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 12:07:08 -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: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ProteoDisco.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings ProteoDisco_1.0.0.tar.gz |
| StartedAt: 2022-04-13 00:55:53 -0400 (Wed, 13 Apr 2022) |
| EndedAt: 2022-04-13 01:08:34 -0400 (Wed, 13 Apr 2022) |
| EllapsedTime: 761.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ProteoDisco.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ProteoDisco.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings ProteoDisco_1.0.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/ProteoDisco.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
incorporateGenomicVariants 29.82 0.72 30.53
generateJunctionModels 12.31 0.98 29.53
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
incorporateGenomicVariants 29.24 0.81 30.05
generateJunctionModels 13.04 0.56 31.39
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
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
'C:/Users/biocbuild/bbs-3.14-bioc/meat/ProteoDisco.Rcheck/00check.log'
for details.
ProteoDisco.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/ProteoDisco_1.0.0.tar.gz && rm -rf ProteoDisco.buildbin-libdir && mkdir ProteoDisco.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ProteoDisco.buildbin-libdir ProteoDisco_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL ProteoDisco_1.0.0.zip && rm ProteoDisco_1.0.0.tar.gz ProteoDisco_1.0.0.zip
###
##############################################################################
##############################################################################
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 232k 100 232k 0 0 311k 0 --:--:-- --:--:-- --:--:-- 312k
install for i386
* 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
converting help for package 'ProteoDisco'
finding HTML links ... done
ProteoDiscography html
ProteoDiscographyExample.hg19 html
checkProteotypicFragments html
dot-checkReferenceAnchor html
exportProteoDiscography html
generateJunctionModels html
generateProteoDiscography html
getDiscography html
importGenomicVariants.MAF html
importGenomicVariants html
importGenomicVariants.VCF html
importSpliceJunctions html
importTranscriptSequences html
incorporateGenomicVariants html
mutantTranscripts html
organism html
print html
seqinfo html
seqlevels html
setGenomicSequences html
setMutantTranscripts html
setTxDb html
show html
summary html
** 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
install for x64
* installing *source* package 'ProteoDisco' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ProteoDisco' as ProteoDisco_1.0.0.zip
* DONE (ProteoDisco)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'ProteoDisco' successfully unpacked and MD5 sums checked
|
ProteoDisco.Rcheck/tests_i386/testthat.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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.
|
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|======================================================================| 100%
ProteoDisco - Generating the annotation database (ProteoDiscography)
ProteoDisco - Importing genomic variants from 1 file(s) to the ProteoDiscography.
ProteoDisco - Importing 1 VCF file(s).
|
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|
|======================================================================| 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).
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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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ProteoDisco - Adding SNV/MNV and InDel mutations to transcript sequences.
ProteoDisco - Incorporating mutations within the CDS sequence(s).
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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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ProteoDisco - Adding mutant transcripts to the ProteoDiscography.
Exporting 99 mutant protein sequences.
Writing to test.FASTA.
[ FAIL 0 | WARN 5 | SKIP 0 | PASS 11 ]
[ FAIL 0 | WARN 5 | SKIP 0 | PASS 11 ]
>
> proc.time()
user system elapsed
127.17 5.75 150.31
|
ProteoDisco.Rcheck/tests_x64/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-w64-mingw32/x64 (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).
|
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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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ProteoDisco - Adding SNV/MNV and InDel mutations to transcript sequences.
ProteoDisco - Incorporating mutations within the CDS sequence(s).
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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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ProteoDisco - Adding mutant transcripts to the ProteoDiscography.
Exporting 99 mutant protein sequences.
Writing to test.FASTA.
[ FAIL 0 | WARN 5 | SKIP 0 | PASS 11 ]
[ FAIL 0 | WARN 5 | SKIP 0 | PASS 11 ]
>
> proc.time()
user system elapsed
126.53 4.12 148.40
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ProteoDisco.Rcheck/examples_i386/ProteoDisco-Ex.timings
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ProteoDisco.Rcheck/examples_x64/ProteoDisco-Ex.timings
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