How do you eventually resolve 'cannot open file 'renv/activate.R'

lychenus13 · November 12, 2021, 4:56am

We are trying to contribute on the study for LegendT2DM.

We realize that the package has to use “renv”. But there was not a lot of success. As we tried to install LegendT2DM from github with

devtools::install_github("ohdsi-studies/LegendT2dm")

it always stop with the errors

Error in file(filename, "r", encoding = encoding) : 
  cannot open the connection
Calls: source -> file
In addition: Warning message:
In file(filename, "r", encoding = encoding) :
  cannot open file 'renv/activate.R': No such file or directory
Execution halted

How to resolve that? The packages somehow worked for previous study Cervello. But it didnt work a month later and I have no idea why.

Tried googling, there was not much information with ‘renv/activate.R’. Tried all solutions but it does not work.

THanks

lychenus13 · November 12, 2021, 5:57am

I checked with devtools::install_github("ohdsi/Achilles") which was previously working

After installing renv, Achilles no longer work and it cannot be ‘reinstalled’. No idea why.

Chungsoo_Kim · November 12, 2021, 6:03am

Hi,

when you turn on the renv environment, the library path will be changed to renv library, not the local R library. If you want to turn off the renv and set the r library to the original one, you can run this:

renv::deactivate()

lychenus13 · November 12, 2021, 6:18am

Sorry I do not think it works. It just goes back to cannot open file 'renv/activate.R': No such file or directory after renv::deactivate()

Seems it cannot be turned off. Skynet??

No idea why.

Chungsoo_Kim · November 12, 2021, 6:32am

That’s odd. you can try renv::init() and select option 2: Discard the lockfile and re-initialize the project. maybe? and then you also try to renv:: activate() again.

schuemie · November 12, 2021, 7:20am

I think the instructions that @msuchard wrote for the LegendT2dm package aren’t very clear. Instead of using devtools::install_github(), as @lychenus13 did, you should clone the LegendT2dm repo.

So, assuming you’re running R-Studio, and have git installed:

In R-Studio, click File → New Project → Version Control → Git → Use ‘https://github.com/ohdsi-studies/LegendT2dm.git’ as repository URL → Create Project
Once Legend2Tdm has been cloned, the project automatically opens in R-Studio. Then follow the instructions in the LegendT2dm README.

lychenus13 · November 12, 2021, 8:21am

i have done importing and restoring renv, very smoothly except for the package cohortmethod

now it says

ERROR: compilation failed for package 'CohortMethod'
Warning in system(paste(cmd, "shlib-clean")) : 'make' not found
Warning in system(cmd) : 'make' not found
* removing 'D:/OHDSI-LegendT2DM/LegendT2dm/renv/staging/1/CohortMethod'
Error: install of package 'CohortMethod' failed [error code 1]

json states that it runs on 4.2.0. do i need to change anything?

perhaps it is R 4.10
edit: R4.0.5 does not fix anything
edit2: it was .Renviron

lychenus13 · November 12, 2021, 9:52am

Now that the packages are succesfully installed. However when i press “install and restart”, the error would be

Error in file(filename, "r", encoding = encoding) : 
  cannot open the connection
Calls: source -> file
In addition: Warning message:
In file(filename, "r", encoding = encoding) :
  cannot open file 'renv/activate.R': No such file or directory
Execution halted

Exited with status 1.

lychenus13 · November 12, 2021, 10:09am

Some how T2DM is built with

Sys.unsetenv("R_PROFILE_USER")
devtools::check()

i do not know why it worked.

now the problem is

Connecting using PostgreSQL driver
Creating cohort table
Creating cohort table took 0.195 secs
Error: '' does not exist in current working directory ('D:/OHDSI-LegendT2DM/LegendT2dm').
In addition: Warning message:
In dir.create(outputFolder, recursive = TRUE) :
  'D:\OHDSI-LegendT2DM\results' already exists
An error report has been created at  D:/OHDSI-LegendT2DM/results//errorReportR.txt

Thread: Main
Message:  Error: '' does not exist in current working directory ('D:/OHDSI-LegendT2DM/LegendT2dm'). 
Level:  FATAL
Time:  2021-11-12 18:08:46

Stack trace:
13: stop("'", path, "' does not exist", if (!is_absolute_path(path)) paste0(" in current working directory ('", getwd
12: check_path(path)
11: standardise_path(file)
10: datasource(file, skip = skip, skip_empty_rows = FALSE, skip_quote = FALSE)
9: read_lines_raw(file, n_max = n_max)
8: unlist(read_lines_raw(file, n_max = n_max))
7: readr::guess_encoding(file = fileName, n_max = min(1e+07))
6: checkInputFileEncoding(pathToCsv)
5: getCohortsJsonAndSqlFromPackage(packageName = packageName, cohortToCreateFile = cohortToCreateFile, cohortIds = c
4: getCohortsJsonAndSql(packageName = packageName, cohortToCreateFile = cohortToCreateFile, baseUrl = baseUrl, cohor
3: CreateAllCohorts.R#63: CohortDiagnostics::instantiateCohortSet(connectionDetails = connectionDetails, cdmDatabase
2: Assessment.R#75: createExposureCohorts(connectionDetails = connectionDetails, cdmDatabaseSchema = cdmDatabaseSche
1: assessPhenotypes(connectionDetails = connectionDetails, cdmDatabaseSchema = cdmDatabaseSchema, oracleTempSchema =

R version:
R version 4.0.5 (2021-03-31)

looks like

was the last place it can ever produce a good log.
What is cohortToCreateFile = cohortToCreateFile?

extra log that might be helpful

2021-11-12 18:44:25	[Main thread]	INFO	LegendT2dm	assessPhenotypes	Starting assessPhenotypes() for LEGEND-T2DM class-vs-class studies
2021-11-12 18:44:25	[Main thread]	INFO	LegendT2dm	createExposureCohorts	Creating class exposure cohorts
2021-11-12 18:44:25	[Main thread]	INFO	LegendT2dm	createExposureCohorts	- Populating table legendt2dm_study_class_cohort
2021-11-12 18:44:25	[Main thread]	WARN	CohortDiagnostics	instantiateCohortSet	OracleTempSchema has been deprecated by DatabaseConnector
2021-11-12 18:44:25	[Main thread]	INFO	CohortDiagnostics	createCohortTable	Creating cohort table
2021-11-12 18:44:25	[Main thread]	DEBUG	CohortDiagnostics	createCohortTable	Created table temp_renv.legendt2dm_study_class_cohort
2021-11-12 18:44:25	[Main thread]	DEBUG	CohortDiagnostics	getCohortsJsonAndSqlFromPackage	Executing on cohorts specified in package - LegendT2dm
2021-11-12 18:44:25	[Main thread]	FATAL	readr	check_path	Error: '' does not exist in current working directory ('D:/OHDSI-LegendT2DM/LegendT2dm').

Where is the “'” ?

lychenus13 · November 16, 2021, 7:39am

So I turned to a untouched fresh PC nearby, reinstall everything and it worked. no idea what went wrong but at least it worked. so the solution is to master uninstall everything and redo.

jposada · November 16, 2021, 1:16pm

I know I am late to the party but if you can give the docker option a try

lychenus13 · November 18, 2021, 2:21am

maybe next time. the code has been running for a few days already dun wanna touch it now. i just want it done eh.

i thought there was a exodus in the dev community when docker was charging people were moving away.

jposada · November 18, 2021, 4:05pm

Docker is still free for our use case. It is for orgs that are pushing and pulling images like crazy, we are not at those levels yet

thomasfalconer · November 30, 2022, 7:50pm

Hi @schuemie , @lychenus13 , @Chungsoo_Kim, can I revive this topic? I’m encountering the same issue as @lychenus13 had, with the error:

installing source package ‘ParallelLogger’ …
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error in file(filename, “r”, encoding = encoding) :
cannot open the connection
Calls: source → file
In addition: Warning message:
In file(filename, “r”, encoding = encoding) :
cannot open file ‘renv/activate.R’: No such file or directory
Execution halted

The package doesn’t matter but WHERE the package lives does matter. Packages on CRAN install fine but packages for which I need to run 'remotes::install_github(…) fail with the above error message.

I noticed that, even when I open a plain RStudio session (outside of an R project), the console reports the following:

Project ‘~’ loaded. [renv 0.15.5]
[Workspace loaded from ~/.RData]

I’ve executed ‘renv::deactivate()’ but, like mentioned, doesn’t resolve the error. I’ve checked to make sure the packages are being downloading into their respective local and renv C drive directories for when I’m not in an R environment and when I am in an R environment, respectively. That also is fine.

Any help on this matter from what has been learned since the original posting will be greatly appreciated. Thanks, all.

thomasfalconer · November 30, 2022, 9:03pm

@schuemie @lychenus13 @Chungsoo_Kim

update: I think I solved the issue. Opening the .Rprofile file in my C:/Users/…/Documents directory with Notepad++ and removing the line ‘source(‘renv/activate.R’)’ seemed to have worked.