Back to Multiple platform build/check report for BioC 3.15 |
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This page was generated on 2022-10-19 13:23:30 -0400 (Wed, 19 Oct 2022).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4386 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" | 4138 |
merida1 | macOS 10.14.6 Mojave | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4205 |
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 |
To the developers/maintainers of the ProteoDisco package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1512/2140 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ProteoDisco 1.2.0 (landing page) Job van Riet
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |||||||||
Package: ProteoDisco |
Version: 1.2.0 |
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_1.2.0.tar.gz |
StartedAt: 2022-10-19 06:27:48 -0400 (Wed, 19 Oct 2022) |
EndedAt: 2022-10-19 06:41:44 -0400 (Wed, 19 Oct 2022) |
EllapsedTime: 835.3 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_1.2.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/ProteoDisco.Rcheck’ * using R version 4.2.1 (2022-06-23) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ProteoDisco/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ProteoDisco’ version ‘1.2.0’ * 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::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::count’ by ‘plyr::count’ when loading ‘ProteoDisco’ Warning: replacing previous import ‘dplyr::desc’ by ‘plyr::desc’ when loading ‘ProteoDisco’ Warning: replacing previous import ‘dplyr::mutate’ by ‘plyr::mutate’ when loading ‘ProteoDisco’ Warning: replacing previous import ‘dplyr::arrange’ by ‘plyr::arrange’ when loading ‘ProteoDisco’ Warning: replacing previous import ‘dplyr::rename’ by ‘plyr::rename’ when loading ‘ProteoDisco’ Warning: replacing previous import ‘dplyr::summarise’ by ‘plyr::summarise’ when loading ‘ProteoDisco’ See ‘/Users/biocbuild/bbs-3.15-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 R 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 ... OK * 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 71.825 0.992 72.923 generateJunctionModels 25.654 1.537 27.147 importGenomicVariants.MAF 5.338 0.320 5.678 importGenomicVariants 5.159 0.109 5.286 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... 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, 2 NOTEs See ‘/Users/biocbuild/bbs-3.15-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/4.2/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::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::count’ by ‘plyr::count’ when loading ‘ProteoDisco’ Warning: replacing previous import ‘dplyr::desc’ by ‘plyr::desc’ when loading ‘ProteoDisco’ Warning: replacing previous import ‘dplyr::mutate’ by ‘plyr::mutate’ when loading ‘ProteoDisco’ Warning: replacing previous import ‘dplyr::arrange’ by ‘plyr::arrange’ when loading ‘ProteoDisco’ Warning: replacing previous import ‘dplyr::rename’ by ‘plyr::rename’ when loading ‘ProteoDisco’ Warning: replacing previous import ‘dplyr::summarise’ by ‘plyr::summarise’ 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::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::count’ by ‘plyr::count’ when loading ‘ProteoDisco’ Warning: replacing previous import ‘dplyr::desc’ by ‘plyr::desc’ when loading ‘ProteoDisco’ Warning: replacing previous import ‘dplyr::mutate’ by ‘plyr::mutate’ when loading ‘ProteoDisco’ Warning: replacing previous import ‘dplyr::arrange’ by ‘plyr::arrange’ when loading ‘ProteoDisco’ Warning: replacing previous import ‘dplyr::rename’ by ‘plyr::rename’ when loading ‘ProteoDisco’ Warning: replacing previous import ‘dplyr::summarise’ by ‘plyr::summarise’ when loading ‘ProteoDisco’ ** testing if installed package can be loaded from final location 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::count’ by ‘plyr::count’ when loading ‘ProteoDisco’ Warning: replacing previous import ‘dplyr::desc’ by ‘plyr::desc’ when loading ‘ProteoDisco’ Warning: replacing previous import ‘dplyr::mutate’ by ‘plyr::mutate’ when loading ‘ProteoDisco’ Warning: replacing previous import ‘dplyr::arrange’ by ‘plyr::arrange’ when loading ‘ProteoDisco’ Warning: replacing previous import ‘dplyr::rename’ by ‘plyr::rename’ when loading ‘ProteoDisco’ Warning: replacing previous import ‘dplyr::summarise’ by ‘plyr::summarise’ when loading ‘ProteoDisco’ ** testing if installed package keeps a record of temporary installation path * DONE (ProteoDisco)
ProteoDisco.Rcheck/tests/testthat.Rout
R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid" Copyright (C) 2022 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (64-bit) 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::failwith' by 'plyr::failwith' when loading 'ProteoDisco' 2: replacing previous import 'dplyr::id' by 'plyr::id' when loading 'ProteoDisco' 3: replacing previous import 'dplyr::summarize' by 'plyr::summarize' when loading 'ProteoDisco' 4: replacing previous import 'dplyr::count' by 'plyr::count' when loading 'ProteoDisco' 5: replacing previous import 'dplyr::desc' by 'plyr::desc' when loading 'ProteoDisco' 6: replacing previous import 'dplyr::mutate' by 'plyr::mutate' when loading 'ProteoDisco' 7: replacing previous import 'dplyr::arrange' by 'plyr::arrange' when loading 'ProteoDisco' 8: replacing previous import 'dplyr::rename' by 'plyr::rename' when loading 'ProteoDisco' 9: replacing previous import 'dplyr::summarise' by 'plyr::summarise' 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. | | | 0% | |======================================================================| 100% ProteoDisco - Generating the annotation database (ProteoDiscography) ProteoDisco - Importing genomic variants from 1 file(s) to the ProteoDiscography. ProteoDisco - Importing 1 VCF file(s). | | | 0% | |======================================================================| 100% ProteoDisco - Calculating a prelim. overlap of genomic mutations with given annotations ProteoDisco - Adding SNV/MNV and InDel mutations to transcript sequences. ProteoDisco - Incorporating mutations within the CDS sequence(s). | | | 0% | |== | 3% | |==== | 6% | |====== | 9% | |======== | 12% | |=========== | 15% | |============= | 18% | |=============== | 21% | |================= | 24% | |=================== | 27% | |===================== | 30% | |======================= | 33% | |========================= | 36% | |============================ | 39% | |============================== | 42% | |================================ | 45% | |================================== | 48% | |==================================== | 52% | |====================================== | 55% | |======================================== | 58% | |========================================== | 61% | |============================================= | 64% | |=============================================== | 67% | |================================================= | 70% | |=================================================== | 73% | |===================================================== | 76% | |======================================================= | 79% | |========================================================= | 82% | |=========================================================== | 85% | |============================================================== | 88% | |================================================================ | 91% | |================================================================== | 94% | |==================================================================== | 97% | |======================================================================| 100% ProteoDisco - Generating mutant transcript sequence(s) by replacing wild-type to mutant CDS. 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ProteoDisco - Adding SNV/MNV and InDel mutations to transcript sequences. ProteoDisco - Incorporating mutations within the CDS sequence(s). | | | 0% | |== | 3% | |==== | 6% | |====== | 9% | |======== | 12% | |=========== | 15% | |============= | 18% | |=============== | 21% | |================= | 24% | |=================== | 27% | |===================== | 30% | |======================= | 33% | |========================= | 36% | |============================ | 39% | |============================== | 42% | |================================ | 45% | |================================== | 48% | |==================================== | 52% | |====================================== | 55% | |======================================== | 58% | |========================================== | 61% | |============================================= | 64% | |=============================================== | 67% | |================================================= | 70% | |=================================================== | 73% | |===================================================== | 76% | |======================================================= | 79% | |========================================================= | 82% | |=========================================================== | 85% | |============================================================== | 88% | |================================================================ | 91% | |================================================================== | 94% | |==================================================================== | 97% | |======================================================================| 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% | |= | 1% | |== | 3% | |=== | 4% | |==== | 6% | |===== | 7% | |====== | 9% | |======= | 10% | |======== | 11% | |========= | 13% | |========== | 14% | |=========== | 16% | |============ | 17% | |============= | 19% | |============== | 20% | |=============== | 21% | |================ | 23% | |================= | 24% | |================== | 26% | |=================== | 27% | |==================== | 29% | |===================== | 30% | |====================== | 31% | |======================= | 33% | |======================== | 34% | |========================= | 36% | |========================== | 37% | |=========================== | 39% | |============================ | 40% | |============================= | 41% | |============================== | 43% | |=============================== | 44% | |================================ | 46% | |================================= | 47% | |================================== | 49% | |=================================== | 50% | |==================================== | 51% | |===================================== | 53% | |====================================== | 54% | |======================================= | 56% | |======================================== | 57% | |========================================= | 59% | |========================================== | 60% | |=========================================== | 61% | |============================================ | 63% | |============================================= | 64% | |============================================== | 66% | |=============================================== | 67% | |================================================ | 69% | |================================================= | 70% | |================================================== | 71% | |=================================================== | 73% | |==================================================== | 74% | |===================================================== | 76% | |====================================================== | 77% | |======================================================= | 79% | |======================================================== | 80% | |========================================================= | 81% | |========================================================== | 83% | |=========================================================== | 84% | |============================================================ | 86% | |============================================================= | 87% | |============================================================== | 89% | |=============================================================== | 90% | |================================================================ | 91% | |================================================================= | 93% | |================================================================== | 94% | |=================================================================== | 96% | |==================================================================== | 97% | |===================================================================== | 99% | |======================================================================| 100% ProteoDisco - Adding mutant transcripts to the ProteoDiscography. Exporting 99 mutant protein sequences. Writing to test.FASTA. [ FAIL 0 | WARN 1 | SKIP 0 | PASS 11 ] [ FAIL 0 | WARN 1 | SKIP 0 | PASS 11 ] > > proc.time() user system elapsed 393.158 221.563 255.200
ProteoDisco.Rcheck/ProteoDisco-Ex.timings
name | user | system | elapsed | |
checkProteotypicFragments | 0.666 | 0.034 | 0.700 | |
exportProteoDiscography | 0.583 | 0.011 | 0.596 | |
generateJunctionModels | 25.654 | 1.537 | 27.147 | |
generateProteoDiscography | 0.005 | 0.001 | 0.005 | |
getDiscography | 0.555 | 0.041 | 0.598 | |
importGenomicVariants.MAF | 5.338 | 0.320 | 5.678 | |
importGenomicVariants | 5.159 | 0.109 | 5.286 | |
importGenomicVariants.VCF | 4.869 | 0.089 | 4.967 | |
importSpliceJunctions | 0.968 | 0.042 | 1.011 | |
importTranscriptSequences | 0.466 | 0.007 | 0.475 | |
incorporateGenomicVariants | 71.825 | 0.992 | 72.923 | |
mutantTranscripts | 0.493 | 0.013 | 0.506 | |
setGenomicSequences | 0.464 | 0.011 | 0.476 | |
setMutantTranscripts | 0.729 | 0.020 | 0.751 | |
setTxDb | 0.431 | 0.007 | 0.440 | |