error at annotate peak step

duncan8659 commented 6 years ago

I'm trying to do the tutorial workflow and I get this message at the annotate peak step:

Warning: 'ensembldb::SeqnameFilter' is deprecated. Use 'SeqNameFilter' instead. See help("Deprecated") Warning: 'ensembldb::GeneidFilter' is deprecated. Use 'GeneIdFilter' instead. See help("Deprecated") Warning: Error in validObject: invalid class "GeneIdFilter" object: 'like' must be in '==' '!=' 'startsWith' 'endsWith' 'contains' Stack trace (innermost first): 126: validObject 125: initialize 124: initialize 123: new 122: ensembldb::GeneidFilter 121: is 120: .processFilterParam 119: .local 118: transcripts 117: transcripts 116: ensembldb::promoters 115: ensembldb::promoters 114: getTSS 113: eval [/Library/Frameworks/R.framework/Versions/3.4/Resources/library/ALTRE/shinyApp/server.R#57] 112: eval 111: withProgress 110: eventReactiveHandler [/Library/Frameworks/R.framework/Versions/3.4/Resources/library/ALTRE/shinyApp/server.R#52] 90: combineAnnotateObj 89: eval 88: eval 87: inherits 86: isTruthy 85: fun 84: dotloop 83: req 82: renderDataTable [/Library/Frameworks/R.framework/Versions/3.4/Resources/library/ALTRE/shinyApp/server.R#280] 81: func 80: origRenderFunc 79: output$table3 2: shiny::runApp 1: runShinyApp Warning: Error in validObject: invalid class "GeneIdFilter" object: 'like' must be in '==' '!=' 'startsWith' 'endsWith' 'contains' Stack trace (innermost first): 93: 92: stop 91: combineAnnotateObj 90: eval 89: eval 88: inherits 87: isTruthy 86: fun 85: dotloop 84: req 83: plotCombineAnnotatePeaks 82: renderUI [/Library/Frameworks/R.framework/Versions/3.4/Resources/library/ALTRE/shinyApp/server.R#315] 81: func 80: origRenderFunc 79: output$annotatebarplot 2: shiny::runApp 1: runShinyApp Warning: Error in validObject: invalid class "GeneIdFilter" object: 'like' must be in '==' '!=' 'startsWith' 'endsWith' 'contains' Stack trace (innermost first): 86: 85: stop 84: combineAnnotateObj 83: vbox_fun [/Library/Frameworks/R.framework/Versions/3.4/Resources/library/ALTRE/shinyApp/server.R#420] 82: shiny::renderUI 81: func 80: origRenderFunc 79: output$statusbox3 2: shiny::runApp 1: runShinyApp

since I'm new to this and would LOVE to use it on my own data any help would be great!

ewymathe commented 6 years ago

Thank you for reporting this, will look into fixing this shortly and will get back to you once it's done.

duncan8659 commented 6 years ago

Thanks so much for the quick response! A colleague suggested that I try the program in an older version of R (I was having the problem with the most recent R for Mac OS 10.11 and higher) and that resolved the error. I can now get all the way through the workflow to the last step (GREAT analysis) but then it fails. Not such a problem for my stuff. I am now however stuck because I need a BED for Drosophila and although I downloaded one from UCSC and formatted it for BED it gives me the following error:

Warning in .Seqinfo.mergexy(x, y) : Each of the 2 combined objects has sequence levels not in the other:

in 'x': chr2L, chr2R, chr3L, chr3R, chrM, chrY_CP007111v1_random, chrUn_CP007081v1, chrUn_DS483755v1, chrUn_DS484007v1, chrUn_DS484314v1, chrUn_DS484484v1, chrUn_CP007080v1, chrUn_DS484309v1, chrUn_CP007075v1, chrUn_CP007077v1, chrUn_CP007079v1, chrUn_CP007120v1, chrUn_DS483629v1, chrUn_DS483675v1, chrUn_DS483724v1, chrUn_DS483746v1, chrUn_DS483749v1, chrUn_DS483751v1, chrUn_DS483773v1, chrUn_DS483817v1, chrUn_DS483849v1, chrUn_DS483853v1, chrUn_DS483880v1, chrUn_DS483944v1, chrUn_DS483956v1, chrUn_DS484004v1, chrUn_DS484058v1, chrUn_DS484064v1, chrUn_DS484116v1, chrUn_DS484148v1, chrUn_DS484188v1, chrUn_DS484189v1, chrUn_DS484225v1, chrUn_DS484244v1, chrUn_DS484246v1, chrUn_DS484257v1, chrUn_DS484277v1, chrUn_DS484282v1, chrUn_DS484369v1, chrUn_DS484383v1, chrUn_DS484394v1, chrUn_DS484454v1, chrUn_DS484469v1, chrUn_DS484472v1, chrUn_DS484566v1, chrUn_DS484588v1, chrUn_DS484673v1, chrUn_DS484707v1, chrUn_DS484722v [... truncated] Warning: Error in [[<-: 1522 elements in value to replace 9248 elements Stack trace (innermost first): 111: [[<- 110: [[<- 109: $<- 108: $<- 107: tssannotgrange 106: combineAnnotatePeaks 105: eval [/Library/Frameworks/R.framework/Versions/3.3/Resources/library/ALTRE/shinyApp/server.R#59] 104: eval 103: withProgress 102: eventReactiveHandler [/Library/Frameworks/R.framework/Versions/3.3/Resources/library/ALTRE/shinyApp/server.R#52] 82: combineAnnotateObj 81: vbox_fun [/Library/Frameworks/R.framework/Versions/3.3/Resources/library/ALTRE/shinyApp/server.R#420] 80: shiny::renderUI 79: func 78: origRenderFunc 77: output$statusbox3 2: shiny::runApp 1: runShinyApp Warning: Error in [[<-: 1522 elements in value to replace 9248 elements Stack trace (innermost first):

I’m thinking that perhaps my BED peak files have some unmapped peaks and that these are not in the TSS file?

My BEDs are mapped to dm6

Dianne Duncan Research Associate Director, Imaging Core Biology Department 149 McDonnell Hall Washington University St Louis MO 63130 314-935-4764

From: Ewy Mathe notifications@github.com Reply-To: Mathelab/ALTRE reply@reply.github.com Date: Tuesday, November 21, 2017 at 9:45 PM To: Mathelab/ALTRE ALTRE@noreply.github.com Cc: "Duncan, Dianne" duncan_d@wustl.edu, Author author@noreply.github.com Subject: Re: [Mathelab/ALTRE] error at annotate peak step (#53)

Thank you for reporting this, will look into fixing this shortly and will get back to you once it's done.

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ewymathe commented 6 years ago

Hi Dianne,

The first issue you brought up (error from deprecated function in getTSS()) is now fixed and pushed. As for this last issue you're raising, yes, it seems to be an annotation issue. Does the TSS annotation file you have contain all the chromosome types that are in your peak files?

Ewy

duncan8659 commented 6 years ago

Wow, thanks for being so responsive! Yes, the latest Drosophila release has lots of unmapped reads so my guess is that they don’t show up in the GTF or BED files from UCSD when you download for refseq genes. I’m going to try running the program after filtering out those few unmapped peaks from my BED files and see if that works. Thanks again. Dianne

Dianne Duncan Research Associate Director, Imaging Core Biology Department 149 McDonnell Hall Washington University St Louis MO 63130 314-935-4764

From: Ewy Mathe notifications@github.com Reply-To: Mathelab/ALTRE reply@reply.github.com Date: Wednesday, November 22, 2017 at 2:56 PM To: Mathelab/ALTRE ALTRE@noreply.github.com Cc: "Duncan, Dianne" duncan_d@wustl.edu, Author author@noreply.github.com Subject: Re: [Mathelab/ALTRE] error at annotate peak step (#53)

Hi Dianne,

The first issue you brought up (error from deprecated function in getTSS()) is now fixed and pushed. As for this last issue you're raising, yes, it seems to be an annotation issue. Does the TSS annotation file you have contain all the chromosome types that are in your peak files?

Ewy

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/Mathelab/ALTRE/issues/53#issuecomment-346470736, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AYz4PpzafczVzxUbpsEnK6yzbRChgCcsks5s5Ip8gaJpZM4QmOAI.

ewymathe commented 6 years ago

Sure thing! OK Dianne, I'm going to close this issue. Feel free to reach out again if filtering out the unmapped peaks doesn't work. Ewy

duncan8659 commented 6 years ago

Hi Ewy I’ve been trying to use ALTRE today and it wasn’t working for me; I re-installed it and I still get the same error message:

Installing ALTRE '/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet CMD INSTALL \ '/private/var/folders/n4/sprgby7d2bd9430f7rs7y6p00000gr/T/Rtmp6R0Hya/devtoolsd0d2acfe68b/Mathelab-ALTRE-e5f07b3' \ --library='/Library/Frameworks/R.framework/Versions/3.3/Resources/library' --install-tests

ERROR: dependency ‘AnnotationFilter’ is not available for package ‘ALTRE’

removing ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/ALTRE’ Installation failed: Command failed (1)

Not sure what I did. I’m not familiar enough with R to figure out how to even look for the missing dependency

Great if you could help!

Dianne Duncan Research Associate Director, Imaging Core Biology Department 149 McDonnell Hall Washington University St Louis MO 63130 314-935-4764

From: Ewy Mathe notifications@github.com Reply-To: Mathelab/ALTRE reply@reply.github.com Date: Wednesday, November 22, 2017 at 2:56 PM To: Mathelab/ALTRE ALTRE@noreply.github.com Cc: "Duncan, Dianne" duncan_d@wustl.edu, Author author@noreply.github.com Subject: Re: [Mathelab/ALTRE] error at annotate peak step (#53)

Hi Dianne,

The first issue you brought up (error from deprecated function in getTSS()) is now fixed and pushed. As for this last issue you're raising, yes, it seems to be an annotation issue. Does the TSS annotation file you have contain all the chromosome types that are in your peak files?

Ewy

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/Mathelab/ALTRE/issues/53#issuecomment-346470736, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AYz4PpzafczVzxUbpsEnK6yzbRChgCcsks5s5Ip8gaJpZM4QmOAI.

Mathelab commented 6 years ago

Hi Dianne,

Can you try installing the AnnotationFilter package, then installing ALTRE?

source("https://bioconductor.org/biocLite.R") biocLite("AnnotationFilter")

Ewy

From: duncan8659 notifications@github.com Reply-To: Mathelab/ALTRE reply@reply.github.com Date: Tuesday, November 28, 2017 at 1:00 PM To: Mathelab/ALTRE ALTRE@noreply.github.com Cc: "Mathe, Ewy" Ewy.Mathe@osumc.edu, State change state_change@noreply.github.com Subject: Re: [Mathelab/ALTRE] error at annotate peak step (#53)

Hi Ewy I’ve been trying to use ALTRE today and it wasn’t working for me; I re-installed it and I still get the same error message:

Installing ALTRE '/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet CMD INSTALL \ '/private/var/folders/n4/sprgby7d2bd9430f7rs7y6p00000gr/T/Rtmp6R0Hya/devtoolsd0d2acfe68b/Mathelab-ALTRE-e5f07b3' \ --library='/Library/Frameworks/R.framework/Versions/3.3/Resources/library' --install-tests

ERROR: dependency ‘AnnotationFilter’ is not available for package ‘ALTRE’

removing ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/ALTRE’ Installation failed: Command failed (1)

Not sure what I did. I’m not familiar enough with R to figure out how to even look for the missing dependency

Great if you could help!

Dianne Duncan Research Associate Director, Imaging Core Biology Department 149 McDonnell Hall Washington University St Louis MO 63130 314-935-4764

From: Ewy Mathe notifications@github.com Reply-To: Mathelab/ALTRE reply@reply.github.com Date: Wednesday, November 22, 2017 at 2:56 PM To: Mathelab/ALTRE ALTRE@noreply.github.com Cc: "Duncan, Dianne" duncan_d@wustl.edu, Author author@noreply.github.com Subject: Re: [Mathelab/ALTRE] error at annotate peak step (#53)

Hi Dianne,

The first issue you brought up (error from deprecated function in getTSS()) is now fixed and pushed. As for this last issue you're raising, yes, it seems to be an annotation issue. Does the TSS annotation file you have contain all the chromosome types that are in your peak files?

Ewy

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/Mathelab/ALTRE/issues/53#issuecomment-346470736, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AYz4PpzafczVzxUbpsEnK6yzbRChgCcsks5s5Ip8gaJpZM4QmOAI.

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duncan8659 commented 6 years ago

Will do!

Dianne Duncan Research Associate Director, Imaging Core Biology Department 149 McDonnell Hall Washington University St Louis MO 63130 314-935-4764

From: Mathelab notifications@github.com Reply-To: Mathelab/ALTRE reply@reply.github.com Date: Tuesday, November 28, 2017 at 12:12 PM To: Mathelab/ALTRE ALTRE@noreply.github.com Cc: "Duncan, Dianne" duncan_d@wustl.edu, Author author@noreply.github.com Subject: Re: [Mathelab/ALTRE] error at annotate peak step (#53)

source("https://bioconductor.org/biocLite.R"https://bioconductor.org/biocLite.R%22) biocLite("AnnotationFilter")

duncan8659 commented 6 years ago

Gives this response:

BioC_mirror: https://bioconductor.org Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.3 (2017-03-06). Installing package(s) ‘AnnotationFilter’ Warning message: package ‘AnnotationFilter’ is not available (for R version 3.3.3)

Dianne Duncan Research Associate Director, Imaging Core Biology Department 149 McDonnell Hall Washington University St Louis MO 63130 314-935-4764

From: Mathelab notifications@github.com Reply-To: Mathelab/ALTRE reply@reply.github.com Date: Tuesday, November 28, 2017 at 12:12 PM To: Mathelab/ALTRE ALTRE@noreply.github.com Cc: "Duncan, Dianne" duncan_d@wustl.edu, Author author@noreply.github.com Subject: Re: [Mathelab/ALTRE] error at annotate peak step (#53)

Hi Dianne,

Can you try installing the AnnotationFilter package, then installing ALTRE?

source("https://bioconductor.org/biocLite.R") biocLite("AnnotationFilter")

Ewy

From: duncan8659 notifications@github.com Reply-To: Mathelab/ALTRE reply@reply.github.com Date: Tuesday, November 28, 2017 at 1:00 PM To: Mathelab/ALTRE ALTRE@noreply.github.com Cc: "Mathe, Ewy" Ewy.Mathe@osumc.edu, State change state_change@noreply.github.com Subject: Re: [Mathelab/ALTRE] error at annotate peak step (#53)

Hi Ewy I’ve been trying to use ALTRE today and it wasn’t working for me; I re-installed it and I still get the same error message:

Installing ALTRE '/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet CMD INSTALL \ '/private/var/folders/n4/sprgby7d2bd9430f7rs7y6p00000gr/T/Rtmp6R0Hya/devtoolsd0d2acfe68b/Mathelab-ALTRE-e5f07b3' \ --library='/Library/Frameworks/R.framework/Versions/3.3/Resources/library' --install-tests

ERROR: dependency ‘AnnotationFilter’ is not available for package ‘ALTRE’

removing ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/ALTRE’ Installation failed: Command failed (1)

Not sure what I did. I’m not familiar enough with R to figure out how to even look for the missing dependency

Great if you could help!

Dianne Duncan Research Associate Director, Imaging Core Biology Department 149 McDonnell Hall Washington University St Louis MO 63130 314-935-4764

From: Ewy Mathe notifications@github.com Reply-To: Mathelab/ALTRE reply@reply.github.com Date: Wednesday, November 22, 2017 at 2:56 PM To: Mathelab/ALTRE ALTRE@noreply.github.com Cc: "Duncan, Dianne" duncan_d@wustl.edu, Author author@noreply.github.com Subject: Re: [Mathelab/ALTRE] error at annotate peak step (#53)

Hi Dianne,

The first issue you brought up (error from deprecated function in getTSS()) is now fixed and pushed. As for this last issue you're raising, yes, it seems to be an annotation issue. Does the TSS annotation file you have contain all the chromosome types that are in your peak files?

Ewy

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/Mathelab/ALTRE/issues/53#issuecomment-346470736, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AYz4PpzafczVzxUbpsEnK6yzbRChgCcsks5s5Ip8gaJpZM4QmOAI.

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Mathelab commented 6 years ago

Ah, unfortunately, AnnotationFilter requires R3.4 or greater. Could you update R? Ewy

From: duncan8659 notifications@github.com Reply-To: Mathelab/ALTRE reply@reply.github.com Date: Tuesday, November 28, 2017 at 1:14 PM To: Mathelab/ALTRE ALTRE@noreply.github.com Cc: "Mathe, Ewy" Ewy.Mathe@osumc.edu, State change state_change@noreply.github.com Subject: Re: [Mathelab/ALTRE] error at annotate peak step (#53)

Gives this response:

BioC_mirror: https://bioconductor.org Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.3 (2017-03-06). Installing package(s) ‘AnnotationFilter’ Warning message: package ‘AnnotationFilter’ is not available (for R version 3.3.3)

Dianne Duncan Research Associate Director, Imaging Core Biology Department 149 McDonnell Hall Washington University St Louis MO 63130 314-935-4764

From: Mathelab notifications@github.com Reply-To: Mathelab/ALTRE reply@reply.github.com Date: Tuesday, November 28, 2017 at 12:12 PM To: Mathelab/ALTRE ALTRE@noreply.github.com Cc: "Duncan, Dianne" duncan_d@wustl.edu, Author author@noreply.github.com Subject: Re: [Mathelab/ALTRE] error at annotate peak step (#53)

Hi Dianne,

Can you try installing the AnnotationFilter package, then installing ALTRE?

source("https://bioconductor.org/biocLite.R") biocLite("AnnotationFilter")

Ewy

From: duncan8659 notifications@github.com Reply-To: Mathelab/ALTRE reply@reply.github.com Date: Tuesday, November 28, 2017 at 1:00 PM To: Mathelab/ALTRE ALTRE@noreply.github.com Cc: "Mathe, Ewy" Ewy.Mathe@osumc.edu, State change state_change@noreply.github.com Subject: Re: [Mathelab/ALTRE] error at annotate peak step (#53)

Hi Ewy I’ve been trying to use ALTRE today and it wasn’t working for me; I re-installed it and I still get the same error message:

Installing ALTRE '/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet CMD INSTALL \ '/private/var/folders/n4/sprgby7d2bd9430f7rs7y6p00000gr/T/Rtmp6R0Hya/devtoolsd0d2acfe68b/Mathelab-ALTRE-e5f07b3' \ --library='/Library/Frameworks/R.framework/Versions/3.3/Resources/library' --install-tests

ERROR: dependency ‘AnnotationFilter’ is not available for package ‘ALTRE’

removing ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/ALTRE’ Installation failed: Command failed (1)

Not sure what I did. I’m not familiar enough with R to figure out how to even look for the missing dependency

Great if you could help!

Dianne Duncan Research Associate Director, Imaging Core Biology Department 149 McDonnell Hall Washington University St Louis MO 63130 314-935-4764

From: Ewy Mathe notifications@github.com Reply-To: Mathelab/ALTRE reply@reply.github.com Date: Wednesday, November 22, 2017 at 2:56 PM To: Mathelab/ALTRE ALTRE@noreply.github.com Cc: "Duncan, Dianne" duncan_d@wustl.edu, Author author@noreply.github.com Subject: Re: [Mathelab/ALTRE] error at annotate peak step (#53)

Hi Dianne,

The first issue you brought up (error from deprecated function in getTSS()) is now fixed and pushed. As for this last issue you're raising, yes, it seems to be an annotation issue. Does the TSS annotation file you have contain all the chromosome types that are in your peak files?

Ewy

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/Mathelab/ALTRE/issues/53#issuecomment-346470736, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AYz4PpzafczVzxUbpsEnK6yzbRChgCcsks5s5Ip8gaJpZM4QmOAI.

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duncan8659 commented 6 years ago

Yep, thanks!

Dianne Duncan Research Associate Director, Imaging Core Biology Department 149 McDonnell Hall Washington University St Louis MO 63130 314-935-4764

From: Mathelab notifications@github.com Reply-To: Mathelab/ALTRE reply@reply.github.com Date: Tuesday, November 28, 2017 at 12:16 PM To: Mathelab/ALTRE ALTRE@noreply.github.com Cc: "Duncan, Dianne" duncan_d@wustl.edu, Author author@noreply.github.com Subject: Re: [Mathelab/ALTRE] error at annotate peak step (#53)

Ah, unfortunately, AnnotationFilter requires R3.4 or greater. Could you update R? Ewy

From: duncan8659 notifications@github.com Reply-To: Mathelab/ALTRE reply@reply.github.com Date: Tuesday, November 28, 2017 at 1:14 PM To: Mathelab/ALTRE ALTRE@noreply.github.com Cc: "Mathe, Ewy" Ewy.Mathe@osumc.edu, State change state_change@noreply.github.com Subject: Re: [Mathelab/ALTRE] error at annotate peak step (#53)

Gives this response:

BioC_mirror: https://bioconductor.org Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.3 (2017-03-06). Installing package(s) ‘AnnotationFilter’ Warning message: package ‘AnnotationFilter’ is not available (for R version 3.3.3)

Dianne Duncan Research Associate Director, Imaging Core Biology Department 149 McDonnell Hall Washington University St Louis MO 63130 314-935-4764

From: Mathelab notifications@github.com Reply-To: Mathelab/ALTRE reply@reply.github.com Date: Tuesday, November 28, 2017 at 12:12 PM To: Mathelab/ALTRE ALTRE@noreply.github.com Cc: "Duncan, Dianne" duncan_d@wustl.edu, Author author@noreply.github.com Subject: Re: [Mathelab/ALTRE] error at annotate peak step (#53)

Hi Dianne,

Can you try installing the AnnotationFilter package, then installing ALTRE?

source("https://bioconductor.org/biocLite.R") biocLite("AnnotationFilter")

Ewy

From: duncan8659 notifications@github.com Reply-To: Mathelab/ALTRE reply@reply.github.com Date: Tuesday, November 28, 2017 at 1:00 PM To: Mathelab/ALTRE ALTRE@noreply.github.com Cc: "Mathe, Ewy" Ewy.Mathe@osumc.edu, State change state_change@noreply.github.com Subject: Re: [Mathelab/ALTRE] error at annotate peak step (#53)

Hi Ewy I’ve been trying to use ALTRE today and it wasn’t working for me; I re-installed it and I still get the same error message:

Installing ALTRE '/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet CMD INSTALL \ '/private/var/folders/n4/sprgby7d2bd9430f7rs7y6p00000gr/T/Rtmp6R0Hya/devtoolsd0d2acfe68b/Mathelab-ALTRE-e5f07b3' \ --library='/Library/Frameworks/R.framework/Versions/3.3/Resources/library' --install-tests

ERROR: dependency ‘AnnotationFilter’ is not available for package ‘ALTRE’

removing ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/ALTRE’ Installation failed: Command failed (1)

Not sure what I did. I’m not familiar enough with R to figure out how to even look for the missing dependency

Great if you could help!

Dianne Duncan Research Associate Director, Imaging Core Biology Department 149 McDonnell Hall Washington University St Louis MO 63130 314-935-4764

From: Ewy Mathe notifications@github.com Reply-To: Mathelab/ALTRE reply@reply.github.com Date: Wednesday, November 22, 2017 at 2:56 PM To: Mathelab/ALTRE ALTRE@noreply.github.com Cc: "Duncan, Dianne" duncan_d@wustl.edu, Author author@noreply.github.com Subject: Re: [Mathelab/ALTRE] error at annotate peak step (#53)

Hi Dianne,

The first issue you brought up (error from deprecated function in getTSS()) is now fixed and pushed. As for this last issue you're raising, yes, it seems to be an annotation issue. Does the TSS annotation file you have contain all the chromosome types that are in your peak files?

Ewy

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duncan8659 commented 6 years ago

Ok so that got rid of that problem, but now I’m back to this issue that I had early on:

Warning: Error in validObject: invalid class "GeneIdFilter" object: 'like' must be in '==' '!=' 'startsWith' 'endsWith' 'contains'

Which my IT friend told me related to the new Mac R version

Dianne Duncan Research Associate Director, Imaging Core Biology Department 149 McDonnell Hall Washington University St Louis MO 63130 314-935-4764

From: Mathelab notifications@github.com Reply-To: Mathelab/ALTRE reply@reply.github.com Date: Tuesday, November 28, 2017 at 12:16 PM To: Mathelab/ALTRE ALTRE@noreply.github.com Cc: "Duncan, Dianne" duncan_d@wustl.edu, Author author@noreply.github.com Subject: Re: [Mathelab/ALTRE] error at annotate peak step (#53)

Ah, unfortunately, AnnotationFilter requires R3.4 or greater. Could you update R? Ewy

From: duncan8659 notifications@github.com Reply-To: Mathelab/ALTRE reply@reply.github.com Date: Tuesday, November 28, 2017 at 1:14 PM To: Mathelab/ALTRE ALTRE@noreply.github.com Cc: "Mathe, Ewy" Ewy.Mathe@osumc.edu, State change state_change@noreply.github.com Subject: Re: [Mathelab/ALTRE] error at annotate peak step (#53)

Gives this response:

BioC_mirror: https://bioconductor.org Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.3 (2017-03-06). Installing package(s) ‘AnnotationFilter’ Warning message: package ‘AnnotationFilter’ is not available (for R version 3.3.3)

Dianne Duncan Research Associate Director, Imaging Core Biology Department 149 McDonnell Hall Washington University St Louis MO 63130 314-935-4764

From: Mathelab notifications@github.com Reply-To: Mathelab/ALTRE reply@reply.github.com Date: Tuesday, November 28, 2017 at 12:12 PM To: Mathelab/ALTRE ALTRE@noreply.github.com Cc: "Duncan, Dianne" duncan_d@wustl.edu, Author author@noreply.github.com Subject: Re: [Mathelab/ALTRE] error at annotate peak step (#53)

Hi Dianne,

Can you try installing the AnnotationFilter package, then installing ALTRE?

source("https://bioconductor.org/biocLite.R") biocLite("AnnotationFilter")

Ewy

From: duncan8659 notifications@github.com Reply-To: Mathelab/ALTRE reply@reply.github.com Date: Tuesday, November 28, 2017 at 1:00 PM To: Mathelab/ALTRE ALTRE@noreply.github.com Cc: "Mathe, Ewy" Ewy.Mathe@osumc.edu, State change state_change@noreply.github.com Subject: Re: [Mathelab/ALTRE] error at annotate peak step (#53)

Hi Ewy I’ve been trying to use ALTRE today and it wasn’t working for me; I re-installed it and I still get the same error message:

Installing ALTRE '/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet CMD INSTALL \ '/private/var/folders/n4/sprgby7d2bd9430f7rs7y6p00000gr/T/Rtmp6R0Hya/devtoolsd0d2acfe68b/Mathelab-ALTRE-e5f07b3' \ --library='/Library/Frameworks/R.framework/Versions/3.3/Resources/library' --install-tests

ERROR: dependency ‘AnnotationFilter’ is not available for package ‘ALTRE’

removing ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/ALTRE’ Installation failed: Command failed (1)

Not sure what I did. I’m not familiar enough with R to figure out how to even look for the missing dependency

Great if you could help!

Dianne Duncan Research Associate Director, Imaging Core Biology Department 149 McDonnell Hall Washington University St Louis MO 63130 314-935-4764

From: Ewy Mathe notifications@github.com Reply-To: Mathelab/ALTRE reply@reply.github.com Date: Wednesday, November 22, 2017 at 2:56 PM To: Mathelab/ALTRE ALTRE@noreply.github.com Cc: "Duncan, Dianne" duncan_d@wustl.edu, Author author@noreply.github.com Subject: Re: [Mathelab/ALTRE] error at annotate peak step (#53)

Hi Dianne,

The first issue you brought up (error from deprecated function in getTSS()) is now fixed and pushed. As for this last issue you're raising, yes, it seems to be an annotation issue. Does the TSS annotation file you have contain all the chromosome types that are in your peak files?

Ewy

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/Mathelab/ALTRE/issues/53#issuecomment-346470736, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AYz4PpzafczVzxUbpsEnK6yzbRChgCcsks5s5Ip8gaJpZM4QmOAI.

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Mathelab commented 6 years ago

Did you try to reinstall the package? That error was fixed and I’m not reproducing it… Ewy

From: duncan8659 notifications@github.com Reply-To: Mathelab/ALTRE reply@reply.github.com Date: Tuesday, November 28, 2017 at 1:48 PM To: Mathelab/ALTRE ALTRE@noreply.github.com Cc: "Mathe, Ewy" Ewy.Mathe@osumc.edu, State change state_change@noreply.github.com Subject: Re: [Mathelab/ALTRE] error at annotate peak step (#53)

Ok so that got rid of that problem, but now I’m back to this issue that I had early on:

Warning: Error in validObject: invalid class "GeneIdFilter" object: 'like' must be in '==' '!=' 'startsWith' 'endsWith' 'contains'

Which my IT friend told me related to the new Mac R version

Dianne Duncan Research Associate Director, Imaging Core Biology Department 149 McDonnell Hall Washington University St Louis MO 63130 314-935-4764

From: Mathelab notifications@github.com Reply-To: Mathelab/ALTRE reply@reply.github.com Date: Tuesday, November 28, 2017 at 12:16 PM To: Mathelab/ALTRE ALTRE@noreply.github.com Cc: "Duncan, Dianne" duncan_d@wustl.edu, Author author@noreply.github.com Subject: Re: [Mathelab/ALTRE] error at annotate peak step (#53)

Ah, unfortunately, AnnotationFilter requires R3.4 or greater. Could you update R? Ewy

From: duncan8659 notifications@github.com Reply-To: Mathelab/ALTRE reply@reply.github.com Date: Tuesday, November 28, 2017 at 1:14 PM To: Mathelab/ALTRE ALTRE@noreply.github.com Cc: "Mathe, Ewy" Ewy.Mathe@osumc.edu, State change state_change@noreply.github.com Subject: Re: [Mathelab/ALTRE] error at annotate peak step (#53)

Gives this response:

BioC_mirror: https://bioconductor.org Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.3 (2017-03-06). Installing package(s) ‘AnnotationFilter’ Warning message: package ‘AnnotationFilter’ is not available (for R version 3.3.3)

Dianne Duncan Research Associate Director, Imaging Core Biology Department 149 McDonnell Hall Washington University St Louis MO 63130 314-935-4764

From: Mathelab notifications@github.com Reply-To: Mathelab/ALTRE reply@reply.github.com Date: Tuesday, November 28, 2017 at 12:12 PM To: Mathelab/ALTRE ALTRE@noreply.github.com Cc: "Duncan, Dianne" duncan_d@wustl.edu, Author author@noreply.github.com Subject: Re: [Mathelab/ALTRE] error at annotate peak step (#53)

Hi Dianne,

Can you try installing the AnnotationFilter package, then installing ALTRE?

source("https://bioconductor.org/biocLite.R") biocLite("AnnotationFilter")

Ewy

From: duncan8659 notifications@github.com Reply-To: Mathelab/ALTRE reply@reply.github.com Date: Tuesday, November 28, 2017 at 1:00 PM To: Mathelab/ALTRE ALTRE@noreply.github.com Cc: "Mathe, Ewy" Ewy.Mathe@osumc.edu, State change state_change@noreply.github.com Subject: Re: [Mathelab/ALTRE] error at annotate peak step (#53)

Hi Ewy I’ve been trying to use ALTRE today and it wasn’t working for me; I re-installed it and I still get the same error message:

Installing ALTRE '/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet CMD INSTALL \ '/private/var/folders/n4/sprgby7d2bd9430f7rs7y6p00000gr/T/Rtmp6R0Hya/devtoolsd0d2acfe68b/Mathelab-ALTRE-e5f07b3' \ --library='/Library/Frameworks/R.framework/Versions/3.3/Resources/library' --install-tests

ERROR: dependency ‘AnnotationFilter’ is not available for package ‘ALTRE’

removing ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/ALTRE’ Installation failed: Command failed (1)

Not sure what I did. I’m not familiar enough with R to figure out how to even look for the missing dependency

Great if you could help!

Dianne Duncan Research Associate Director, Imaging Core Biology Department 149 McDonnell Hall Washington University St Louis MO 63130 314-935-4764

From: Ewy Mathe notifications@github.com Reply-To: Mathelab/ALTRE reply@reply.github.com Date: Wednesday, November 22, 2017 at 2:56 PM To: Mathelab/ALTRE ALTRE@noreply.github.com Cc: "Duncan, Dianne" duncan_d@wustl.edu, Author author@noreply.github.com Subject: Re: [Mathelab/ALTRE] error at annotate peak step (#53)

Hi Dianne,

The first issue you brought up (error from deprecated function in getTSS()) is now fixed and pushed. As for this last issue you're raising, yes, it seems to be an annotation issue. Does the TSS annotation file you have contain all the chromosome types that are in your peak files?

Ewy

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/Mathelab/ALTRE/issues/53#issuecomment-346470736, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AYz4PpzafczVzxUbpsEnK6yzbRChgCcsks5s5Ip8gaJpZM4QmOAI.

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duncan8659 commented 6 years ago

Ok Ill try again

Dianne Duncan Research Associate Director, Imaging Core Biology Department 149 McDonnell Hall Washington University St Louis MO 63130 314-935-4764

From: Mathelab notifications@github.com Reply-To: Mathelab/ALTRE reply@reply.github.com Date: Tuesday, November 28, 2017 at 2:05 PM To: Mathelab/ALTRE ALTRE@noreply.github.com Cc: "Duncan, Dianne" duncan_d@wustl.edu, Author author@noreply.github.com Subject: Re: [Mathelab/ALTRE] error at annotate peak step (#53)

Did you try to reinstall the package? That error was fixed and I’m not reproducing it… Ewy

From: duncan8659 notifications@github.com Reply-To: Mathelab/ALTRE reply@reply.github.com Date: Tuesday, November 28, 2017 at 1:48 PM To: Mathelab/ALTRE ALTRE@noreply.github.com Cc: "Mathe, Ewy" Ewy.Mathe@osumc.edu, State change state_change@noreply.github.com Subject: Re: [Mathelab/ALTRE] error at annotate peak step (#53)

Ok so that got rid of that problem, but now I’m back to this issue that I had early on:

Warning: Error in validObject: invalid class "GeneIdFilter" object: 'like' must be in '==' '!=' 'startsWith' 'endsWith' 'contains'

Which my IT friend told me related to the new Mac R version

Dianne Duncan Research Associate Director, Imaging Core Biology Department 149 McDonnell Hall Washington University St Louis MO 63130 314-935-4764

From: Mathelab notifications@github.com Reply-To: Mathelab/ALTRE reply@reply.github.com Date: Tuesday, November 28, 2017 at 12:16 PM To: Mathelab/ALTRE ALTRE@noreply.github.com Cc: "Duncan, Dianne" duncan_d@wustl.edu, Author author@noreply.github.com Subject: Re: [Mathelab/ALTRE] error at annotate peak step (#53)

Ah, unfortunately, AnnotationFilter requires R3.4 or greater. Could you update R? Ewy

From: duncan8659 notifications@github.com Reply-To: Mathelab/ALTRE reply@reply.github.com Date: Tuesday, November 28, 2017 at 1:14 PM To: Mathelab/ALTRE ALTRE@noreply.github.com Cc: "Mathe, Ewy" Ewy.Mathe@osumc.edu, State change state_change@noreply.github.com Subject: Re: [Mathelab/ALTRE] error at annotate peak step (#53)

Gives this response:

BioC_mirror: https://bioconductor.org Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.3 (2017-03-06). Installing package(s) ‘AnnotationFilter’ Warning message: package ‘AnnotationFilter’ is not available (for R version 3.3.3)

Dianne Duncan Research Associate Director, Imaging Core Biology Department 149 McDonnell Hall Washington University St Louis MO 63130 314-935-4764

From: Mathelab notifications@github.com Reply-To: Mathelab/ALTRE reply@reply.github.com Date: Tuesday, November 28, 2017 at 12:12 PM To: Mathelab/ALTRE ALTRE@noreply.github.com Cc: "Duncan, Dianne" duncan_d@wustl.edu, Author author@noreply.github.com Subject: Re: [Mathelab/ALTRE] error at annotate peak step (#53)

Hi Dianne,

Can you try installing the AnnotationFilter package, then installing ALTRE?

source("https://bioconductor.org/biocLite.R") biocLite("AnnotationFilter")

Ewy

From: duncan8659 notifications@github.com Reply-To: Mathelab/ALTRE reply@reply.github.com Date: Tuesday, November 28, 2017 at 1:00 PM To: Mathelab/ALTRE ALTRE@noreply.github.com Cc: "Mathe, Ewy" Ewy.Mathe@osumc.edu, State change state_change@noreply.github.com Subject: Re: [Mathelab/ALTRE] error at annotate peak step (#53)

Hi Ewy I’ve been trying to use ALTRE today and it wasn’t working for me; I re-installed it and I still get the same error message:

Installing ALTRE '/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet CMD INSTALL \ '/private/var/folders/n4/sprgby7d2bd9430f7rs7y6p00000gr/T/Rtmp6R0Hya/devtoolsd0d2acfe68b/Mathelab-ALTRE-e5f07b3' \ --library='/Library/Frameworks/R.framework/Versions/3.3/Resources/library' --install-tests

ERROR: dependency ‘AnnotationFilter’ is not available for package ‘ALTRE’

removing ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/ALTRE’ Installation failed: Command failed (1)

Not sure what I did. I’m not familiar enough with R to figure out how to even look for the missing dependency

Great if you could help!

Dianne Duncan Research Associate Director, Imaging Core Biology Department 149 McDonnell Hall Washington University St Louis MO 63130 314-935-4764

From: Ewy Mathe notifications@github.com Reply-To: Mathelab/ALTRE reply@reply.github.com Date: Wednesday, November 22, 2017 at 2:56 PM To: Mathelab/ALTRE ALTRE@noreply.github.com Cc: "Duncan, Dianne" duncan_d@wustl.edu, Author author@noreply.github.com Subject: Re: [Mathelab/ALTRE] error at annotate peak step (#53)

Hi Dianne,

The first issue you brought up (error from deprecated function in getTSS()) is now fixed and pushed. As for this last issue you're raising, yes, it seems to be an annotation issue. Does the TSS annotation file you have contain all the chromosome types that are in your peak files?

Ewy

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Mathelab commented 6 years ago

Just to confirm, this error appears when you run getTSS()? If it’s still not working, could you share that file with me so I can test? Ewy

From: duncan8659 notifications@github.com Reply-To: Mathelab/ALTRE reply@reply.github.com Date: Tuesday, November 28, 2017 at 3:05 PM To: Mathelab/ALTRE ALTRE@noreply.github.com Cc: "Mathe, Ewy" Ewy.Mathe@osumc.edu, State change state_change@noreply.github.com Subject: Re: [Mathelab/ALTRE] error at annotate peak step (#53)

Ok Ill try again

Dianne Duncan Research Associate Director, Imaging Core Biology Department 149 McDonnell Hall Washington University St Louis MO 63130 314-935-4764

From: Mathelab notifications@github.com Reply-To: Mathelab/ALTRE reply@reply.github.com Date: Tuesday, November 28, 2017 at 2:05 PM To: Mathelab/ALTRE ALTRE@noreply.github.com Cc: "Duncan, Dianne" duncan_d@wustl.edu, Author author@noreply.github.com Subject: Re: [Mathelab/ALTRE] error at annotate peak step (#53)

Did you try to reinstall the package? That error was fixed and I’m not reproducing it… Ewy

From: duncan8659 notifications@github.com Reply-To: Mathelab/ALTRE reply@reply.github.com Date: Tuesday, November 28, 2017 at 1:48 PM To: Mathelab/ALTRE ALTRE@noreply.github.com Cc: "Mathe, Ewy" Ewy.Mathe@osumc.edu, State change state_change@noreply.github.com Subject: Re: [Mathelab/ALTRE] error at annotate peak step (#53)

Ok so that got rid of that problem, but now I’m back to this issue that I had early on:

Warning: Error in validObject: invalid class "GeneIdFilter" object: 'like' must be in '==' '!=' 'startsWith' 'endsWith' 'contains'

Which my IT friend told me related to the new Mac R version

Dianne Duncan Research Associate Director, Imaging Core Biology Department 149 McDonnell Hall Washington University St Louis MO 63130 314-935-4764

From: Mathelab notifications@github.com Reply-To: Mathelab/ALTRE reply@reply.github.com Date: Tuesday, November 28, 2017 at 12:16 PM To: Mathelab/ALTRE ALTRE@noreply.github.com Cc: "Duncan, Dianne" duncan_d@wustl.edu, Author author@noreply.github.com Subject: Re: [Mathelab/ALTRE] error at annotate peak step (#53)

Ah, unfortunately, AnnotationFilter requires R3.4 or greater. Could you update R? Ewy

From: duncan8659 notifications@github.com Reply-To: Mathelab/ALTRE reply@reply.github.com Date: Tuesday, November 28, 2017 at 1:14 PM To: Mathelab/ALTRE ALTRE@noreply.github.com Cc: "Mathe, Ewy" Ewy.Mathe@osumc.edu, State change state_change@noreply.github.com Subject: Re: [Mathelab/ALTRE] error at annotate peak step (#53)

Gives this response:

BioC_mirror: https://bioconductor.org Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.3 (2017-03-06). Installing package(s) ‘AnnotationFilter’ Warning message: package ‘AnnotationFilter’ is not available (for R version 3.3.3)

Dianne Duncan Research Associate Director, Imaging Core Biology Department 149 McDonnell Hall Washington University St Louis MO 63130 314-935-4764

From: Mathelab notifications@github.com Reply-To: Mathelab/ALTRE reply@reply.github.com Date: Tuesday, November 28, 2017 at 12:12 PM To: Mathelab/ALTRE ALTRE@noreply.github.com Cc: "Duncan, Dianne" duncan_d@wustl.edu, Author author@noreply.github.com Subject: Re: [Mathelab/ALTRE] error at annotate peak step (#53)

Hi Dianne,

Can you try installing the AnnotationFilter package, then installing ALTRE?

source("https://bioconductor.org/biocLite.R") biocLite("AnnotationFilter")

Ewy

From: duncan8659 notifications@github.com Reply-To: Mathelab/ALTRE reply@reply.github.com Date: Tuesday, November 28, 2017 at 1:00 PM To: Mathelab/ALTRE ALTRE@noreply.github.com Cc: "Mathe, Ewy" Ewy.Mathe@osumc.edu, State change state_change@noreply.github.com Subject: Re: [Mathelab/ALTRE] error at annotate peak step (#53)

Hi Ewy I’ve been trying to use ALTRE today and it wasn’t working for me; I re-installed it and I still get the same error message:

Installing ALTRE '/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet CMD INSTALL \ '/private/var/folders/n4/sprgby7d2bd9430f7rs7y6p00000gr/T/Rtmp6R0Hya/devtoolsd0d2acfe68b/Mathelab-ALTRE-e5f07b3' \ --library='/Library/Frameworks/R.framework/Versions/3.3/Resources/library' --install-tests

ERROR: dependency ‘AnnotationFilter’ is not available for package ‘ALTRE’

removing ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/ALTRE’ Installation failed: Command failed (1)

Not sure what I did. I’m not familiar enough with R to figure out how to even look for the missing dependency

Great if you could help!

Dianne Duncan Research Associate Director, Imaging Core Biology Department 149 McDonnell Hall Washington University St Louis MO 63130 314-935-4764

From: Ewy Mathe notifications@github.com Reply-To: Mathelab/ALTRE reply@reply.github.com Date: Wednesday, November 22, 2017 at 2:56 PM To: Mathelab/ALTRE ALTRE@noreply.github.com Cc: "Duncan, Dianne" duncan_d@wustl.edu, Author author@noreply.github.com Subject: Re: [Mathelab/ALTRE] error at annotate peak step (#53)

Hi Dianne,

The first issue you brought up (error from deprecated function in getTSS()) is now fixed and pushed. As for this last issue you're raising, yes, it seems to be an annotation issue. Does the TSS annotation file you have contain all the chromosome types that are in your peak files?

Ewy

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duncan8659 commented 6 years ago

Ok that did it, thanks so much!

Dianne Duncan Research Associate Director, Imaging Core Biology Department 149 McDonnell Hall Washington University St Louis MO 63130 314-935-4764

From: Mathelab notifications@github.com Reply-To: Mathelab/ALTRE reply@reply.github.com Date: Tuesday, November 28, 2017 at 2:05 PM To: Mathelab/ALTRE ALTRE@noreply.github.com Cc: "Duncan, Dianne" duncan_d@wustl.edu, Author author@noreply.github.com Subject: Re: [Mathelab/ALTRE] error at annotate peak step (#53)

Did you try to reinstall the package? That error was fixed and I’m not reproducing it… Ewy

From: duncan8659 notifications@github.com Reply-To: Mathelab/ALTRE reply@reply.github.com Date: Tuesday, November 28, 2017 at 1:48 PM To: Mathelab/ALTRE ALTRE@noreply.github.com Cc: "Mathe, Ewy" Ewy.Mathe@osumc.edu, State change state_change@noreply.github.com Subject: Re: [Mathelab/ALTRE] error at annotate peak step (#53)

Ok so that got rid of that problem, but now I’m back to this issue that I had early on:

Warning: Error in validObject: invalid class "GeneIdFilter" object: 'like' must be in '==' '!=' 'startsWith' 'endsWith' 'contains'

Which my IT friend told me related to the new Mac R version

Dianne Duncan Research Associate Director, Imaging Core Biology Department 149 McDonnell Hall Washington University St Louis MO 63130 314-935-4764

From: Mathelab notifications@github.com Reply-To: Mathelab/ALTRE reply@reply.github.com Date: Tuesday, November 28, 2017 at 12:16 PM To: Mathelab/ALTRE ALTRE@noreply.github.com Cc: "Duncan, Dianne" duncan_d@wustl.edu, Author author@noreply.github.com Subject: Re: [Mathelab/ALTRE] error at annotate peak step (#53)

Ah, unfortunately, AnnotationFilter requires R3.4 or greater. Could you update R? Ewy

From: duncan8659 notifications@github.com Reply-To: Mathelab/ALTRE reply@reply.github.com Date: Tuesday, November 28, 2017 at 1:14 PM To: Mathelab/ALTRE ALTRE@noreply.github.com Cc: "Mathe, Ewy" Ewy.Mathe@osumc.edu, State change state_change@noreply.github.com Subject: Re: [Mathelab/ALTRE] error at annotate peak step (#53)

Gives this response:

BioC_mirror: https://bioconductor.org Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.3 (2017-03-06). Installing package(s) ‘AnnotationFilter’ Warning message: package ‘AnnotationFilter’ is not available (for R version 3.3.3)

Dianne Duncan Research Associate Director, Imaging Core Biology Department 149 McDonnell Hall Washington University St Louis MO 63130 314-935-4764

From: Mathelab notifications@github.com Reply-To: Mathelab/ALTRE reply@reply.github.com Date: Tuesday, November 28, 2017 at 12:12 PM To: Mathelab/ALTRE ALTRE@noreply.github.com Cc: "Duncan, Dianne" duncan_d@wustl.edu, Author author@noreply.github.com Subject: Re: [Mathelab/ALTRE] error at annotate peak step (#53)

Hi Dianne,

Can you try installing the AnnotationFilter package, then installing ALTRE?

source("https://bioconductor.org/biocLite.R") biocLite("AnnotationFilter")

Ewy

From: duncan8659 notifications@github.com Reply-To: Mathelab/ALTRE reply@reply.github.com Date: Tuesday, November 28, 2017 at 1:00 PM To: Mathelab/ALTRE ALTRE@noreply.github.com Cc: "Mathe, Ewy" Ewy.Mathe@osumc.edu, State change state_change@noreply.github.com Subject: Re: [Mathelab/ALTRE] error at annotate peak step (#53)

Hi Ewy I’ve been trying to use ALTRE today and it wasn’t working for me; I re-installed it and I still get the same error message:

Installing ALTRE '/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet CMD INSTALL \ '/private/var/folders/n4/sprgby7d2bd9430f7rs7y6p00000gr/T/Rtmp6R0Hya/devtoolsd0d2acfe68b/Mathelab-ALTRE-e5f07b3' \ --library='/Library/Frameworks/R.framework/Versions/3.3/Resources/library' --install-tests

ERROR: dependency ‘AnnotationFilter’ is not available for package ‘ALTRE’

removing ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/ALTRE’ Installation failed: Command failed (1)

Not sure what I did. I’m not familiar enough with R to figure out how to even look for the missing dependency

Great if you could help!

Dianne Duncan Research Associate Director, Imaging Core Biology Department 149 McDonnell Hall Washington University St Louis MO 63130 314-935-4764

From: Ewy Mathe notifications@github.com Reply-To: Mathelab/ALTRE reply@reply.github.com Date: Wednesday, November 22, 2017 at 2:56 PM To: Mathelab/ALTRE ALTRE@noreply.github.com Cc: "Duncan, Dianne" duncan_d@wustl.edu, Author author@noreply.github.com Subject: Re: [Mathelab/ALTRE] error at annotate peak step (#53)

Hi Dianne,

The first issue you brought up (error from deprecated function in getTSS()) is now fixed and pushed. As for this last issue you're raising, yes, it seems to be an annotation issue. Does the TSS annotation file you have contain all the chromosome types that are in your peak files?

Ewy

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Mathelab commented 6 years ago

Great! Ewy

From: duncan8659 notifications@github.com Reply-To: Mathelab/ALTRE reply@reply.github.com Date: Tuesday, November 28, 2017 at 3:22 PM To: Mathelab/ALTRE ALTRE@noreply.github.com Cc: "Mathe, Ewy" Ewy.Mathe@osumc.edu, State change state_change@noreply.github.com Subject: Re: [Mathelab/ALTRE] error at annotate peak step (#53)

Ok that did it, thanks so much!

Dianne Duncan Research Associate Director, Imaging Core Biology Department 149 McDonnell Hall Washington University St Louis MO 63130 314-935-4764

From: Mathelab notifications@github.com Reply-To: Mathelab/ALTRE reply@reply.github.com Date: Tuesday, November 28, 2017 at 2:05 PM To: Mathelab/ALTRE ALTRE@noreply.github.com Cc: "Duncan, Dianne" duncan_d@wustl.edu, Author author@noreply.github.com Subject: Re: [Mathelab/ALTRE] error at annotate peak step (#53)

Did you try to reinstall the package? That error was fixed and I’m not reproducing it… Ewy

From: duncan8659 notifications@github.com Reply-To: Mathelab/ALTRE reply@reply.github.com Date: Tuesday, November 28, 2017 at 1:48 PM To: Mathelab/ALTRE ALTRE@noreply.github.com Cc: "Mathe, Ewy" Ewy.Mathe@osumc.edu, State change state_change@noreply.github.com Subject: Re: [Mathelab/ALTRE] error at annotate peak step (#53)

Ok so that got rid of that problem, but now I’m back to this issue that I had early on:

Warning: Error in validObject: invalid class "GeneIdFilter" object: 'like' must be in '==' '!=' 'startsWith' 'endsWith' 'contains'

Which my IT friend told me related to the new Mac R version

Dianne Duncan Research Associate Director, Imaging Core Biology Department 149 McDonnell Hall Washington University St Louis MO 63130 314-935-4764

From: Mathelab notifications@github.com Reply-To: Mathelab/ALTRE reply@reply.github.com Date: Tuesday, November 28, 2017 at 12:16 PM To: Mathelab/ALTRE ALTRE@noreply.github.com Cc: "Duncan, Dianne" duncan_d@wustl.edu, Author author@noreply.github.com Subject: Re: [Mathelab/ALTRE] error at annotate peak step (#53)

Ah, unfortunately, AnnotationFilter requires R3.4 or greater. Could you update R? Ewy

From: duncan8659 notifications@github.com Reply-To: Mathelab/ALTRE reply@reply.github.com Date: Tuesday, November 28, 2017 at 1:14 PM To: Mathelab/ALTRE ALTRE@noreply.github.com Cc: "Mathe, Ewy" Ewy.Mathe@osumc.edu, State change state_change@noreply.github.com Subject: Re: [Mathelab/ALTRE] error at annotate peak step (#53)

Gives this response:

BioC_mirror: https://bioconductor.org Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.3 (2017-03-06). Installing package(s) ‘AnnotationFilter’ Warning message: package ‘AnnotationFilter’ is not available (for R version 3.3.3)

Dianne Duncan Research Associate Director, Imaging Core Biology Department 149 McDonnell Hall Washington University St Louis MO 63130 314-935-4764

From: Mathelab notifications@github.com Reply-To: Mathelab/ALTRE reply@reply.github.com Date: Tuesday, November 28, 2017 at 12:12 PM To: Mathelab/ALTRE ALTRE@noreply.github.com Cc: "Duncan, Dianne" duncan_d@wustl.edu, Author author@noreply.github.com Subject: Re: [Mathelab/ALTRE] error at annotate peak step (#53)

Hi Dianne,

Can you try installing the AnnotationFilter package, then installing ALTRE?

source("https://bioconductor.org/biocLite.R") biocLite("AnnotationFilter")

Ewy

From: duncan8659 notifications@github.com Reply-To: Mathelab/ALTRE reply@reply.github.com Date: Tuesday, November 28, 2017 at 1:00 PM To: Mathelab/ALTRE ALTRE@noreply.github.com Cc: "Mathe, Ewy" Ewy.Mathe@osumc.edu, State change state_change@noreply.github.com Subject: Re: [Mathelab/ALTRE] error at annotate peak step (#53)

Hi Ewy I’ve been trying to use ALTRE today and it wasn’t working for me; I re-installed it and I still get the same error message:

Installing ALTRE '/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet CMD INSTALL \ '/private/var/folders/n4/sprgby7d2bd9430f7rs7y6p00000gr/T/Rtmp6R0Hya/devtoolsd0d2acfe68b/Mathelab-ALTRE-e5f07b3' \ --library='/Library/Frameworks/R.framework/Versions/3.3/Resources/library' --install-tests

ERROR: dependency ‘AnnotationFilter’ is not available for package ‘ALTRE’

removing ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/ALTRE’ Installation failed: Command failed (1)

Not sure what I did. I’m not familiar enough with R to figure out how to even look for the missing dependency

Great if you could help!

Dianne Duncan Research Associate Director, Imaging Core Biology Department 149 McDonnell Hall Washington University St Louis MO 63130 314-935-4764

From: Ewy Mathe notifications@github.com Reply-To: Mathelab/ALTRE reply@reply.github.com Date: Wednesday, November 22, 2017 at 2:56 PM To: Mathelab/ALTRE ALTRE@noreply.github.com Cc: "Duncan, Dianne" duncan_d@wustl.edu, Author author@noreply.github.com Subject: Re: [Mathelab/ALTRE] error at annotate peak step (#53)

Hi Dianne,

The first issue you brought up (error from deprecated function in getTSS()) is now fixed and pushed. As for this last issue you're raising, yes, it seems to be an annotation issue. Does the TSS annotation file you have contain all the chromosome types that are in your peak files?

Ewy

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/Mathelab/ALTRE/issues/53#issuecomment-346470736, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AYz4PpzafczVzxUbpsEnK6yzbRChgCcsks5s5Ip8gaJpZM4QmOAI.

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Mathelab / ALTRE

error at annotate peak step #53