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cmap / cmapR

Tools for manipulating annotated data matrices
BSD 3-Clause "New" or "Revised" License
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Error in parse.gctx(gct_file, matrix_only = TRUE) : could not find function "parse.gctx", error message shows up for all other functions too #28

Closed Jimmay13 closed 5 years ago

Jimmay13 commented 5 years ago

I recently spent 8+ hours trying to get your package functions to work. At first, all that worked was the parse.gctx function. After reinstalling your package and the other packages necessary, now the parse.gctx function doesnt work either.

library(cmapR) library(rhdf5) gct_file <- system.file("/Users/jamesordaya/Downloads/GinnysBioinformaticsFolder/GSE70138_Broad_LINCS_Level3_INF_mlr12k_n78980x22268_2015-06-30.gct", package="cmapR") (ds <- parse.gctx(gct_file, matrix_only=TRUE)) print(my_ds) is my code. I also tried all other functions which get a similar error message

"Error in parse.gctx(gct_file, matrix_only = FALSE) : could not find function "parse.gctx""

I dont know what to do. I must be honest, I am still pretty new to R developer packages from GitHub so I may need a bit more direction than others but, like I said, I was able to get the parse function to work before the reinstall and now it has the same errors all the other functions had before (and afterwards).

tnat1031 commented 5 years ago

Hi @Jimmay13 ,

Thanks for using this package and my apologies for the delayed reply. Seems like perhaps there is an issue with the cmapR install. Does the code

library(cmapR)

work successfully? If so, can you please also run this and post the output:

find.package("cmapR")

Thanks, Ted

felon02 commented 4 years ago

i met the same problem with Jimmay13. here's my input, output and my R version: image

tnat1031 commented 4 years ago

Hi @felon2, @Jimmay13,

My apologies for the confusion. We're in the process of submitting to Bioconductor and have changed the some of the function naming conventions to comply with their standards. Function names that used to contain '.' have been replaced with '_'. Hence, parse.gctx is now parse_gctx and so on. Please try that and see if it works. There is additional info and examples in the vignettes/tutorial.Rmd.

Thanks a lot, Ted

On Thu, Jan 16, 2020 at 10:49 PM felon02 notifications@github.com wrote:

i met the same problem with Jimmay13. here's my input, output and my R version: [image: image] https://user-images.githubusercontent.com/30990200/72582937-5f11e880-391f-11ea-80b1-e59da177317d.png

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