Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-10-19 13:20:25 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (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

CHECK results for InPAS on nebbiolo1


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? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 959/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
InPAS 2.4.0  (landing page)
Jianhong Ou
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/InPAS
git_branch: RELEASE_3_15
git_last_commit: 2de589d
git_last_commit_date: 2022-04-26 11:24:21 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: InPAS
Version: 2.4.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:InPAS.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings InPAS_2.4.0.tar.gz
StartedAt: 2022-10-18 20:12:43 -0400 (Tue, 18 Oct 2022)
EndedAt: 2022-10-18 20:18:22 -0400 (Tue, 18 Oct 2022)
EllapsedTime: 338.9 seconds
RetCode: 0
Status:   OK  
CheckDir: InPAS.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:InPAS.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings InPAS_2.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/InPAS.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘InPAS/DESCRIPTION’ ... OK
* this is package ‘InPAS’ version ‘2.4.0’
* 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 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   21.771  0.475  22.194
get_chromosomes   8.378  0.188   8.516
extract_UTR3Anno  6.082  0.284   6.366
* 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
  ‘/home/biocbuild/bbs-3.15-bioc/meat/InPAS.Rcheck/00check.log’
for details.



Installation output

InPAS.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL InPAS
###
##############################################################################
##############################################################################


* installing to library ‘/home/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
** 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)

Tests output

InPAS.Rcheck/tests/runTests.Rout


R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
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.

> 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, 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
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
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

The following object is masked from 'package:rtracklayer':

    values

The following object is masked from 'package:GenomicRanges':

    values

The following object is masked from 'package:S4Vectors':

    values

> 
> BiocGenerics:::testPackage("InPAS")
InPAS : Version 2.4.0
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 Tue Oct 18 20:18:08 2022.

coverage per sample per chromosome done at Tue Oct 18 20:18:08 2022.

total coverage start at Tue Oct 18 20:18:08 2022.

total coverage done at Tue Oct 18 20:18:08 2022.

backgroud around 3utr done at Tue Oct 18 20:18:08 2022.

utr3 TotalCov done at Tue Oct 18 20:18:08 2022.

chromsome chr1 coverage merged.

Preparation for CPsite search done at Tue Oct 18 20:18:08 2022.

No readable configuration file found
Created registry in '/tmp/RtmpeK73CQ/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 Tue Oct 18 20:18:17 2022.

coverage per sample per chromosome done at Tue Oct 18 20:18:17 2022.

total coverage start at Tue Oct 18 20:18:17 2022.

total coverage done at Tue Oct 18 20:18:17 2022.

backgroud around 3utr done at Tue Oct 18 20:18:17 2022.

utr3 TotalCov done at Tue Oct 18 20:18:17 2022.

chromsome chr1 coverage merged.

Preparation for CPsite search done at Tue Oct 18 20:18:17 2022.

No readable configuration file found
Created registry in '/tmp/RtmpeK73CQ/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 -- Tue Oct 18 20:18:18 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 
 31.403   1.296  32.720 

Example timings

InPAS.Rcheck/InPAS-Ex.timings

nameusersystemelapsed
addInPASTxDb0.2190.0080.227
assemble_allCov0.0000.0020.002
extract_UTR3Anno6.0820.2846.366
filter_testOut0.1230.0160.140
gcComp0.0000.0010.000
gcContents0.0000.0010.001
getInPASTxDb0.1620.0020.164
get_UTR3eSet0.0080.0000.008
get_chromosomes8.3780.1888.516
get_seqLen0.2360.0000.236
get_ssRleCov0.0020.0000.002
get_usage4plot21.771 0.47522.194
parse_TxDb2.6310.0802.711
run_coverageQC0.0040.0000.004
run_singleGroupAnalysis0.010.000.01
run_singleSampleAnalysis0.0030.0000.003
search_CPs0.0020.0040.006
setup_CPsSearch0.0030.0000.003
setup_GSEA0.0250.0080.032
setup_sqlitedb0.0010.0000.001
test_dPDUI0.0270.0000.028