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This page was generated on 2021-09-24 15:06:44 -0400 (Fri, 24 Sep 2021).

CHECK results for InPAS on machv2

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.

raw results

Package 923/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
InPAS 2.0.0  (landing page)
Jianhong Ou
Snapshot Date: 2021-09-23 04:50:12 -0400 (Thu, 23 Sep 2021)
git_url: https://git.bioconductor.org/packages/InPAS
git_branch: RELEASE_3_13
git_last_commit: d402f5c
git_last_commit_date: 2021-05-19 12:12:03 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: InPAS
Version: 2.0.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:InPAS.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings InPAS_2.0.0.tar.gz
StartedAt: 2021-09-23 19:59:09 -0400 (Thu, 23 Sep 2021)
EndedAt: 2021-09-23 20:06:15 -0400 (Thu, 23 Sep 2021)
EllapsedTime: 426.5 seconds
RetCode: 0
Status:   OK  
CheckDir: InPAS.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:InPAS.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings InPAS_2.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/InPAS.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘InPAS/DESCRIPTION’ ... OK
* this is package ‘InPAS’ version ‘2.0.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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 ... 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   31.317  1.142  32.461
extract_UTR3Anno 10.768  0.446  11.229
* 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-3.13-bioc/meat/InPAS.Rcheck/00check.log’
for details.



Installation output

InPAS.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL InPAS
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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)

Tests output

InPAS.Rcheck/tests/runTests.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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
[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 /private/tmp/Rtmpt2f3oB/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 /private/tmp/Rtmpt2f3oB/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 Sep 23 20:06:07 2021 
*********************************************** 
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 
 35.336   1.275  36.607 

Example timings

InPAS.Rcheck/InPAS-Ex.timings

nameusersystemelapsed
assemble_allCov0.0050.0010.006
extract_UTR3Anno10.768 0.44611.229
filter_testOut0.1850.0140.199
gcComp000
gcContents0.0000.0010.001
get_UTR3eSet0.0230.0030.026
get_seqLen0.1560.0150.178
get_ssRleCov0.0020.0010.003
get_usage4plot31.317 1.14232.461
parse_TxDb3.1500.0383.189
run_coverageQC0.0040.0010.004
run_singleGroupAnalysis0.0110.0000.012
run_singleSampleAnalysis0.0030.0000.003
search_CPs0.0110.0010.013
setup_GSEA0.0000.0000.001
setup_sqlitedb0.0010.0000.001
test_dPDUI0.0250.0010.026