Error in installConda() : conda installation failed with status code '2'

[maqingyue]

Hello, thank you very much for developing this software. I encountered the following error while running writeH5AD locally. How can I correct it?

writeH5AD(sce, file = 'D:/filtered_featured_bc_matrix.h5ad')
Error in installConda() : conda installation failed with status code '2'

[LTLA]

Is there any other error message? Because that could mean anything.

[maqingyue]

There is no other error reporting information. This is the entire process.

a <- readRDS("D:/BGI_learning/select-samples/results/liver/aging009-10.0.3.10.rds")
sce<- as.SingleCellExperiment(a)
writeH5AD(sce, file = 'D:/filtered_featured_bc_matrix.h5ad')
Error in installConda() : conda installation failed with status code '2'

[vjcitn]

Is your disk full? Do you have permissions to install software on the machine? Does example(basiliskRun) succeed?

[LTLA]

basilisk.utils::installConda doesn't intercept any error messages, so if nothing's being shown, then I don't know what's going on. Maybe the initial download of the installer was corrupted - you could try flushing the contents of basilisk.utils::getExternalDir(). If that still doesn't work, do debug(basilisk.utils::installConda) and step through the function until you get to

https://github.com/LTLA/basilisk.utils/blob/7ee52130919df88316f29e0be8cbd4aa4f32a6c2/R/installConda.R#L123

See what paste(c(tmploc, inst_args)) says, and try running that command on the command line.

[maqingyue]

@LTLA , This is the result of my following your instructions.

Browse[6]> paste(c(tmploc, inst_args))
[1] "C:/Users/maqingyue/AppData/Local/R/cache/R/basilisk/Miniconda3-py37_4.8.3-Windows-x86_64.exe"
[2] "/InstallationType=JustMe"
[3] "/AddToPath=0"
[4] "/RegisterPython=0"
[5] "/S"
[6] "/NoRegistry=1"
[7] "/D=C:\Users\MAQING1\AppData\Local\R\cache\R\basilisk\18E7611.1\0"
Browse[6]>
Error in installConda() : conda installation failed with status code '2'
debug: if (!success) {
unlink2(dest_path, recursive = TRUE)
}
Browse[6]>
debug: unlink2(dest_path, recursive = TRUE)
Browse[6]>

The parameter "status" may come from "status<- system2 (tmploc, inst_args)" or "status<- system2 (" bash ", inst_args)". Then I also ran these two sentences of code, hoping that this will help solve the problem.
Browse[7]> system2(tmploc, inst_args)
Browse[7]> system2("bash", inst_args)
/usr/bin/bash: /InstallationType=JustMe: No such file or directory

[maqingyue]

@vjcitn , There is still space on my disk. This is my personal computer, and I should have installation permissions. Is the example (basiliskRun) you mentioned the following code? I ran the following section and finally got the same error.

my_env <- basilisk::BasiliskEnvironment(envname="my_env_name",
pkgname="name.of.package",
packages=c("pandas==0.25.1"))

res <- basilisk::basiliskRun(env=my_env, fun=function(args) {
out <- reticulate::import("pandas")
return(some_r_object)
})

[vjcitn]

example(basiliskRun) can be run directly right after library(basilisk). It should produce output like

> example(basiliskRun)

bslskR> ## Don't show: 
bslskR> basilisk.utils::installConda()
[1] FALSE

bslskR> ## End(Don't show)
bslskR> 
bslskR> # Creating an environment (note, this is not necessary
bslskR> # when supplying a BasiliskEnvironment to basiliskStart):
bslskR> tmploc <- file.path(tempdir(), "my_package_A")

bslskR> if (!file.exists(tmploc)) {
bslskR+     setupBasiliskEnv(tmploc, c('pandas=1.4.3'))
bslskR+ }
+ '/home/stvjc/.cache/R/basilisk/1.11.3/0/bin/conda' 'create' '--yes' '--prefix' '/tmp/Rtmps76fUd/my_package_A' 'python=3.8.13' '--quiet' '-c' 'conda-forge'
Collecting package metadata (current_repodata.json): ...working... 

If you have never seen a response like that shown above, your system will need to be modified to allow user-level conda manipulations.

[maqingyue]

@vjcitn , I really don't have the corresponding output. Errors are almost identical. I don't know why personal computer need to be modified to allow user-level conda. Is the change you said changed here(fig1)? I did not successfully correct this error.

example(basiliskRun)

bslskR> ## Don't show:
bslskR> basilisk.utils::installConda()
Error in basilisk.utils::installConda() :
conda installation failed with status code '2'

fig1

[vjcitn]

What is the result of reticulate::py_config()?

[maqingyue]

@vjcitn, the result of reticulate::py_config() is following:

reticulate::py_config()
python: C:/Users/maqingyue/AppData/Local/r-miniconda/envs/r-reticulate/python.exe
libpython: C:/Users/maqingyue/AppData/Local/r-miniconda/envs/r-reticulate/python38.dll
pythonhome: C:/Users/maqingyue/AppData/Local/r-miniconda/envs/r-reticulate
version: 3.8.13 | packaged by conda-forge | (default, Mar 25 2022, 05:59:00) [MSC v.1929 64 bit (AMD64)]
Architecture: 64bit
numpy: C:/Users/maqingyue/AppData/Local/r-miniconda/envs/r-reticulate/Lib/site-packages/numpy
numpy_version: 1.23.4

[LTLA]

[1] "C:/Users/maqingyue/AppData/Local/R/cache/R/basilisk/Miniconda3-py37_4.8.3-Windows-x86_64.exe"

You're using an out-of-date version. Latest basilisk.utils should pull down py38_4.12.0, not py37_4.8.3.

In any case, you need to figure out if the Conda installer runs at all on your computer. As I said, you need to extract the commands used by installConda and run them on the command line. In your case, it would be something like:

C:/Users/maqingyue/AppData/Local/R/cache/R/basilisk/Miniconda3-py37_4.8.3-Windows-x86_64.exe /InstallationType=JustMe /AddToPath=0 /RegisterPython=0 /S /NoRegistry=1 /D=C:\Users\MAQING~1\AppData\Local\R\cache\R\basilisk\18E761~1.1\0

Not tested, of course, but I will leave the rest to you.

If this doesn't work on the command line, then it's not a basilisk problem, it's a conda problem, and that's beyond my ability to help. basilisk just wraps the conda installer at this point, so if the latter doesn't work, the former won't either.

[maqingyue]

@vjcitn , @LTLA , Thank you for your patience and I will continue to try to solve this problem.

[alanocallaghan]

I've run into the same error on windows devel GHA: https://github.com/alanocallaghan/densvis/actions/runs/5884832224/job/15960238189

Not sure if exactly the same reason as on GHA, but the installer runs fine if I open it directly, but silently fails with the system2 call

[alanocallaghan]

Seems like most basilisk dependencies are failing on palomino in bioc-devel with this error:

• BiocSklearn
• cfTools
• densvis
• MOFA2
• orthos
• pareg
• snifter
• spatialDE
• velociraptor
• zellkonverter
• FLAMES

I haven't checked the rest in detail, but it seems they either explicitly don't support windows, or they don't load conda during R CMD build/check

I've tried switching conda versions with snifter, and anything past 4.12 doesn't work on windows. Does basilisk need any newer conda features? If we have to stick with 22+, then I'm going to have to remove windows support to get bioc checks to pass.