Job van Riet
| Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022) |
| git_url: https://git.bioconductor.org/packages/ProteoDisco |
| git_branch: RELEASE_3_14 |
| git_last_commit: efdf16d |
| git_last_commit_date: 2021-10-26 13:12:13 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:05:47 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| 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 1475/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ProteoDisco 1.0.0 (landing page) Job van Riet
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: ProteoDisco |
| Version: 1.0.0 |
| Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:ProteoDisco.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings ProteoDisco_1.0.0.tar.gz |
| StartedAt: 2022-04-12 08:50:29 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 08:57:31 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 422.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ProteoDisco.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:ProteoDisco.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings ProteoDisco_1.0.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/ProteoDisco.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-pc-linux-gnu (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 ‘1.0.0’
* 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 ... OK
* 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 ... OK
* 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 ... OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
incorporateGenomicVariants 26.708 0.716 27.424
generateJunctionModels 11.804 0.576 15.337
* 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: 1 NOTE
See
‘/home/biocbuild/bbs-3.14-bioc/meat/ProteoDisco.Rcheck/00check.log’
for details.
ProteoDisco.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL ProteoDisco ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’ * installing *source* package ‘ProteoDisco’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘print’ in package ‘ProteoDisco’ Creating a new generic function for ‘summary’ in package ‘ProteoDisco’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ProteoDisco)
ProteoDisco.Rcheck/tests/testthat.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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)
Attaching package: 'ProteoDisco'
The following object is masked from 'package:methods':
show
The following objects are masked from 'package:base':
print, summary
>
> 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.
Working on sample: validationSet_hg19.vcf (33 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.
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 0 | SKIP 0 | PASS 11 ]
>
> proc.time()
user system elapsed
217.684 143.460 145.226
ProteoDisco.Rcheck/ProteoDisco-Ex.timings
| name | user | system | elapsed | |
| checkProteotypicFragments | 1.207 | 0.116 | 1.323 | |
| exportProteoDiscography | 0.331 | 0.004 | 0.335 | |
| generateJunctionModels | 11.804 | 0.576 | 15.337 | |
| generateProteoDiscography | 0.003 | 0.000 | 0.003 | |
| getDiscography | 2.865 | 0.383 | 0.270 | |
| importGenomicVariants.MAF | 2.799 | 0.148 | 2.947 | |
| importGenomicVariants | 2.625 | 0.027 | 2.653 | |
| importGenomicVariants.VCF | 2.546 | 0.073 | 2.618 | |
| importSpliceJunctions | 0.458 | 0.008 | 0.465 | |
| importTranscriptSequences | 0.312 | 0.024 | 0.335 | |
| incorporateGenomicVariants | 26.708 | 0.716 | 27.424 | |
| mutantTranscripts | 0.195 | 0.003 | 0.198 | |
| organism | 0.147 | 0.005 | 0.150 | |
| 0.254 | 0.000 | 0.254 | ||
| seqinfo | 0.161 | 0.000 | 0.161 | |
| seqlevels | 0.159 | 0.000 | 0.159 | |
| setGenomicSequences | 0.179 | 0.000 | 0.179 | |
| setMutantTranscripts | 0.293 | 0.000 | 0.292 | |
| setTxDb | 0.183 | 0.012 | 0.195 | |
| show | 0.179 | 0.000 | 0.179 | |
| summary | 0.181 | 0.000 | 0.181 | |