Job van Riet
| Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/ProteoDisco |
| git_branch: RELEASE_3_20 |
| git_last_commit: 89c9e43 |
| git_last_commit_date: 2024-10-29 11:03:45 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-12-23 12:05 -0500 (Mon, 23 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 1609/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ProteoDisco 1.12.0 (landing page) Job van Riet
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
|
To the developers/maintainers of the ProteoDisco package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ProteoDisco.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: ProteoDisco |
| Version: 1.12.0 |
| Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ProteoDisco.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings ProteoDisco_1.12.0.tar.gz |
| StartedAt: 2024-12-20 04:50:00 -0500 (Fri, 20 Dec 2024) |
| EndedAt: 2024-12-20 05:01:32 -0500 (Fri, 20 Dec 2024) |
| EllapsedTime: 692.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: ProteoDisco.Rcheck |
| Warnings: 2 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ProteoDisco.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings ProteoDisco_1.12.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/ProteoDisco.Rcheck'
* using R version 4.4.2 (2024-10-31 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.3.0
GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'ProteoDisco/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ProteoDisco' version '1.12.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'ProteoDisco' can be installed ... WARNING
Found the following significant warnings:
Warning: replacing previous import 'dplyr::rename' by 'plyr::rename' when loading 'ProteoDisco'
Warning: replacing previous import 'dplyr::count' by 'plyr::count' when loading 'ProteoDisco'
Warning: replacing previous import 'dplyr::failwith' by 'plyr::failwith' when loading 'ProteoDisco'
Warning: replacing previous import 'dplyr::id' by 'plyr::id' when loading 'ProteoDisco'
Warning: replacing previous import 'dplyr::summarize' by 'plyr::summarize' when loading 'ProteoDisco'
Warning: replacing previous import 'dplyr::summarise' by 'plyr::summarise' when loading 'ProteoDisco'
Warning: replacing previous import 'dplyr::mutate' by 'plyr::mutate' when loading 'ProteoDisco'
Warning: replacing previous import 'dplyr::desc' by 'plyr::desc' when loading 'ProteoDisco'
Warning: replacing previous import 'dplyr::arrange' by 'plyr::arrange' when loading 'ProteoDisco'
See 'F:/biocbuild/bbs-3.20-bioc/meat/ProteoDisco.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... NOTE
Warning: no function found corresponding to methods exports from 'ProteoDisco' for: 'show'
A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.
Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... NOTE
checkRd: (-1) checkProteotypicFragments.Rd:25: Lost braces; missing escapes or markup?
25 | \item{x}{({ProteoDiscography}): ProteoDiscography object which stores the annotation and genomic sequences.}
| ^
checkRd: (-1) checkProteotypicFragments.Rd:39: Lost braces; missing escapes or markup?
39 | {ProteoDiscography} with an additional column specifying the number of proteotypic fragments per record.
| ^
checkRd: (-1) generateJunctionModels.Rd:36: Lost braces; missing escapes or markup?
36 | of the given {ProteoDiscography}; strand-information is taken into account. If no strand-information is given, the nearest (or overlapping) known
| ^
checkRd: (-1) importGenomicVariants.MAF.Rd:17: Lost braces; missing escapes or markup?
17 | \item{ProteoDiscography}{({ProteoDiscography}): ProteoDiscography object which stores the annotation and genomic sequences.}
| ^
checkRd: (-1) importGenomicVariants.Rd:40: Lost braces; missing escapes or markup?
40 | into the {ProteoDiscography} as a {VRanges}. This genomic variants can later be incorporated within transcript
| ^
checkRd: (-1) importGenomicVariants.Rd:40: Lost braces; missing escapes or markup?
40 | into the {ProteoDiscography} as a {VRanges}. This genomic variants can later be incorporated within transcript
| ^
checkRd: (-1) importGenomicVariants.Rd:19: Lost braces; missing escapes or markup?
19 | \item{ProteoDiscography}{({ProteoDiscography}): ProteoDiscography object which stores the annotation and genomic sequences.}
| ^
checkRd: (-1) importGenomicVariants.VCF.Rd:17: Lost braces; missing escapes or markup?
17 | \item{ProteoDiscography}{({ProteoDiscography}): ProteoDiscography object which stores the annotation and genomic sequences.}
| ^
checkRd: (-1) importSpliceJunctions.Rd:39: Lost braces; missing escapes or markup?
39 | Input should be a {tibble} containing the following columns:
| ^
checkRd: (-1) importSpliceJunctions.Rd:18: Lost braces; missing escapes or markup?
18 | \item{ProteoDiscography}{({ProteoDiscography}): ProteoDiscography object which stores the annotation and genomic sequences.}
| ^
checkRd: (-1) importTranscriptSequences.Rd:15: Lost braces; missing escapes or markup?
15 | \item{ProteoDiscography}{({ProteoDiscography}): ProteoDiscography object which stores the annotation and genomic sequences.}
| ^
checkRd: (-1) incorporateGenomicVariants.Rd:34: Lost braces; missing escapes or markup?
34 | \code{incorporateMutations} Incorporates SNV, MNV and InDels present in the {ProteoDiscography} on the transcripts.
| ^
checkRd: (-1) incorporateGenomicVariants.Rd:17: Lost braces; missing escapes or markup?
17 | \item{ProteoDiscography}{({ProteoDiscography}): ProteoDiscography object which stores the annotation and genomic sequences.}
| ^
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
generic 'show' and siglist 'ProteoDiscography'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... NOTE
Error loading dataset 'ProteoDiscographyExample.hg19':
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'x' in selecting a method for function 'seqlevels': UCSC library operation failed
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
incorporateGenomicVariants 41.00 1.25 42.25
generateJunctionModels 15.03 0.78 39.73
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'testthat.R'
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 WARNINGs, 3 NOTEs
See
'F:/biocbuild/bbs-3.20-bioc/meat/ProteoDisco.Rcheck/00check.log'
for details.
ProteoDisco.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL ProteoDisco ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'ProteoDisco' ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading Warning: replacing previous import 'dplyr::rename' by 'plyr::rename' when loading 'ProteoDisco' Warning: replacing previous import 'dplyr::count' by 'plyr::count' when loading 'ProteoDisco' Warning: replacing previous import 'dplyr::failwith' by 'plyr::failwith' when loading 'ProteoDisco' Warning: replacing previous import 'dplyr::id' by 'plyr::id' when loading 'ProteoDisco' Warning: replacing previous import 'dplyr::summarize' by 'plyr::summarize' when loading 'ProteoDisco' Warning: replacing previous import 'dplyr::summarise' by 'plyr::summarise' when loading 'ProteoDisco' Warning: replacing previous import 'dplyr::mutate' by 'plyr::mutate' when loading 'ProteoDisco' Warning: replacing previous import 'dplyr::desc' by 'plyr::desc' when loading 'ProteoDisco' Warning: replacing previous import 'dplyr::arrange' by 'plyr::arrange' when loading 'ProteoDisco' ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: replacing previous import 'dplyr::rename' by 'plyr::rename' when loading 'ProteoDisco' Warning: replacing previous import 'dplyr::count' by 'plyr::count' when loading 'ProteoDisco' Warning: replacing previous import 'dplyr::failwith' by 'plyr::failwith' when loading 'ProteoDisco' Warning: replacing previous import 'dplyr::id' by 'plyr::id' when loading 'ProteoDisco' Warning: replacing previous import 'dplyr::summarize' by 'plyr::summarize' when loading 'ProteoDisco' Warning: replacing previous import 'dplyr::summarise' by 'plyr::summarise' when loading 'ProteoDisco' Warning: replacing previous import 'dplyr::mutate' by 'plyr::mutate' when loading 'ProteoDisco' Warning: replacing previous import 'dplyr::desc' by 'plyr::desc' when loading 'ProteoDisco' Warning: replacing previous import 'dplyr::arrange' by 'plyr::arrange' when loading 'ProteoDisco' ** testing if installed package can be loaded from final location Warning: replacing previous import 'dplyr::rename' by 'plyr::rename' when loading 'ProteoDisco' Warning: replacing previous import 'dplyr::count' by 'plyr::count' when loading 'ProteoDisco' Warning: replacing previous import 'dplyr::failwith' by 'plyr::failwith' when loading 'ProteoDisco' Warning: replacing previous import 'dplyr::id' by 'plyr::id' when loading 'ProteoDisco' Warning: replacing previous import 'dplyr::summarize' by 'plyr::summarize' when loading 'ProteoDisco' Warning: replacing previous import 'dplyr::summarise' by 'plyr::summarise' when loading 'ProteoDisco' Warning: replacing previous import 'dplyr::mutate' by 'plyr::mutate' when loading 'ProteoDisco' Warning: replacing previous import 'dplyr::desc' by 'plyr::desc' when loading 'ProteoDisco' Warning: replacing previous import 'dplyr::arrange' by 'plyr::arrange' when loading 'ProteoDisco' ** testing if installed package keeps a record of temporary installation path * DONE (ProteoDisco)
ProteoDisco.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> Sys.setenv("R_TESTS" = "")
>
> library(testthat)
> library(ProteoDisco)
Warning messages:
1: replacing previous import 'dplyr::rename' by 'plyr::rename' when loading 'ProteoDisco'
2: replacing previous import 'dplyr::count' by 'plyr::count' when loading 'ProteoDisco'
3: replacing previous import 'dplyr::failwith' by 'plyr::failwith' when loading 'ProteoDisco'
4: replacing previous import 'dplyr::id' by 'plyr::id' when loading 'ProteoDisco'
5: replacing previous import 'dplyr::summarize' by 'plyr::summarize' when loading 'ProteoDisco'
6: replacing previous import 'dplyr::summarise' by 'plyr::summarise' when loading 'ProteoDisco'
7: replacing previous import 'dplyr::mutate' by 'plyr::mutate' when loading 'ProteoDisco'
8: replacing previous import 'dplyr::desc' by 'plyr::desc' when loading 'ProteoDisco'
9: replacing previous import 'dplyr::arrange' by 'plyr::arrange' when loading 'ProteoDisco'
>
> testthat::test_check("ProteoDisco")
ProteoDisco - Importing manual transcript sequences to the ProteoDiscography.
ProteoDisco - Importing splice-junctions to the ProteoDiscography.
ProteoDisco - Generating splice-junctions models based on 9 unique (sample-specific or aggregated) splice-junctions.
Retrieving all CDS-records from the TxDb.
|
| | 0%Retrieving overlapping or adjacent CDS for each splice-junction: testSJ
Retrieving 5'-adjacent or overlapping CDS.
Retrieving 3'-adjacent or overlapping CDS.
|
|======================================================================| 100%
ProteoDisco - Ignoring subsetting on shared seqlevels as a BSgenome was given.
ProteoDisco - Generating the annotation database (ProteoDiscography)
ProteoDisco - Importing genomic variants from 1 file(s) to the ProteoDiscography.
ProteoDisco - Importing 1 VCF file(s).
|
| | 0%ProteoDisco - Importing F:/biocbuild/bbs-3.20-bioc/R/library/ProteoDisco/extdata/validationSet_hg19.vcf
ProteoDisco - Checking sanity of reference anchors for validationSet_hg19.vcf.
ProteoDisco - Checking sanity of reference anchors in chr1 (using 1 threads)
ProteoDisco - Checking sanity of reference anchors in chr2 (using 1 threads)
ProteoDisco - Checking sanity of reference anchors in chr3 (using 1 threads)
ProteoDisco - Checking sanity of reference anchors in chr6 (using 1 threads)
ProteoDisco - Checking sanity of reference anchors in chr7 (using 1 threads)
ProteoDisco - Checking sanity of reference anchors in chr10 (using 1 threads)
ProteoDisco - Checking sanity of reference anchors in chr11 (using 1 threads)
ProteoDisco - Checking sanity of reference anchors in chr13 (using 1 threads)
ProteoDisco - Checking sanity of reference anchors in chr14 (using 1 threads)
ProteoDisco - Checking sanity of reference anchors in chr17 (using 1 threads)
ProteoDisco - Checking sanity of reference anchors in chr19 (using 1 threads)
ProteoDisco - Checking sanity of reference anchors in chrX (using 1 threads)
|
|======================================================================| 100%
ProteoDisco - Calculating a prelim. overlap of genomic mutations with given annotations
ProteoDisco - Adding SNV/MNV and InDel mutations to transcript sequences.
ProteoDisco - Finding overlap of mutations with CDS within the TxDb.
ProteoDisco - Incorporating mutations within the CDS sequence(s).
Working on sample: validationSet_hg19.vcf (28 overlapping CDS; 4 threads)
|
| | 0% Working on CDS: 114412 (validationSet_hg19.vcf)
|
|== | 3% Working on CDS: 126702 (validationSet_hg19.vcf)
|
|==== | 6% Working on CDS: 13114 (validationSet_hg19.vcf)
|
|====== | 9% Working on CDS: 147351 (validationSet_hg19.vcf)
|
|======== | 12% Working on CDS: 157704 (validationSet_hg19.vcf)
|
|=========== | 15% Working on CDS: 157710 (validationSet_hg19.vcf)
|
|============= | 18% Working on CDS: 183308 (validationSet_hg19.vcf)
|
|=============== | 21% Working on CDS: 183309 (validationSet_hg19.vcf)
|
|================= | 24% Working on CDS: 186841 (validationSet_hg19.vcf)
|
|=================== | 27% Working on CDS: 197660 (validationSet_hg19.vcf)
|
|===================== | 30% Working on CDS: 197662 (validationSet_hg19.vcf)
|
|======================= | 33% Working on CDS: 220567 (validationSet_hg19.vcf)
|
|========================= | 36% Working on CDS: 25123 (validationSet_hg19.vcf)
|
|============================ | 39% Working on CDS: 25135 (validationSet_hg19.vcf)
|
|============================== | 42% Working on CDS: 25146 (validationSet_hg19.vcf)
|
|================================ | 45% Working on CDS: 25149 (validationSet_hg19.vcf)
|
|================================== | 48% Working on CDS: 38664 (validationSet_hg19.vcf)
|
|==================================== | 52% Working on CDS: 38670 (validationSet_hg19.vcf)
|
|====================================== | 55% Working on CDS: 49583 (validationSet_hg19.vcf)
|
|======================================== | 58% Working on CDS: 49584 (validationSet_hg19.vcf)
|
|========================================== | 61% Working on CDS: 73734 (validationSet_hg19.vcf)
|
|============================================= | 64% Working on CDS: 73737 (validationSet_hg19.vcf)
|
|=============================================== | 67% Working on CDS: 77574 (validationSet_hg19.vcf)
|
|================================================= | 70% Working on CDS: 77575 (validationSet_hg19.vcf)
|
|=================================================== | 73% Working on CDS: 77579 (validationSet_hg19.vcf)
|
|===================================================== | 76% Working on CDS: 77580 (validationSet_hg19.vcf)
|
|======================================================= | 79% Working on CDS: 77581 (validationSet_hg19.vcf)
|
|========================================================= | 82% Working on CDS: 84767 (validationSet_hg19.vcf)
|
|=========================================================== | 85% Working on CDS: 84768 (validationSet_hg19.vcf)
|
|============================================================== | 88% Working on CDS: 84771 (validationSet_hg19.vcf)
|
|================================================================ | 91% Working on CDS: 84772 (validationSet_hg19.vcf)
|
|================================================================== | 94% Working on CDS: 85674 (validationSet_hg19.vcf)
|
|==================================================================== | 97% Working on CDS: 85702 (validationSet_hg19.vcf)
|
|======================================================================| 100%
ProteoDisco - Generating mutant transcript sequence(s) by replacing wild-type to mutant CDS.
Working on sample: validationSet_hg19.vcf (33 mutant CDS; 4 threads)
|
| | 0% Working on TX: 12501 (validationSet_hg19.vcf)
|
|= | 1% Working on TX: 12503 (validationSet_hg19.vcf)
|
|== | 3% Working on TX: 12504 (validationSet_hg19.vcf)
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|=== | 4% Working on TX: 16025 (validationSet_hg19.vcf)
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|==== | 6% Working on TX: 24255 (validationSet_hg19.vcf)
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|===== | 7% Working on TX: 25556 (validationSet_hg19.vcf)
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|====== | 9% Working on TX: 25557 (validationSet_hg19.vcf)
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|======= | 10% Working on TX: 25558 (validationSet_hg19.vcf)
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|======== | 11% Working on TX: 25559 (validationSet_hg19.vcf)
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|========= | 13% Working on TX: 25560 (validationSet_hg19.vcf)
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|========== | 14% Working on TX: 25561 (validationSet_hg19.vcf)
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|=========== | 16% Working on TX: 25562 (validationSet_hg19.vcf)
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|============ | 17% Working on TX: 25563 (validationSet_hg19.vcf)
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|============= | 19% Working on TX: 25565 (validationSet_hg19.vcf)
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|============== | 20% Working on TX: 25568 (validationSet_hg19.vcf)
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|=============== | 21% Working on TX: 25569 (validationSet_hg19.vcf)
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|================ | 23% Working on TX: 25570 (validationSet_hg19.vcf)
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|================= | 24% Working on TX: 25571 (validationSet_hg19.vcf)
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|================== | 26% Working on TX: 25572 (validationSet_hg19.vcf)
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|=================== | 27% Working on TX: 25573 (validationSet_hg19.vcf)
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|==================== | 29% Working on TX: 28087 (validationSet_hg19.vcf)
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|===================== | 30% Working on TX: 28088 (validationSet_hg19.vcf)
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|============================================================== | 89% Working on TX: 8423 (validationSet_hg19.vcf)
|
|=============================================================== | 90% Working on TX: 8424 (validationSet_hg19.vcf)
|
|================================================================ | 91% Working on TX: 8425 (validationSet_hg19.vcf)
|
|================================================================= | 93% Working on TX: 8426 (validationSet_hg19.vcf)
|
|================================================================== | 94% Working on TX: 8427 (validationSet_hg19.vcf)
|
|=================================================================== | 96% Working on TX: 8431 (validationSet_hg19.vcf)
|
|==================================================================== | 97% Working on TX: 8432 (validationSet_hg19.vcf)
|
|===================================================================== | 99% Working on TX: 8433 (validationSet_hg19.vcf)
|
|======================================================================| 100%
Retrieving 3' UTR
ProteoDisco - Adding mutant transcripts to the ProteoDiscography.
ProteoDisco - Adding SNV/MNV and InDel mutations to transcript sequences.
ProteoDisco - Finding overlap of mutations with CDS within the TxDb.
ProteoDisco - Incorporating mutations within the CDS sequence(s).
Working on sample: validationSet_hg19.vcf (28 overlapping CDS; 4 threads)
|
| | 0% Working on CDS: 114412 (validationSet_hg19.vcf)
|
|== | 3% Working on CDS: 126702 (validationSet_hg19.vcf)
|
|==== | 6% Working on CDS: 13114 (validationSet_hg19.vcf)
|
|====== | 9% Working on CDS: 147351 (validationSet_hg19.vcf)
|
|======== | 12% Working on CDS: 157704 (validationSet_hg19.vcf)
|
|=========== | 15% Working on CDS: 157710 (validationSet_hg19.vcf)
|
|============= | 18% Working on CDS: 183308 (validationSet_hg19.vcf)
|
|=============== | 21% Working on CDS: 183309 (validationSet_hg19.vcf)
|
|================= | 24% Working on CDS: 186841 (validationSet_hg19.vcf)
|
|=================== | 27% Working on CDS: 197660 (validationSet_hg19.vcf)
|
|===================== | 30% Working on CDS: 197662 (validationSet_hg19.vcf)
|
|======================= | 33% Working on CDS: 220567 (validationSet_hg19.vcf)
|
|========================= | 36% Working on CDS: 25123 (validationSet_hg19.vcf)
|
|============================ | 39% Working on CDS: 25135 (validationSet_hg19.vcf)
|
|============================== | 42% Working on CDS: 25146 (validationSet_hg19.vcf)
|
|================================ | 45% Working on CDS: 25149 (validationSet_hg19.vcf)
|
|================================== | 48% Working on CDS: 38664 (validationSet_hg19.vcf)
|
|==================================== | 52% Working on CDS: 38670 (validationSet_hg19.vcf)
|
|====================================== | 55% Working on CDS: 49583 (validationSet_hg19.vcf)
|
|======================================== | 58% Working on CDS: 49584 (validationSet_hg19.vcf)
|
|========================================== | 61% Working on CDS: 73734 (validationSet_hg19.vcf)
|
|============================================= | 64% Working on CDS: 73737 (validationSet_hg19.vcf)
|
|=============================================== | 67% Working on CDS: 77574 (validationSet_hg19.vcf)
|
|================================================= | 70% Working on CDS: 77575 (validationSet_hg19.vcf)
|
|=================================================== | 73% Working on CDS: 77579 (validationSet_hg19.vcf)
|
|===================================================== | 76% Working on CDS: 77580 (validationSet_hg19.vcf)
|
|======================================================= | 79% Working on CDS: 77581 (validationSet_hg19.vcf)
|
|========================================================= | 82% Working on CDS: 84767 (validationSet_hg19.vcf)
|
|=========================================================== | 85% Working on CDS: 84768 (validationSet_hg19.vcf)
|
|============================================================== | 88% Working on CDS: 84771 (validationSet_hg19.vcf)
|
|================================================================ | 91% Working on CDS: 84772 (validationSet_hg19.vcf)
|
|================================================================== | 94% Working on CDS: 85674 (validationSet_hg19.vcf)
|
|==================================================================== | 97% Working on CDS: 85702 (validationSet_hg19.vcf)
|
|======================================================================| 100%
ProteoDisco - Generating mutant transcript sequence(s) by replacing wild-type to mutant CDS.
Working on sample: validationSet_hg19.vcf (34 mutant CDS; 4 threads)
|
| | 0% Working on TX: 12501 (validationSet_hg19.vcf)
|
|= | 1% Working on TX: 12503 (validationSet_hg19.vcf)
|
|== | 3% Working on TX: 12504 (validationSet_hg19.vcf)
|
|=== | 4% Working on TX: 16025 (validationSet_hg19.vcf)
|
|==== | 6% Working on TX: 24255 (validationSet_hg19.vcf)
|
|===== | 7% Working on TX: 25556 (validationSet_hg19.vcf)
|
|====== | 9% Working on TX: 25557 (validationSet_hg19.vcf)
|
|======= | 10% Working on TX: 25558 (validationSet_hg19.vcf)
|
|======== | 11% Working on TX: 25559 (validationSet_hg19.vcf)
|
|========= | 13% Working on TX: 25560 (validationSet_hg19.vcf)
|
|========== | 14% Working on TX: 25561 (validationSet_hg19.vcf)
|
|=========== | 16% Working on TX: 25562 (validationSet_hg19.vcf)
|
|============ | 17% Working on TX: 25563 (validationSet_hg19.vcf)
|
|============= | 19% Working on TX: 25565 (validationSet_hg19.vcf)
|
|============== | 20% Working on TX: 25568 (validationSet_hg19.vcf)
|
|=============== | 21% Working on TX: 25569 (validationSet_hg19.vcf)
|
|================ | 23% Working on TX: 25570 (validationSet_hg19.vcf)
|
|================= | 24% Working on TX: 25571 (validationSet_hg19.vcf)
|
|================== | 26% Working on TX: 25572 (validationSet_hg19.vcf)
|
|=================== | 27% Working on TX: 25573 (validationSet_hg19.vcf)
|
|==================== | 29% Working on TX: 28087 (validationSet_hg19.vcf)
|
|===================== | 30% Working on TX: 28088 (validationSet_hg19.vcf)
|
|====================== | 31% Working on TX: 28089 (validationSet_hg19.vcf)
|
|======================= | 33% Working on TX: 28090 (validationSet_hg19.vcf)
|
|======================== | 34% Working on TX: 28435 (validationSet_hg19.vcf)
|
|========================= | 36% Working on TX: 28436 (validationSet_hg19.vcf)
|
|========================== | 37% Working on TX: 28437 (validationSet_hg19.vcf)
|
|=========================== | 39% Working on TX: 28438 (validationSet_hg19.vcf)
|
|============================ | 40% Working on TX: 28439 (validationSet_hg19.vcf)
|
|============================= | 41% Working on TX: 28440 (validationSet_hg19.vcf)
|
|============================== | 43% Working on TX: 28441 (validationSet_hg19.vcf)
|
|=============================== | 44% Working on TX: 28442 (validationSet_hg19.vcf)
|
|================================ | 46% Working on TX: 38563 (validationSet_hg19.vcf)
|
|================================= | 47% Working on TX: 42727 (validationSet_hg19.vcf)
|
|================================== | 49% Working on TX: 42728 (validationSet_hg19.vcf)
|
|=================================== | 50% Working on TX: 42732 (validationSet_hg19.vcf)
|
|==================================== | 51% Working on TX: 4414 (validationSet_hg19.vcf)
|
|===================================== | 53% Working on TX: 4415 (validationSet_hg19.vcf)
|
|====================================== | 54% Working on TX: 49484 (validationSet_hg19.vcf)
|
|======================================= | 56% Working on TX: 53489 (validationSet_hg19.vcf)
|
|======================================== | 57% Working on TX: 53490 (validationSet_hg19.vcf)
|
|========================================= | 59% Working on TX: 53491 (validationSet_hg19.vcf)
|
|========================================== | 60% Working on TX: 53492 (validationSet_hg19.vcf)
|
|=========================================== | 61% Working on TX: 53493 (validationSet_hg19.vcf)
|
|============================================ | 63% Working on TX: 53494 (validationSet_hg19.vcf)
|
|============================================= | 64% Working on TX: 62635 (validationSet_hg19.vcf)
|
|============================================== | 66% Working on TX: 62636 (validationSet_hg19.vcf)
|
|=============================================== | 67% Working on TX: 62643 (validationSet_hg19.vcf)
|
|================================================ | 69% Working on TX: 62644 (validationSet_hg19.vcf)
|
|================================================= | 70% Working on TX: 62645 (validationSet_hg19.vcf)
|
|================================================== | 71% Working on TX: 62648 (validationSet_hg19.vcf)
|
|=================================================== | 73% Working on TX: 62651 (validationSet_hg19.vcf)
|
|==================================================== | 74% Working on TX: 63850 (validationSet_hg19.vcf)
|
|===================================================== | 76% Working on TX: 63851 (validationSet_hg19.vcf)
|
|====================================================== | 77% Working on TX: 63852 (validationSet_hg19.vcf)
|
|======================================================= | 79% Working on TX: 63853 (validationSet_hg19.vcf)
|
|======================================================== | 80% Working on TX: 63854 (validationSet_hg19.vcf)
|
|========================================================= | 81% Working on TX: 63855 (validationSet_hg19.vcf)
|
|========================================================== | 83% Working on TX: 63856 (validationSet_hg19.vcf)
|
|=========================================================== | 84% Working on TX: 67278 (validationSet_hg19.vcf)
|
|============================================================ | 86% Working on TX: 76042 (validationSet_hg19.vcf)
|
|============================================================= | 87% Working on TX: 76044 (validationSet_hg19.vcf)
|
|============================================================== | 89% Working on TX: 8423 (validationSet_hg19.vcf)
|
|=============================================================== | 90% Working on TX: 8424 (validationSet_hg19.vcf)
|
|================================================================ | 91% Working on TX: 8425 (validationSet_hg19.vcf)
|
|================================================================= | 93% Working on TX: 8426 (validationSet_hg19.vcf)
|
|================================================================== | 94% Working on TX: 8427 (validationSet_hg19.vcf)
|
|=================================================================== | 96% Working on TX: 8431 (validationSet_hg19.vcf)
|
|==================================================================== | 97% Working on TX: 8432 (validationSet_hg19.vcf)
|
|===================================================================== | 99% Working on TX: 8433 (validationSet_hg19.vcf)
|
|======================================================================| 100%
Retrieving 3' UTR
ProteoDisco - Adding mutant transcripts to the ProteoDiscography.
ProteoDisco - Exporting mutant protein isoforms.
Exporting 99 mutant protein sequences.
Writing to test.FASTA.
[ FAIL 0 | WARN 8 | SKIP 0 | PASS 11 ]
[ FAIL 0 | WARN 8 | SKIP 0 | PASS 11 ]
>
> proc.time()
user system elapsed
231.48 7.00 261.42
ProteoDisco.Rcheck/ProteoDisco-Ex.timings
| name | user | system | elapsed | |
| checkProteotypicFragments | 0.50 | 0.20 | 0.78 | |
| exportProteoDiscography | 0.38 | 0.25 | 0.64 | |
| generateJunctionModels | 15.03 | 0.78 | 39.73 | |
| generateProteoDiscography | 0 | 0 | 0 | |
| getDiscography | 0.31 | 0.20 | 0.52 | |
| importGenomicVariants.MAF | 4.37 | 0.19 | 4.56 | |
| importGenomicVariants | 3.83 | 0.02 | 3.84 | |
| importGenomicVariants.VCF | 3.86 | 0.06 | 3.92 | |
| importSpliceJunctions | 0.34 | 0.09 | 0.44 | |
| importTranscriptSequences | 0.25 | 0.00 | 0.25 | |
| incorporateGenomicVariants | 41.00 | 1.25 | 42.25 | |
| mutantTranscripts | 0.36 | 0.23 | 0.60 | |
| setGenomicSequences | 0.33 | 0.19 | 0.51 | |
| setMutantTranscripts | 0.48 | 0.19 | 0.68 | |
| setTxDb | 0.38 | 0.25 | 0.62 | |