package installed. So install it install.packages("rmarkdown"). And maybe lot it library(rmarkdown)

[hadley]

If anyone sees this again, please file a reprex and I'll look into it.