Jianhong Ou
| Snapshot Date: 2024-03-27 14:05:05 -0400 (Wed, 27 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/InPAS |
| git_branch: RELEASE_3_18 |
| git_last_commit: a2f3538 |
| git_last_commit_date: 2023-10-24 10:42:15 -0400 (Tue, 24 Oct 2023) |
| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2024-03-29 11:37:50 -0400 (Fri, 29 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4669 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4404 |
| merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4427 |
| 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 1024/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| InPAS 2.10.0 (landing page) Jianhong Ou
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the InPAS package: - 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 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: InPAS |
| Version: 2.10.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:InPAS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings InPAS_2.10.0.tar.gz |
| StartedAt: 2024-03-28 04:12:31 -0400 (Thu, 28 Mar 2024) |
| EndedAt: 2024-03-28 04:26:19 -0400 (Thu, 28 Mar 2024) |
| EllapsedTime: 828.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: InPAS.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:InPAS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings InPAS_2.10.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/InPAS.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘InPAS/DESCRIPTION’ ... OK
* this is package ‘InPAS’ version ‘2.10.0’
* 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 ‘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 startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
‘adjust_distalCPs’ ‘adjust_proximalCPs’ ‘adjust_proximalCPsByNBC’
‘adjust_proximalCPsByPWM’ ‘calculate_mse’ ‘find_valleyBySpline’
‘get_PAscore’ ‘get_PAscore2’ ‘remove_convergentUTR3s’
‘search_distalCPs’ ‘search_proximalCPs’
* 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 35.723 2.008 43.650
extract_UTR3Anno 12.561 0.662 14.809
get_chromosomes 10.123 0.269 11.334
parse_TxDb 4.230 0.172 5.097
* 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: 1 NOTE
See
‘/Users/biocbuild/bbs-3.18-bioc/meat/InPAS.Rcheck/00check.log’
for details.
InPAS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL InPAS ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/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 ** 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)
InPAS.Rcheck/tests/runTests.Rout
R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (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.
> pkgs_required <- c(
+ "BSgenome.Mmusculus.UCSC.mm10",
+ "TxDb.Mmusculus.UCSC.mm10.knownGene",
+ "EnsDb.Mmusculus.v79",
+ "rtracklayer",
+ "GenomicRanges",
+ "RUnit",
+ "limma", "future.apply"
+ )
> for (pkg in pkgs_required)
+ {
+ require(pkg, character.only = TRUE) || stop(pkg, " can't be loaded!")
+ }
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, aperm, 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 object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
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: BiocIO
Loading required package: rtracklayer
Attaching package: 'rtracklayer'
The following object is masked from 'package:BiocIO':
FileForFormat
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")'.
Loading required package: EnsDb.Mmusculus.v79
Loading required package: ensembldb
Loading required package: AnnotationFilter
Attaching package: 'ensembldb'
The following object is masked from 'package:stats':
filter
Loading required package: RUnit
Loading required package: limma
Attaching package: 'limma'
The following object is masked from 'package:BiocGenerics':
plotMA
Loading required package: future.apply
Loading required package: future
Attaching package: 'future'
The following object is masked from 'package:AnnotationFilter':
value
>
> BiocGenerics:::testPackage("InPAS")
InPAS : Version 2.10.0
For more information see our website : https://bioconductor.org/packages/release/bioc/vignettes/InPAS/inst/doc/InPAS.html
If you encounter a bug, please report : https://github.com/jianhong/InPAS/InPAS/issues
coverage per sample per chromosome start at Thu Mar 28 04:25:42 2024.
coverage per sample per chromosome done at Thu Mar 28 04:25:42 2024.
total coverage start at Thu Mar 28 04:25:42 2024.
total coverage done at Thu Mar 28 04:25:42 2024.
backgroud around 3utr done at Thu Mar 28 04:25:42 2024.
utr3 TotalCov done at Thu Mar 28 04:25:42 2024.
chromsome chr1 coverage merged.
Preparation for CPsite search done at Thu Mar 28 04:25:42 2024.
No readable configuration file found
Created registry in '/private/tmp/RtmpwkBJYC/006.CPsites.out_chr1' using cluster functions 'Interactive'
Adding 1 jobs ...
Submitting 1 jobs in 1 chunks using cluster functions 'Interactive' ...
coverage per sample per chromosome start at Thu Mar 28 04:25:56 2024.
coverage per sample per chromosome done at Thu Mar 28 04:25:56 2024.
total coverage start at Thu Mar 28 04:25:57 2024.
total coverage done at Thu Mar 28 04:25:57 2024.
backgroud around 3utr done at Thu Mar 28 04:25:57 2024.
utr3 TotalCov done at Thu Mar 28 04:25:57 2024.
chromsome chr1 coverage merged.
Preparation for CPsite search done at Thu Mar 28 04:25:57 2024.
No readable configuration file found
Created registry in '/private/tmp/RtmpwkBJYC/006.CPsites.out_chr1' using cluster functions 'Interactive'
Adding 1 jobs ...
Submitting 1 jobs in 1 chunks using cluster functions 'Interactive' ...
Error in get_ssRleCov(bedgraph = filenames[i], tag = tags[i], genome = genome, :
seqlevelsStyle of genome is different from bedgraph file.
RUNIT TEST PROTOCOL -- Thu Mar 28 04:26:00 2024
***********************************************
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
54.710 2.740 66.814
InPAS.Rcheck/InPAS-Ex.timings
| name | user | system | elapsed | |
| addInPASTxDb | 0.523 | 0.030 | 0.618 | |
| assemble_allCov | 0.007 | 0.002 | 0.009 | |
| extract_UTR3Anno | 12.561 | 0.662 | 14.809 | |
| filter_testOut | 0.288 | 0.037 | 0.343 | |
| gcComp | 0.000 | 0.001 | 0.001 | |
| gcContents | 0.000 | 0.000 | 0.001 | |
| getInPASTxDb | 0.295 | 0.023 | 0.340 | |
| get_UTR3eSet | 0.029 | 0.004 | 0.039 | |
| get_chromosomes | 10.123 | 0.269 | 11.334 | |
| get_seqLen | 0.348 | 0.035 | 0.417 | |
| get_ssRleCov | 0.005 | 0.002 | 0.008 | |
| get_usage4plot | 35.723 | 2.008 | 43.650 | |
| parse_TxDb | 4.230 | 0.172 | 5.097 | |
| run_coverageQC | 0.012 | 0.004 | 0.017 | |
| run_singleGroupAnalysis | 0.019 | 0.001 | 0.026 | |
| run_singleSampleAnalysis | 0.006 | 0.001 | 0.007 | |
| search_CPs | 0.023 | 0.005 | 0.033 | |
| setup_CPsSearch | 0.011 | 0.003 | 0.018 | |
| setup_GSEA | 0.049 | 0.006 | 0.064 | |
| setup_sqlitedb | 0.002 | 0.001 | 0.004 | |
| test_dPDUI | 0.041 | 0.004 | 0.049 | |