Job van Riet
| Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024) |
| git_url: https://git.bioconductor.org/packages/ProteoDisco |
| git_branch: RELEASE_3_19 |
| git_last_commit: e7dc7fb |
| git_last_commit_date: 2024-04-30 11:36:56 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-06-11 14:44 -0400 (Tue, 11 Jun 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4757 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4491 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4522 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4468 |
| 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 1622/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ProteoDisco 1.10.0 (landing page) Job van Riet
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
|
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: 1.10.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ProteoDisco.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ProteoDisco_1.10.0.tar.gz |
| StartedAt: 2024-06-11 01:53:40 -0400 (Tue, 11 Jun 2024) |
| EndedAt: 2024-06-11 02:06:20 -0400 (Tue, 11 Jun 2024) |
| EllapsedTime: 760.5 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: ProteoDisco.Rcheck |
| Warnings: 2 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ProteoDisco.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ProteoDisco_1.10.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/ProteoDisco.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ProteoDisco/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ProteoDisco’ version ‘1.10.0’
* 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 for sufficient/correct file permissions ... 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 ‘/Users/biocbuild/bbs-3.19-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 39.602 1.087 46.320
generateJunctionModels 22.827 1.390 30.951
importGenomicVariants.MAF 4.460 0.345 7.286
importGenomicVariants 4.240 0.099 6.037
importGenomicVariants.VCF 4.175 0.094 5.595
* 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
‘/Users/biocbuild/bbs-3.19-bioc/meat/ProteoDisco.Rcheck/00check.log’
for details.
ProteoDisco.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ProteoDisco ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/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 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
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 /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/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)
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ProteoDisco - Generating mutant transcript sequence(s) by replacing wild-type to mutant CDS.
Working on sample: validationSet_hg19.vcf (33 mutant CDS; 4 threads)
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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)
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ProteoDisco - Generating mutant transcript sequence(s) by replacing wild-type to mutant CDS.
Working on sample: validationSet_hg19.vcf (34 mutant CDS; 4 threads)
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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 3 | SKIP 0 | PASS 11 ]
[ FAIL 0 | WARN 3 | SKIP 0 | PASS 11 ]
>
> proc.time()
user system elapsed
174.373 50.292 193.125
ProteoDisco.Rcheck/ProteoDisco-Ex.timings
| name | user | system | elapsed | |
| checkProteotypicFragments | 0.405 | 0.023 | 0.589 | |
| exportProteoDiscography | 0.411 | 0.019 | 0.616 | |
| generateJunctionModels | 22.827 | 1.390 | 30.951 | |
| generateProteoDiscography | 0.003 | 0.003 | 0.007 | |
| getDiscography | 0.421 | 0.050 | 0.705 | |
| importGenomicVariants.MAF | 4.460 | 0.345 | 7.286 | |
| importGenomicVariants | 4.240 | 0.099 | 6.037 | |
| importGenomicVariants.VCF | 4.175 | 0.094 | 5.595 | |
| importSpliceJunctions | 0.447 | 0.041 | 0.737 | |
| importTranscriptSequences | 0.263 | 0.009 | 0.414 | |
| incorporateGenomicVariants | 39.602 | 1.087 | 46.320 | |
| mutantTranscripts | 0.351 | 0.012 | 0.561 | |
| setGenomicSequences | 0.351 | 0.011 | 0.552 | |
| setMutantTranscripts | 0.459 | 0.010 | 0.710 | |
| setTxDb | 0.400 | 0.012 | 0.627 | |