Error in default(grDevices::dev.size("px")[1]) : could not find function "default"

[clemenceROBERT]

Hello,

I am getting the following error message:
Error in default(grDevices::dev.size("px")[1]) : could not find function "default"
when running the taxa abundace plot script, copied directly from R history on the web browser:
mbSet<-PlotTaxaAundanceBar(mbSet, "taxa_alpha_0","Phylum","viability", "null",
"barraw",10, "set3","sum",10, "bottom", "F", "png")

Did anyone ever encountered the same issue and has a workaround please?

[Aciole-David]

Hi, @clemenceROBERT
Did you install the package and its dependencies wthout error?

[clemenceROBERT]

Dear Aciole, yes I did, with just a little bit troubleshooting for the Tax4fun issue. In fact I can see them in tht list of the “Packages” tab, and libraries loading runs without error (and I get the tick marks). Thank you Clémence ROBERT, PHD R&D Specialist [Logo]<https://www.complifegroup.com/> Complife Italia Corso Trieste 15/A 28100 Novara (NO) - Italy T: +39 0321 660835 www.complifegroup.com<http://complifegroup.com/> ***@***.***<https://www.pchi-china.com/en/page/showInformation> ***@***.***<https://www.in-cosmetics.com/global/en-gb/help/venue-and-travel.html> Think before you print DISCLAIMER Le informazioni contenute in questo messaggio di posta elettronica sono riservate e confidenziali e ne è vietata la diffusione in qualunque modo eseguita. Qualora Lei non fosse la persona a cui il presente messaggio è destinato La invitiamo ad eliminarlo e a non leggerlo, dandocene gentilmente comunicazione al seguente indirizzo di posta elettronica: ***@***.******@***.***> The information contained in this e-mail and any attachments are confidential and may also be privileged. If you are not named recipient, please notify immediately at this e-mail address: ***@***.******@***.***>and do not disclose the contents to another person, use it for any purpose, or store or copy the information in any medium.

…

________________________________ From: Aciole.D ***@***.***> Sent: Thursday, March 7, 2024 6:48:48 PM To: xia-lab/MicrobiomeAnalystR ***@***.***> Cc: Clemence Robert ***@***.***>; Mention ***@***.***> Subject: Re: [xia-lab/MicrobiomeAnalystR] Error in default(grDevices::dev.size("px")[1]) : could not find function "default" (Issue #31) Vous ne recevez pas souvent de courriers de la part de ***@***.*** Découvrez pourquoi cela est important<https://aka.ms/LearnAboutSenderIdentification> Hi, @clemenceROBERT<https://github.com/clemenceROBERT> Did you install the package and its dependencies wthout error? — Reply to this email directly, view it on GitHub<#31 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/BFLKAIAAWFNBE7GGLN7A6ELYXCSABAVCNFSM6AAAAABEJLXVHOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSOBUGEYTCOBYGI>. You are receiving this because you were mentioned.Message ID: ***@***.***>

[Aciole-David]

Ok, let's see;
First, what is your current system specs?
Did you run all the previous steps for creating/parsing the mbset object?
If so, would you please share your code?

[Aciole-David]

Also, are you closing the plot's device view with dev.off() or something like that ?
grDevices::dev.size guesses the current graphics device size; if there's no device at the moment, maybe calling an empty plot before may pass the error
I can't test right now, sorry, but if you're not in a hurry I'd provide a dummy code

Cheers

[clemenceROBERT]

Hi, I am running on Windows 11/x64, with Rstudio version 2023.12.1.0. Here is the code I am entering: * otu_table <- read.csv("data_raw/otu_table_OR.csv") * metadata <- read.csv("data_raw/metadata_file_OR.csv") * taxonomy_table <- read.csv("data_raw/taxonomy_table_OR.csv") * library(MicrobiomeAnalystR) * mbSet<-Init.mbSetObj() * mbSet<-SetModuleType(mbSet, "mdp") * mbSet<-Read16SAbundData(mbSet, "data_raw/otu_table_OR.csv","text","Others/Not_specific","T","false") * mbSet<-ReadSampleTable(mbSet, "data_raw/metadata_file_OR.txt") * mbSet<-Read16STaxaTable(mbSet, "data_raw/taxonomy_table_OR.csv") * mbSet<-SanityCheckData(mbSet, "text"); * mbSet<-SanityCheckSampleData(mbSet); * mbSet<-SetMetaAttributes(mbSet, "1") * mbSet<-PlotLibSizeView(mbSet, "norm_libsizes_0","png"); * mbSet<-CreatePhyloseqObj(mbSet, "text","Others/Not_specific","F" , "false") * * mbSet<-ApplyAbundanceFilter(mbSet, "mean", 4, 0.2) * mbSet<-ApplyVarianceFilter(mbSet, "iqr", 0.1) * mbSet<-PerformNormalization(mbSet, "none", "colsum", "none", "true") * * mbSet<-PlotTaxaAundanceBar(mbSet, "taxa_alpha_0","Phylum","viability", "null", * "barraw",10, "set3","sum",10, "bottom", "F", "png") And this is the complete error message that I get: * ERROR in default (grDevices::dev.size("px")[1]): could not find function "default" As I may have mentioned before, I controlled that both the grDevices and the plotly libraries were installed and loaded. I had run into a bit of trouble while installing the MicrobiomeAnalystR package, but ended up being able to go around it (manual installation of Tax4fun), and did not get error messages concerning either the library or the mbset object. I hope it makes the situation clearer, looking forward to your reply. Thanks again for your help, Clémence ROBERT, PHD R&D Specialist [Logo]<https://www.complifegroup.com/> Complife Italia Corso Trieste 15/A 28100 Novara (NO) - Italy T: +39 0321 660835 www.complifegroup.com<http://complifegroup.com/> ***@***.***<https://www.pchi-china.com/en/page/showInformation> ***@***.***<https://www.in-cosmetics.com/global/en-gb/help/venue-and-travel.html> Think before you print DISCLAIMER Le informazioni contenute in questo messaggio di posta elettronica sono riservate e confidenziali e ne è vietata la diffusione in qualunque modo eseguita. Qualora Lei non fosse la persona a cui il presente messaggio è destinato La invitiamo ad eliminarlo e a non leggerlo, dandocene gentilmente comunicazione al seguente indirizzo di posta elettronica: ***@***.******@***.***> The information contained in this e-mail and any attachments are confidential and may also be privileged. If you are not named recipient, please notify immediately at this e-mail address: ***@***.******@***.***>and do not disclose the contents to another person, use it for any purpose, or store or copy the information in any medium.

…

________________________________ From: Aciole.D ***@***.***> Sent: Saturday, March 9, 2024 3:52:55 PM To: xia-lab/MicrobiomeAnalystR ***@***.***> Cc: Clemence Robert ***@***.***>; Mention ***@***.***> Subject: Re: [xia-lab/MicrobiomeAnalystR] Error in default(grDevices::dev.size("px")[1]) : could not find function "default" (Issue #31) Vous ne recevez pas souvent de courriers de la part de ***@***.*** Découvrez pourquoi cela est important<https://aka.ms/LearnAboutSenderIdentification> Ok, let's see; First, what is your current system specs? Did you run all the previous steps for creating/parsing the mbset object? If so, would you please share your code? — Reply to this email directly, view it on GitHub<#31 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/BFLKAIGTSDREDOYBTHRKZB3YXMO4PAVCNFSM6AAAAABEJLXVHOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSOBWHA3TMOJWHA>. You are receiving this because you were mentioned.Message ID: ***@***.***>

[clemenceROBERT]

Hello, did you have the opportunity to look at my code and identify the problem I have with grdevices/dev size? Thank you for your support, Clémence ROBERT, PHD R&D Specialist [Logo]<https://www.complifegroup.com/> Complife Italia Corso Trieste 15/A 28100 Novara (NO) - Italy T: +39 0321 660835 www.complifegroup.com<http://complifegroup.com/> ***@***.***<https://www.pchi-china.com/en/page/showInformation> ***@***.***<https://www.in-cosmetics.com/global/en-gb/help/venue-and-travel.html> Think before you print DISCLAIMER Le informazioni contenute in questo messaggio di posta elettronica sono riservate e confidenziali e ne è vietata la diffusione in qualunque modo eseguita. Qualora Lei non fosse la persona a cui il presente messaggio è destinato La invitiamo ad eliminarlo e a non leggerlo, dandocene gentilmente comunicazione al seguente indirizzo di posta elettronica: ***@***.******@***.***> The information contained in this e-mail and any attachments are confidential and may also be privileged. If you are not named recipient, please notify immediately at this e-mail address: ***@***.******@***.***>and do not disclose the contents to another person, use it for any purpose, or store or copy the information in any medium.

…

________________________________ From: Clemence Robert ***@***.***> Sent: Monday, March 11, 2024 10:29:31 AM To: xia-lab/MicrobiomeAnalystR ***@***.***>; xia-lab/MicrobiomeAnalystR ***@***.***> Cc: Mention ***@***.***> Subject: RE: [xia-lab/MicrobiomeAnalystR] Error in default(grDevices::dev.size("px")[1]) : could not find function "default" (Issue #31) Hi, I am running on Windows 11/x64, with Rstudio version 2023.12.1.0. Here is the code I am entering: * otu_table <- read.csv("data_raw/otu_table_OR.csv") * metadata <- read.csv("data_raw/metadata_file_OR.csv") * taxonomy_table <- read.csv("data_raw/taxonomy_table_OR.csv") * library(MicrobiomeAnalystR) * mbSet<-Init.mbSetObj() * mbSet<-SetModuleType(mbSet, "mdp") * mbSet<-Read16SAbundData(mbSet, "data_raw/otu_table_OR.csv","text","Others/Not_specific","T","false") * mbSet<-ReadSampleTable(mbSet, "data_raw/metadata_file_OR.txt") * mbSet<-Read16STaxaTable(mbSet, "data_raw/taxonomy_table_OR.csv") * mbSet<-SanityCheckData(mbSet, "text"); * mbSet<-SanityCheckSampleData(mbSet); * mbSet<-SetMetaAttributes(mbSet, "1") * mbSet<-PlotLibSizeView(mbSet, "norm_libsizes_0","png"); * mbSet<-CreatePhyloseqObj(mbSet, "text","Others/Not_specific","F" , "false") * * mbSet<-ApplyAbundanceFilter(mbSet, "mean", 4, 0.2) * mbSet<-ApplyVarianceFilter(mbSet, "iqr", 0.1) * mbSet<-PerformNormalization(mbSet, "none", "colsum", "none", "true") * * mbSet<-PlotTaxaAundanceBar(mbSet, "taxa_alpha_0","Phylum","viability", "null", * "barraw",10, "set3","sum",10, "bottom", "F", "png") And this is the complete error message that I get: * ERROR in default (grDevices::dev.size("px")[1]): could not find function "default" As I may have mentioned before, I controlled that both the grDevices and the plotly libraries were installed and loaded. I had run into a bit of trouble while installing the MicrobiomeAnalystR package, but ended up being able to go around it (manual installation of Tax4fun), and did not get error messages concerning either the library or the mbset object. I hope it makes the situation clearer, looking forward to your reply. Thanks again for your help, Clémence ROBERT, PHD R&D Specialist [Logo]<https://www.complifegroup.com/> Complife Italia Corso Trieste 15/A 28100 Novara (NO) - Italy T: +39 0321 660835 www.complifegroup.com<http://complifegroup.com/> ***@***.***<https://www.pchi-china.com/en/page/showInformation> ***@***.***<https://www.in-cosmetics.com/global/en-gb/help/venue-and-travel.html> Think before you print DISCLAIMER Le informazioni contenute in questo messaggio di posta elettronica sono riservate e confidenziali e ne è vietata la diffusione in qualunque modo eseguita. Qualora Lei non fosse la persona a cui il presente messaggio è destinato La invitiamo ad eliminarlo e a non leggerlo, dandocene gentilmente comunicazione al seguente indirizzo di posta elettronica: ***@***.******@***.***> The information contained in this e-mail and any attachments are confidential and may also be privileged. If you are not named recipient, please notify immediately at this e-mail address: ***@***.******@***.***>and do not disclose the contents to another person, use it for any purpose, or store or copy the information in any medium.

________________________________ From: Aciole.D ***@***.***> Sent: Saturday, March 9, 2024 3:52:55 PM To: xia-lab/MicrobiomeAnalystR ***@***.***> Cc: Clemence Robert ***@***.***>; Mention ***@***.***> Subject: Re: [xia-lab/MicrobiomeAnalystR] Error in default(grDevices::dev.size("px")[1]) : could not find function "default" (Issue #31) Vous ne recevez pas souvent de courriers de la part de ***@***.*** Découvrez pourquoi cela est important<https://aka.ms/LearnAboutSenderIdentification> Ok, let's see; First, what is your current system specs? Did you run all the previous steps for creating/parsing the mbset object? If so, would you please share your code? — Reply to this email directly, view it on GitHub<#31 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/BFLKAIGTSDREDOYBTHRKZB3YXMO4PAVCNFSM6AAAAABEJLXVHOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSOBWHA3TMOJWHA>. You are receiving this because you were mentioned.Message ID: ***@***.***>

[Aciole-David]

Hello,
Your error is not reproducible on my system.
You did mentioned RStudio version, but please always state which R version is being used. This is easier to try helping.
E.g., have you installed Rtools for your specific R version?

[clemenceROBERT]

Hello, my apologies, here is the R version that I am using: 4.3.2 And yes, I did have to install the Rtools package manually. Thank you for your support, Clémence ROBERT, PHD R&D Specialist [Logo]<https://www.complifegroup.com/> Complife Italia Corso Trieste 15/A 28100 Novara (NO) - Italy T: +39 0321 660835 www.complifegroup.com<http://complifegroup.com/> ***@***.***<https://www.pchi-china.com/en/page/showInformation> ***@***.***<https://www.in-cosmetics.com/global/en-gb/help/venue-and-travel.html> Think before you print DISCLAIMER Le informazioni contenute in questo messaggio di posta elettronica sono riservate e confidenziali e ne è vietata la diffusione in qualunque modo eseguita. Qualora Lei non fosse la persona a cui il presente messaggio è destinato La invitiamo ad eliminarlo e a non leggerlo, dandocene gentilmente comunicazione al seguente indirizzo di posta elettronica: ***@***.******@***.***> The information contained in this e-mail and any attachments are confidential and may also be privileged. If you are not named recipient, please notify immediately at this e-mail address: ***@***.******@***.***>and do not disclose the contents to another person, use it for any purpose, or store or copy the information in any medium.

…

________________________________ From: Aciole.D ***@***.***> Sent: Friday, March 22, 2024 4:02:10 PM To: xia-lab/MicrobiomeAnalystR ***@***.***> Cc: Clemence Robert ***@***.***>; Mention ***@***.***> Subject: Re: [xia-lab/MicrobiomeAnalystR] Error in default(grDevices::dev.size("px")[1]) : could not find function "default" (Issue #31) Vous ne recevez pas souvent de courriers de la part de ***@***.*** Découvrez pourquoi cela est important<https://aka.ms/LearnAboutSenderIdentification> Hello, Your error is not reproducible on my system. You did mentioned RStudio version, but please always state which R version is being used. This is easier to try helping. E.g., have you installed Rtools for your specific R version? — Reply to this email directly, view it on GitHub<#31 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/BFLKAIGIQCFGCJJ5D3TMOJ3YZRBXFAVCNFSM6AAAAABEJLXVHOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMJVGI4TEOJXGM>. You are receiving this because you were mentioned.Message ID: ***@***.***>