Error downloading and reading the library (No package called FField)

[Sudheshna30]

Error: package or namespace load failed for ‘GenVisR’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): there is no package called ‘FField’

[blackbeerd]

I was just searching for a solution for similar error... Trying to install genvisr on a linux cluster in a conda R=4.2 environment. "FFiled not available for this version of R"

But the Bioc page for this says to open R (4.2) and install GenVisR...? https://bioconductor.org/packages/release/bioc/html/GenVisR.html

Is this a version mistake?

[Sudheshna30]

I was just searching for a solution for similar error... Trying to install genvisr on a linux cluster in a conda R=4.2 environment. "FFiled not available for this version of R"

But the Bioc page for this says to open R (4.2) and install GenVisR...? https://bioconductor.org/packages/release/bioc/html/GenVisR.html

Is this a version mistake?

Im not sure. I'm on the same version of R and the same thing confused me as well

[blackbeerd]

I was just searching for a solution for similar error... Trying to install genvisr on a linux cluster in a conda R=4.2 environment. "FFiled not available for this version of R" But the Bioc page for this says to open R (4.2) and install GenVisR...? https://bioconductor.org/packages/release/bioc/html/GenVisR.html Is this a version mistake?

Im not sure. I'm on the same version of R and the same thing confused me as well

Thanks for the sanity check! Let me know if you find a solution (I will as well). I was thinking of trying to install with an earlier version of Bioc (and R), but I haven't checked how recent the FField package (which version of R, that is)...

[Sudheshna30]

I was just searching for a solution for similar error... Trying to install genvisr on a linux cluster in a conda R=4.2 environment. "FFiled not available for this version of R" But the Bioc page for this says to open R (4.2) and install GenVisR...? https://bioconductor.org/packages/release/bioc/html/GenVisR.html Is this a version mistake?

Im not sure. I'm on the same version of R and the same thing confused me as well

Thanks for the sanity check! Let me know if you find a solution (I will as well). I was thinking of trying to install with an earlier version of Bioc (and R), but I haven't checked how recent the FField package (which version of R, that is)...

I found this https://cran.r-project.org/web/packages/FField/index.html

[blackbeerd]

I was just searching for a solution for similar error... Trying to install genvisr on a linux cluster in a conda R=4.2 environment. "FFiled not available for this version of R" But the Bioc page for this says to open R (4.2) and install GenVisR...? https://bioconductor.org/packages/release/bioc/html/GenVisR.html Is this a version mistake?

Im not sure. I'm on the same version of R and the same thing confused me as well

Thanks for the sanity check! Let me know if you find a solution (I will as well). I was thinking of trying to install with an earlier version of Bioc (and R), but I haven't checked how recent the FField package (which version of R, that is)...

I found this https://cran.r-project.org/web/packages/FField/index.html

So I got mine working.

Here's what I did, not sure it's applicable to your situation?\ 1) in R (version 4.2) I installed the devel version of Bioc (https://contributions.bioconductor.org/use-devel.html) if (!requireNamespace("BiocManager", quietly=TRUE)) install.packages("BiocManager") BiocManager::install(version = "devel")

1a) I reran GenVisR install in R BiocManager::install("GenVisR")

and saw that stringi was not installing, so I quit R and installed via conda in bash. This thread was useful: https://github.com/gagolews/stringi/issues/302 - suggests apt install instead of conda if you're not using conda

2) conda install -c conda-forge r-stringi 3) Started R 4) Ran GenVisR install again (BiocManager::install("GenVisR")), but enter "n" when it asked if I wanted to update stringi. 5) Loaded GenVisR library (library(GenVisR)) 6) Tried the sample data following commands in waterfall plot tutorial here: https://genviz.org/module-03-genvisr/0003/02/01/waterfall_GenVisR/

Good luck!

[Sudheshna30]

@blackbeerd downloading devel and running GenVis worked for me! Thanks to you!

[zlskidmore]

re-opening this, the FField package is now deprecated, it's only used in the lolliplot() function, and i have a working replacement I just need to strip out the dependency and the old lolliplot function

[Sudheshna30]

re-opening this, the FField package is now deprecated, it's only used in the lolliplot() function, and i have a working replacement I just need to strip out the dependency and the old lolliplot function

@zlskidmore May I know how to do that?

[zlskidmore]

if you clone the repo, you'll find FField calls in the DESCRIPTION and NAMESPACE files, they need to be removed, along with the entire lolliplot() function which is located in R/deprecated.R

[bounlu]

Will you push the fixed version soon?

[zlskidmore]

Currently at a conference, it should be pushed by end of the week

[Hejhacz]

Hello!

@zlskidmore Could I know when the fixed version will be available to install?

I'm a newbie and really would like to use GenVisR but I do not know how to deal with this FField error :(

[csmatyi]

BiocManager::install("GenVisR")

I tried doing what you said but no luck, FField still keeps coming up: My error:

---

library("GenVisR") Error: package or namespace load failed for ‘GenVisR’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): there is no package called ‘FField’

[mheskett]

I was just searching for a solution for similar error... Trying to install genvisr on a linux cluster in a conda R=4.2 environment. "FFiled not available for this version of R" But the Bioc page for this says to open R (4.2) and install GenVisR...? https://bioconductor.org/packages/release/bioc/html/GenVisR.html Is this a version mistake?

Im not sure. I'm on the same version of R and the same thing confused me as well

Thanks for the sanity check! Let me know if you find a solution (I will as well). I was thinking of trying to install with an earlier version of Bioc (and R), but I haven't checked how recent the FField package (which version of R, that is)...

I found this https://cran.r-project.org/web/packages/FField/index.html

So I got mine working.

Here's what I did, not sure it's applicable to your situation?\

1. in R (version 4.2) I installed the devel version of Bioc (https://contributions.bioconductor.org/use-devel.html) if (!requireNamespace("BiocManager", quietly=TRUE)) install.packages("BiocManager") BiocManager::install(version = "devel")

1a) I reran GenVisR install in R BiocManager::install("GenVisR")

and saw that stringi was not installing, so I quit R and installed via conda in bash. This thread was useful: gagolews/stringi#302 - suggests apt install instead of conda if you're not using conda

2. conda install -c conda-forge r-stringi
3. Started R
4. Ran GenVisR install again (BiocManager::install("GenVisR")), but enter "n" when it asked if I wanted to update stringi.
5. Loaded GenVisR library (library(GenVisR))
6. Tried the sample data following commands in waterfall plot tutorial here: https://genviz.org/module-03-genvisr/0003/02/01/waterfall_GenVisR/

Good luck!

thanks for this. at that point using the package is not worth it because i could spend days trying to reproduce this. hopefully the developers are willing to help out!

[zlskidmore]

I appreciate everyone's patience a fix has been pushed up, you should be able to install from github now, or from the bioc-devel branch once the nightly builds complete. Please re-open if there are still issues after 24 hours.

[jon4thin]

I am unable to get Lolliplot() to work and I am not sure if this is expected or not: https://github.com/griffithlab/GenVisR/issues/394