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Constantly showing alerts about not finding file #7427

Open rjake opened 4 years ago

rjake commented 4 years ago

System details

RStudio Edition : Desktop
RStudio Version : 1.3.1056
OS Version      :  Windows 10
R Version       :  3.6.3

Steps to reproduce the problem

I don't know what causes this to pop up.

Describe the problem in detail

This popup displays every 5 second or so. Very distracting and no clear way to resolve other than hitting ok or restarting RStudio image The log has a bunch of these entries

23 Jul 2020 14:52:28 [rsession-rileyj3] 
ERROR system error 2 (The system cannot find the file specified)

OCCURRED AT class rstudio::core::Error __cdecl rstudio::session::source_database::get(
  const class std::basic_string < char ,
  struct std::char_traits < char > ,
  class std::allocator < char > > & ,
  bool,
  class rstudio_boost::shared_ptr < class rstudio::session::source_database::SourceDocument >
) 
src / cpp / session / SessionSourceDatabase.cpp:693

LOGGED FROM: struct SEXPREC * __cdecl 
  rstudio::session::modules::r_packages::`anonymous -  namespace'::rs_getKnitParamsForDocument(struct SEXPREC *) 
src/cpp/session/modules/SessionRCompletions.cpp:463
RStudio Diagnostics Report ``` RStudio Diagnostics Report ========================== WARNING: This report may contain sensitive security information and / or personally identifiable information. Please audit the below and redact any sensitive information before submitting your diagnostics report. Generated: Thu Jul 23 11:11:20 2020 RStudio Version -------------------------------------------------- 1.3.1056 Session Information -------------------------------------------------- R version 3.6.3 (2020-02-29) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 17763) Matrix products: default 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] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] Rcpp_1.0.2 pillar_1.4.2 compiler_3.6.3 forcats_0.4.0 base64enc_0.1-3 tools_3.6.3 [7] odbc_1.2.2 zeallot_0.1.0 bit_1.1-14 tibble_2.1.3 gtable_0.3.0 pkgconfig_2.0.3 [13] rlang_0.4.5 DBI_1.1.0 rstudioapi_0.11 xfun_0.9 knitr_1.24 withr_2.1.2 [19] styler_1.1.1 stringr_1.4.0 dplyr_0.8.3 vctrs_0.2.0 hms_0.5.2 bit64_0.9-7 [25] grid_3.6.3 tidyselect_0.2.5 prettycode_1.0.2 glue_1.3.1 R6_2.4.0 purrr_0.3.3 [31] ggplot2_3.3.0 blob_1.2.0 magrittr_1.5 backports_1.1.4 scales_1.0.0 assertthat_0.2.1 [37] colorspace_1.4-1 tinytex_0.20 stringi_1.4.3 munsell_0.5.0 crayon_1.3.4 System Information -------------------------------------------------- sysname : Windows release : 10 x64 version : build 17763 nodename : C85B76FDE126 machine : x86-64 login : rileyj3 user : rileyj3 effective_user : rileyj3 Platform Information -------------------------------------------------- OS.type : windows file.sep : / dynlib.ext : .dll GUI : RStudio endian : little pkgType : win.binary path.sep : ; r_arch : x64 Environment Variables -------------------------------------------------- __COMPAT_LAYER : PerProcessSystemDPIForceOff ALLUSERSPROFILE : C:\ProgramData APPDATA : C:\Users\rileyj3\AppData\Roaming CLICOLOR_FORCE : 1 CommonProgramFiles : C:\Program Files\Common Files CommonProgramFiles(x86) : C:\Program Files (x86)\Common Files CommonProgramW6432 : C:\Program Files\Common Files COMPUTERNAME : C85B76FDE126 ComSpec : C:\WINDOWS\system32\cmd.exe DADIR : C:\Program Files (x86)\CheckPoint\Endpoint Security\Endpoint Common DB_ENVIRONMENT : UAT DEFLOGDIR : C:\ProgramData\McAfee\Endpoint Security\Logs DISPLAY : :0 DriverData : C:\Windows\System32\Drivers\DriverData DSN : QMR_DEV GFORTRAN_STDERR_UNIT : -1 GFORTRAN_STDOUT_UNIT : -1 HOME : C:\Users\rileyj3\Documents HOMEDRIVE : H: HOMEPATH : \ HOMESHARE : \\chop.edu\personalshare\hd6\rileyj3 JIA_API_TOKEN : *** redacted *** LOCALAPPDATA : C:\Users\rileyj3\AppData\Local LOGONSERVER : \\ENTWDCPW11 MPLENGINE : tkAgg MSYS2_ENV_CONV_EXCL : R_ARCH NUMBER_OF_PROCESSORS : 4 OneDrive : C:\Users\rileyj3\OneDrive OneDriveConsumer : C:\Users\rileyj3\OneDrive OS : Windows_NT PATH : C:/Apps/Oracle/instantclient_18_5;C:\Program Files\R\R-3.6.3\bin\x64;C:\Rtools\bin;C:\Program Files\ImageMagick-7.0.7-Q16;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\WINDOWS\System32\WindowsPowerShell\v1.0\;C:\Program Files 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Files\R\R-3.5.2\bin;C:\Users\rileyj3\AppData\Local\Microsoft\WindowsApps;C:\Users\rileyj3\AppData\Local\Programs\Python\Python38-32;C:\Users\rileyj3\AppData\Local\Programs\Python\Python38-32\Lib;C:\Users\rileyj3\AppData\Local\Programs\Python\Python38-32\Lib\site-packages;C:\Users\rileyj3\AppData\Local\Programs\Python\Python38-32\Scripts; PATHEXT : .COM;.EXE;.BAT;.CMD;.VBS;.VBE;.JS;.JSE;.WSF;.WSH;.MSC PROCESSOR_ARCHITECTURE : AMD64 PROCESSOR_IDENTIFIER : Intel64 Family 6 Model 142 Stepping 9, GenuineIntel PROCESSOR_LEVEL : 6 PROCESSOR_REVISION : 8e09 ProgramData : C:\ProgramData ProgramFiles : C:\Program Files ProgramFiles(x86) : C:\Program Files (x86) ProgramW6432 : C:\Program Files PSModulePath : C:\Program Files\WindowsPowerShell\Modules;C:\WINDOWS\system32\WindowsPowerShell\v1.0\Modules PUBLIC : C:\Users\Public PY_HOME : C:\Users\rileyj3\AppData\Local\Programs\Python\Python38-32 PYTHONPATH : 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desktop RSTUDIO_SESSION_PORT : 24909 RSTUDIO_USER_IDENTITY : rileyj3 RSTUDIO_WINUTILS : C:/Users/rileyj3/Documents/RStudio/bin/winutils RTOOLS40_HOME : C:\rtools40 SESSIONNAME : Console SystemDrive : C: SystemRoot : C:\WINDOWS TEMP : C:\Users\rileyj3\AppData\Local\Temp TERM : xterm-256color TMP : C:\Users\rileyj3\AppData\Local\Temp TZDIR : C:/PROGRA~1/R/R-36~1.3/share/zoneinfo UATDATA : C:\WINDOWS\CCM\UATData\D9F8C395-CAB8-491d-B8AC-179A1FE1BE77 USERDNSDOMAIN : CHOP.EDU USERDOMAIN : CHOP-EDU USERDOMAIN_ROAMINGPROFILE : CHOP-EDU USERPROFILE : C:\Users\rileyj3 windir : C:\WINDOWS R Version -------------------------------------------------- platform : x86_64-w64-mingw32 arch : x86_64 os : mingw32 system : x86_64, mingw32 status : major : 3 minor : 6.3 year : 2020 month : 02 day : 29 svn rev : 77875 language : R version.string : R version 3.6.3 (2020-02-29) nickname : Holding the Windsock R Home -------------------------------------------------- C:/PROGRA~1/R/R-36~1.3 R Search Path 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It is always run on startup. ### Additional commands can be placed in site or user Rprofile files ### (see ?Rprofile). ### Copyright (C) 1995-2015 The R Core Team ### Notice that it is a bad idea to use this file as a template for ### personal startup files, since things will be executed twice and in ### the wrong environment (user profiles are run in .GlobalEnv). .GlobalEnv <- globalenv() attach(NULL, name = "Autoloads") .AutoloadEnv <- as.environment(2) assign(".Autoloaded", NULL, envir = .AutoloadEnv) T <- TRUE F <- FALSE R.version <- structure(R.Version(), class = "simple.list") version <- R.version # for S compatibility ## for backwards compatibility only R.version.string <- R.version$version.string ## NOTA BENE: options() for non-base package functionality are in places like ## --------- ../utils/R/zzz.R options(keep.source = interactive()) options(warn = 0) # options(repos = c(CRAN="@CRAN@")) # options(BIOC = "http://www.bioconductor.org") options(timeout = 60) options(encoding = "native.enc") options(show.error.messages = TRUE) ## keep in sync with PrintDefaults() in ../../main/print.c : options(scipen = 0) options(max.print = 99999)# max. #{entries} in internal printMatrix() options(add.smooth = TRUE)# currently only used in 'plot.lm' options(stringsAsFactors = TRUE) if(!interactive() && is.null(getOption("showErrorCalls"))) options(showErrorCalls = TRUE) local({dp <- Sys.getenv("R_DEFAULT_PACKAGES") if(identical(dp, "")) ## it fact methods is done first dp <- c("datasets", "utils", "grDevices", "graphics", "stats", "methods") else if(identical(dp, "NULL")) dp <- character(0) else dp <- strsplit(dp, ",")[[1]] dp <- sub("[[:blank:]]*([[:alnum:]]+)", "\\1", dp) # strip whitespace options(defaultPackages = dp) }) ## Expand R_LIBS_* environment variables. Sys.setenv(R_LIBS_SITE = .expand_R_libs_env_var(Sys.getenv("R_LIBS_SITE"))) Sys.setenv(R_LIBS_USER = .expand_R_libs_env_var(Sys.getenv("R_LIBS_USER"))) local({ if(nzchar(tl <- Sys.getenv("R_SESSION_TIME_LIMIT_CPU"))) setSessionTimeLimit(cpu = tl) if(nzchar(tl <- Sys.getenv("R_SESSION_TIME_LIMIT_ELAPSED"))) setSessionTimeLimit(elapsed = tl) }) .First.sys <- function() { for(pkg in getOption("defaultPackages")) { res <- require(pkg, quietly = TRUE, warn.conflicts = FALSE, character.only = TRUE) if(!res) warning(gettextf('package %s in options("defaultPackages") was not found', sQuote(pkg)), call. = FALSE, domain = NA) } } ## called at C level in the startup process prior to .First.sys .OptRequireMethods <- function() { pkg <- "methods" # done this way to avoid R CMD check warning if(pkg %in% getOption("defaultPackages")) if(!require(pkg, quietly = TRUE, warn.conflicts = FALSE, character.only = TRUE)) warning('package "methods" in options("defaultPackages") was not found', call. = FALSE) } if(nzchar(Sys.getenv("R_BATCH"))) { .Last.sys <- function() { cat("> proc.time()\n") print(proc.time()) } ## avoid passing on to spawned R processes ## A system has been reported without Sys.unsetenv, so try this try(Sys.setenv(R_BATCH="")) } local({ if(nzchar(rv <- Sys.getenv("_R_RNG_VERSION_"))) suppressWarnings(RNGversion(rv)) }) ###-*- R -*- ## this will break if R is on a network share .Library <- file.path(chartr("\\", "/", R.home()), "library") .Library.site <- Sys.getenv("R_LIBS_SITE") .Library.site <- if(!nchar(.Library.site)) file.path(R.home(), "site-library") else unlist(strsplit(.Library.site, ";")) .Library.site <- .Library.site[file.exists(.Library.site)] if(!nzchar(Sys.getenv("R_LIBS_USER"))) Sys.setenv(R_LIBS_USER= file.path(Sys.getenv("R_USER"), "R", "win-library", paste(R.version$major, sub("\\..*$", "", R.version$minor), sep=".") )) invisible(.libPaths(c(unlist(strsplit(Sys.getenv("R_LIBS"), ";")), unlist(strsplit(Sys.getenv("R_LIBS_USER"), ";")) ))) local({ popath <- Sys.getenv("R_TRANSLATIONS", "") if(!nzchar(popath)) { paths <- file.path(.libPaths(), "translations", "DESCRIPTION") popath <- dirname(paths[file.exists(paths)][1]) } bindtextdomain("R", popath) bindtextdomain("R-base", popath) bindtextdomain("RGui", popath) assign(".popath", popath, .BaseNamespaceEnv) }) if(nzchar(Sys.getenv("R_PAPERSIZE"))) { options(papersize = Sys.getenv("R_PAPERSIZE")) } else { if(grepl("(canada|united.states)", Sys.getlocale("LC_MONETARY"), ignore.case = TRUE)) options(papersize = "letter") else options(papersize = "a4") } options(pager = if(length(grep("--ess", commandArgs()))) "console" else "internal", useFancyQuotes = (.Platform$GUI == "Rgui"), pdfviewer = Sys.getenv("R_PDFVIEWER", file.path(R.home("bin"), "open.exe"))) if(.Platform$GUI == "Rgui") Sys.setenv(GFORTRAN_STDOUT_UNIT = "-1", GFORTRAN_STDERR_UNIT = "-1") local({ br <- Sys.getenv("R_BROWSER", NA_character_) if(!is.na(br)) options(browser = br) tests_startup <- Sys.getenv("R_TESTS") if(nzchar(tests_startup)) source(tests_startup) ca_cert <- Sys.getenv("CURL_CA_BUNDLE", NA_character_) if(!is.na(ca_cert) && file.exists(ca_path <- file.path(R.home("etc"), "curl-ca-bundle.crt"))) Sys.setenv(CURL_CA_BUNDLE = ca_path) }) R Site Profile: C:/PROGRA~1/R/R-36~1.3/etc/Rprofile.site -------------------------------------------------- # Things you might want to change # options(papersize="a4") # options(editor="notepad") # options(pager="internal") # set the default help type # options(help_type="text") options(help_type="html") # set a site library # .Library.site <- file.path(chartr("\\", "/", R.home()), "site-library") # set a CRAN mirror # local({r <- getOption("repos") # r["CRAN"] <- "http://my.local.cran" # options(repos=r)}) # Give a fortune cookie, but only to interactive sessions # (This would need the fortunes package to be installed.) # if (interactive()) # fortunes::fortune() R User Profile: C:/Users/rileyj3/Documents/.Rprofile -------------------------------------------------- # Options ---- options( repos = c( CRAN = "https://cran.rstudio.com/", CHOPRAN = "https://github.research.chop.edu/pages/CQI/chopran/" ), scipen = 999 ) # functions ---- .rm_ls <- function(regex, negate = FALSE) { # x <- 1;x2 <- 2; y <- 1;regex <- "^[xy]"; negate <- FALSE obj_list <- ls(envir = globalenv()) to_remove <- obj_list[stringr::str_detect(obj_list, regex, negate = negate)] rm(list = to_remove, envir = globalenv()) } # .rm_ls("^[xy]") .rprofile <- function(edit_r_profile) { usethis::edit_r_profile() } # set working directory to file location .set_here <- function(return = FALSE) { context <- rstudioapi::getSourceEditorContext() wd <- paste0('setwd("', dirname(context$path), '")') if (return) { cat(wd) } else { context rstudioapi::modifyRange( context$selection[[1]]$range, wd, id = context$id ) } } .custom_functions <- function() { r_profile <- parse("~/.Rprofile") fn_code <- as.character(r_profile[grep("^\\.", r_profile)]) new_fn <- stringr::str_remove( stringr::str_extract(fn_code, "^[^\\{]*"), " <- function" ) # stringr::str_remove_all(fn_code, " .*|\\n|\\}") message("\nYou added these functions:") print( styler::style_text( text = trimws(new_fn) ) ) } .custom_functions() R Site Environ: C:/PROGRA~1/R/R-36~1.3/etc/Renviron.site -------------------------------------------------- (File does not exist) R User Environ: C:/Users/rileyj3/Documents/.Renviron -------------------------------------------------- PATH = C:/Apps/Oracle/instantclient_18_5;"${PATH} R Temporary Directory -------------------------------------------------- C:\Users\rileyj3\AppData\Local\Temp\RtmpSwYOP0 Files in R Temporary Directory -------------------------------------------------- rs-graphics-dc2a93ab-d0f5-45bf-b191-4788f345b369 ```

Describe the behavior you expected

No popup

kevinushey commented 4 years ago

Note: bugs of this form can be reproduced by (for example) removing the RStudio state folder(s) while an RStudio session is open.

ahcyip commented 3 years ago

I also see this all the time. @rjake

If it's something about the folders and auto-save, I'm thinking this may be an issue of my code/files being stored in a backed-up Dropbox or Google Drive folder where the file/folders are being updated/changed behind the scenes all the time. @kevinushey thanks for your attention and tips!