Jianhong Ou
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/InPAS |
| git_branch: master |
| git_last_commit: 320001a |
| git_last_commit_date: 2021-11-20 04:40:58 -0400 (Sat, 20 Nov 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:07:49 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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 InPAS package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/InPAS.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 937/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| InPAS 2.3.1 (landing page) Jianhong Ou
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: InPAS |
| Version: 2.3.1 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:InPAS.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings InPAS_2.3.1.tar.gz |
| StartedAt: 2022-03-17 19:22:35 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 19:27:27 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 291.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: InPAS.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:InPAS.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings InPAS_2.3.1.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/InPAS.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'InPAS/DESCRIPTION' ... OK
* this is package 'InPAS' version '2.3.1'
* 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 'InPAS' 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 ... OK
* checking LazyData ... OK
* 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
get_usage4plot 21.72 2.14 23.78
extract_UTR3Anno 6.58 0.42 7.00
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'runTests.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: OK
InPAS.Rcheck/00install.out
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL InPAS
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'InPAS' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'InPAS'
finding HTML links ... done
InPAS html
UTR3eSet-class html
finding level-2 HTML links ... done
adjust_distalCPs html
adjust_proximalCPs html
adjust_proximalCPsByNBC html
adjust_proximalCPsByPWM html
assemble_allCov html
assign_feature html
compensation html
extract_UTR3Anno html
fft.smooth html
filter_testOut html
find_segmentationSites html
find_valley html
fix_dbLockError html
gcComp html
gcContents html
get_PAscore html
get_PAscore2 html
get_UTR3CDS html
get_UTR3TotalCov html
get_UTR3eSet html
get_UTR3region html
get_depthWeight html
get_regionCov html
get_seqLen html
get_ssRleCov html
get_totalCov html
get_usage4plot html
get_zScoreCutoff html
mapComp html
parse_TxDb html
plot_utr3Usage html
polish_CPs html
remove_convergentUTR3s html
run_coverageQC html
run_fisherExactTest html
run_limmaAnalysis html
run_singleGroupAnalysis html
run_singleSampleAnalysis html
search_CPs html
search_distalCPs html
search_proximalCPs html
setup_CPsSearch html
setup_GSEA html
setup_sqlitedb html
test_dPDUI html
trim_seqnames html
utr3.mm10 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
* DONE (InPAS)
Making 'packages.html' ... done
InPAS.Rcheck/tests/runTests.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 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.
> require("BSgenome.Mmusculus.UCSC.mm10") || stop("can not load mm10 BSgenome.")
Loading required package: BSgenome.Mmusculus.UCSC.mm10
Loading required package: BSgenome
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Loading required package: rtracklayer
[1] TRUE
> require("TxDb.Mmusculus.UCSC.mm10.knownGene") || stop("can not load mm10 TxDb")
Loading required package: TxDb.Mmusculus.UCSC.mm10.knownGene
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
[1] TRUE
> require("rtracklayer") || stop("can not load rtracklayer.")
[1] TRUE
> require("GenomicRanges") || stop("can't load GenomicRanges")
[1] TRUE
> require("limma") || stop("can not load limma")
Loading required package: limma
Attaching package: 'limma'
The following object is masked from 'package:BiocGenerics':
plotMA
[1] TRUE
> BiocGenerics:::testPackage("InPAS")
total backgroud ... done.
total coverage ... done.
backgroud around 3utr ... done.
save utr3TotalCov for chr1 at D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpMxkirU\CPsites.out/chr1_utr3TotalCov.RDS ... done.
chromsome chr1 coverage merged.
chromsome chr1 quality filtered by first 100nt coverage.
chromsome chr1 distal search ... start.
chromsome chr1 distal search ... done.
chromsome chr1 distal adjust ... start.
chromsome chr1 proximal search ... start.
chromsome chr1 proximal searched ... done.
chromsome chr1 proximal adjust ... start.
total backgroud ... done.
total coverage ... done.
backgroud around 3utr ... done.
save utr3TotalCov for chr1 at D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpMxkirU\CPsites.out/chr1_utr3TotalCov.RDS ... done.
chromsome chr1 coverage merged.
chromsome chr1 quality filtered by first 100nt coverage.
chromsome chr1 distal search ... start.
chromsome chr1 distal search ... done.
chromsome chr1 distal adjust ... start.
chromsome chr1 proximal search ... start.
chromsome chr1 proximal searched ... done.
chromsome chr1 proximal adjust ... start.
Error in get_ssRleCov(bedgraph = filenames[i], tag = tags[i], genome = genome, :
seqlevelsStyle of genome is different from bedgraph file.
In addition: Warning message:
call dbDisconnect() when finished working with a connection
RUNIT TEST PROTOCOL -- Thu Mar 17 19:27:16 2022
***********************************************
Number of test functions: 3
Number of errors: 0
Number of failures: 0
1 Test Suite :
InPAS RUnit Tests - 3 test functions, 0 errors, 0 failures
Number of test functions: 3
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
20.57 1.46 22.09
InPAS.Rcheck/InPAS-Ex.timings
| name | user | system | elapsed | |
| assemble_allCov | 0 | 0 | 0 | |
| extract_UTR3Anno | 6.58 | 0.42 | 7.00 | |
| filter_testOut | 0.12 | 0.00 | 0.13 | |
| gcComp | 0 | 0 | 0 | |
| gcContents | 0 | 0 | 0 | |
| get_UTR3eSet | 0.01 | 0.00 | 0.02 | |
| get_seqLen | 0.11 | 0.02 | 0.12 | |
| get_ssRleCov | 0.02 | 0.00 | 0.02 | |
| get_usage4plot | 21.72 | 2.14 | 23.78 | |
| parse_TxDb | 2.41 | 0.08 | 2.50 | |
| run_coverageQC | 0 | 0 | 0 | |
| run_singleGroupAnalysis | 0.01 | 0.00 | 0.02 | |
| run_singleSampleAnalysis | 0 | 0 | 0 | |
| search_CPs | 0.02 | 0.00 | 0.02 | |
| setup_GSEA | 0 | 0 | 0 | |
| setup_sqlitedb | 0 | 0 | 0 | |
| test_dPDUI | 0.02 | 0.00 | 0.01 | |