Error when running prepare_annotation_files() from vignette

[Joseph-Waldron]

When I run then prepare_annotation_files() function from the vignette I get the following error

Error: disjointExons() is defunct in BioC 3.15. Please use exonicParts() instead.

[Tim-Yu]

Hi Joe,

I think I have resolve this problem and created a pull request here, before they merge or anything, you can try reinstall via my fork?

BW,
Tim

[Joseph-Waldron]

Hi Tim Thanks very much for this. I am on annual leave at the moment but will make sure to give this a try as soon as I'm back which is on the 31st Aug and I'll let you know how it goes Many thanks Joe Get Outlook for Android<https://aka.ms/AAb9ysg>

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________________________________ From: Tim Yu ***@***.***> Sent: Thursday, August 25, 2022 3:46:42 PM To: lcalviell/ORFquant ***@***.***> Cc: Joseph-Waldron ***@***.***>; Author ***@***.***> Subject: Re: [lcalviell/ORFquant] Error when running prepare_annotation_files() from vignette (Issue #20) Hi Joe, I think I have resolve this problem and created a pull request here, before they merge or anything, you can try reinstall via my fork? BW, Tim — Reply to this email directly, view it on GitHub<#20 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AJUXPEBOL6MO7QN6UHGMU2DV26BNFANCNFSM526BWYCA>. You are receiving this because you authored the thread.Message ID: ***@***.***>

[Joseph-Waldron]

Hi Tim This looks to have worked I think, although I still get the following warnings. Are any of these anything to worry about? Many thanks for this Joe Warning messages: 1: In forgeBSgenomeDataPkg(y, seqs_srcdir = seqs_srcdir, destdir = destdir, : field 'provider_version' is deprecated in favor of 'genome' 2: In forgeBSgenomeDataPkg(y, seqs_srcdir = seqs_srcdir, destdir = destdir, : field 'release_name' is deprecated 3: In .get_cds_IDX(mcols0$type, mcols0$phase) : The "phase" metadata column contains non-NA values for features of type stop_codon. This information was ignored. 4: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 554 out-of-bound ranges located on sequences ENST00000624155.1, ENST00000252835.4, ENST00000426208.5, ENST00000416740.1, ENST00000612978.4, ENST00000613577.4, ENST00000613597.1, ENST00000623496.1, ENST00000438587.5, ENST00000455750.5, ENST00000622227.4, ENST00000412544.5, ENST00000431124.5, ENST00000395109.6, ENST00000413258.1, ENST00000621939.1, ENST00000412786.5, ENST00000432198.5, ENST00000434168.5, ENST00000457069.1, ENST00000432879.5, ENST00000411892.5, ENST00000416427.5, ENST00000421656.5, ENST00000423859.5, ENST00000418705.2, ENST00000436518.5, ENST00000420626.1, ENST00000405993.2, ENST00000445987.5, ENST00000414658.5, ENST00000432052.5, ENST00000438962.1, ENST00000445189.5, ENST00000451058.5, ENST00000457322.5, ENST00000428629.5, ENST00000424287.5, ENST00000423862.5, ENST00000439214.1, ENST00000441376.6, ENST00000434714.5, ENST00000442047.2, ENST00000425975.1, ENST00000458567.5, ENST00000390282.2, ENST00000390283.2, ENST00000390284.2, ENST0 [... truncated] 5: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 554 out-of-bound ranges located on sequences ENST00000624155.1, ENST00000252835.4, ENST00000426208.5, ENST00000416740.1, ENST00000612978.4, ENST00000613577.4, ENST00000613597.1, ENST00000623496.1, ENST00000438587.5, ENST00000455750.5, ENST00000622227.4, ENST00000412544.5, ENST00000431124.5, ENST00000395109.6, ENST00000413258.1, ENST00000621939.1, ENST00000412786.5, ENST00000432198.5, ENST00000434168.5, ENST00000457069.1, ENST00000432879.5, ENST00000411892.5, ENST00000416427.5, ENST00000421656.5, ENST00000423859.5, ENST00000418705.2, ENST00000436518.5, ENST00000420626.1, ENST00000405993.2, ENST00000445987.5, ENST00000414658.5, ENST00000432052.5, ENST00000438962.1, ENST00000445189.5, ENST00000451058.5, ENST00000457322.5, ENST00000428629.5, ENST00000424287.5, ENST00000423862.5, ENST00000439214.1, ENST00000441376.6, ENST00000434714.5, ENST00000442047.2, ENST00000425975.1, ENST00000458567.5, ENST00000390282.2, ENST00000390283.2, ENST00000390284.2, ENST0 [... truncated]

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________________________________ From: Tim Yu ***@***.***> Sent: 25 August 2022 15:46 To: lcalviell/ORFquant ***@***.***> Cc: Joseph-Waldron ***@***.***>; Author ***@***.***> Subject: Re: [lcalviell/ORFquant] Error when running prepare_annotation_files() from vignette (Issue #20) Hi Joe, I think I have resolve this problem and created a pull request here, before they merge or anything, you can try reinstall via my fork? BW, Tim — Reply to this email directly, view it on GitHub<#20 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AJUXPEBOL6MO7QN6UHGMU2DV26BNFANCNFSM526BWYCA>. You are receiving this because you authored the thread.Message ID: ***@***.***>

[Tim-Yu]

Hi Joe,

I am not quite sure about this. Are you running their vignette or it was on your data? (I am thinking if it is due to using the different genome build?)

BW,
Tim