Errors when following the vignette

[carlosf79]

To the authors:

When running the command suppressWarnings(suppressMessages(LoadPrimetimeObjs())) # loads the processed data into R, I get the error Error in hash(c(4, 8, 3, 9, 6, 1, 2, 10, 5, 7), c(1, 2, 3, 4, 9, 10, 5, : could not find function "hash". Do you know I could fix this?

Also, the function act.zscore.lst <- LoadMaraOutput(act.dir = "data/sleep_deprivation_gene_exprs_all") needs to point to a directory, however I do not understand which one should I point it to. Are the data included in the package or should I download additional datasets?

Thank you very much!

[carlosf79]

Hello, update: I have solved the issue with the hash function by installing the package hash.

However, I cannot load the data in the R session. I cannot open the connection or does not find a file named /home/yeung/projects/sleep_deprivation/Robjs/combat_sleuth_filt/dat_combat_countsfilt.5.5.Robj. I could not find similarly named files within the installed package (by looking in the installed files). How could I solve this?

Thank you very much!

[jakeyeung]

Hi Carlos, First of all, thanks for your interest! I have fixed it now. You can try to re-install the package and it should be fixed. Apologies for the missing data. Turns out github has a hard limit if 100 MB per file. I have now added the .Robj in zenodo: https://zenodo.org/record/4057008 <https://zenodo.org/record/4057008> The problematic function you talked about, GetCountsMatrix() is now fixed so that it does not try to find that hard-linked file. Rather, it downloads the file from zenodo to data directory and then loads it. Let me know if you have any other questions, Kindest regards, Jake

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On 28 Sep 2020, at 15:36, carlosf79 ***@***.***> wrote: Hello, update: I have solved the issue with the hash function by installing the package hash. However, I cannot load the data in the R session. I cannot open the connection or does not find a file named /home/yeung/projects/sleep_deprivation/Robjs/combat_sleuth_filt/dat_combat_countsfilt.5.5.Robj. I could not find similarly named files within the installed package (by looking in the installed files). How could I solve this? Thank you very much! — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#1 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AA42NMJBUWSRM6DRD4LAH6LSICNOVANCNFSM4R27UJ7Q>.

[carlosf79]

Dear Jake,

thanks a lot for having updated the package. It still has some issues, as the suppressWarnings(suppressMessages(LoadPrimetimeObjs())) function does not properly download from zenodo (giving this error:
[1] "Did not find \"data/dat_combat_countsfilt.5.5.Robj\", downloading from zenodo" [1] "https://zenodo.org/record/4057008/files/dat_combat_countsfilt.5.5.Robj?download=1" Error in readChar(con, 5L, useBytes = TRUE) : cannot open the connection

However, I managed to get the plotting to work by: 1) downloading the dat_combat_countsfilt.5.5.Robj from zenodo and putting it in a subfolder named "data" within the working directory. I have also downloaded the master from GitHub, to which I can point LoadMaraOutput (I guess that I could use the other files on zenodo, but I have not tried).

In this way, the package works, thanks for providing them, it is a great way to browse your very interesting data! :)