Problem in importing EEMs by the "important_function = csv2"
GuoZhongyuPhD opened this issue · comments
Hi,
I imported my EEMs data by the following codes. I have to use the important_function = csv2 because the column is emission.
folder <- system.file("EEMs_data",package = "staRdom")
eem_list <- eem_read(folder, recursive = TRUE, import_function = eem_csv2) #Import EEMs files
But error occurred which was "Error in x[!is.na(em), !is.na(ex)] : (subscript) logical subscript too long"
I also tried those codes with the example data and the same error occurred. But we I replace csv2 by csv, it succeeded. But that means the column is excitation which is opposite compared with my EEMs.
Could anyone help me?
This issue will be fixed a the next version.
Dear Matthias
First I want to say thank you for the great work that you have been doing with this package. It has been helping me a lot for the last two years. Nevertheless, I recently experienced an issue with the package because I can´t run the ´eem_read´ function, even with the examples that are given on the vignettes.
I am really ashamed because probably could be a simple error, however, I am not doing this for the first time and I have already tried with several procedures but the error is the same:
Error in .eem_csv(file) : argument "file" is missing, with no default or
Error in file.info(file) : invalid filename argument
In advance, I would appreciate your help.
Regards
Dear Rolandu,
I just tried to read the example EEMs and had no problem, could you please provide me with more information: Which versions of staRdom and eemR are you using? Could you please send me some of your code, so I can better understand, what the issue is.
best wishes
Matthias
Dear Mathias
Probably it could be associated with a newer package version because yesterday I´ve tried it on another computer (with R version 3.6.1 and a version of the staRdom that is not updated since January 2020) and I do not replicate any problem at all, in fact, I was able to run all the analysis for some samples.
However, on my personal computer, I can´t even run the examples. I have these versions: R 4.1.3, eemR 1.0.1, and for staRDOM 1.1.26.
The code that I´m trying to run is very simple
``
LDM<- system.file("extdata/EEMs", package = "staRdom") # folder containing example EEMs
eem_list <- eem_read(LDM, recursive = TRUE, import_function = eem_csv) # in case you use your own data, just replace folder by a path. e.g. "C:/folder/another folder" and change import_function according to instrument.
#eem_LMD
eem_list
``
The error is the following: Error in file.info(file): invalid filename argument
As I said earlier, this code works on another computer with an older version of the packages I am used to putting my data in the extdata folder and I only replace "exdata/EEMs" for "extdata/mydata/fluorescence" or "extdata/mydata/absorbance" for the case of the correction and slope parameters.
Regards
I just rerun reading the EEMs with the exact versions, you mentioned (R 4.1.3, eemR 1.0.1, staRdom 1.1.26) and I unfortunately could still not reproduce the issue.
I would advise you, not to put your data into the extdata folder of the package, staRdom is perfectly able to access any folder you want to and I cannot guarantee, there is no problem with this practice.
I am happy to help you, if you could provide more information and please check, if there are still problems when you use folders outside the package.
Is there any more information on this issue? Does the problem still persist?