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This page was generated on 2024-02-18 02:28:41 -0500 (Sun, 18 Feb 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4657
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" 4397
merida1macOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4424
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" 4400
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 1015/2244HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
InPAS 2.11.0  (landing page)
Jianhong Ou
Snapshot Date: 2024-02-16 14:10:20 -0500 (Fri, 16 Feb 2024)
git_url: https://git.bioconductor.org/packages/InPAS
git_branch: devel
git_last_commit: 1c9a765
git_last_commit_date: 2023-10-24 10:42:15 -0500 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 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 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for InPAS on merida1


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.

raw results


Summary

Package: InPAS
Version: 2.11.0
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_2.11.0.tar.gz
StartedAt: 2024-02-17 05:26:54 -0500 (Sat, 17 Feb 2024)
EndedAt: 2024-02-17 05:41:04 -0500 (Sat, 17 Feb 2024)
EllapsedTime: 849.6 seconds
RetCode: 0
Status:   OK  
CheckDir: InPAS.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### 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_2.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/InPAS.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* using platform: x86_64-apple-darwin20
* 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 ‘2.11.0’
* 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 whether 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 ... NOTE
Documented arguments not in \usage in Rd file 'get_UTR3TotalCov.Rd':
  ‘gcCompensationensation’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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   35.122  2.116  45.685
extract_UTR3Anno 13.503  0.644  16.709
get_chromosomes  10.173  0.280  12.056
parse_TxDb        4.245  0.182   5.417
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/InPAS.Rcheck/00check.log’
for details.



Installation output

InPAS.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-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)

Tests output

InPAS.Rcheck/tests/runTests.Rout


R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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, 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 2.11.0
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 Sat Feb 17 05:40:24 2024.

coverage per sample per chromosome done at Sat Feb 17 05:40:24 2024.

total coverage start at Sat Feb 17 05:40:24 2024.

total coverage done at Sat Feb 17 05:40:24 2024.

backgroud around 3utr done at Sat Feb 17 05:40:24 2024.

utr3 TotalCov done at Sat Feb 17 05:40:24 2024.

chromsome chr1 coverage merged.

Preparation for CPsite search done at Sat Feb 17 05:40:25 2024.

No readable configuration file found
Created registry in '/private/tmp/RtmpPA6BcX/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 Sat Feb 17 05:40:40 2024.

coverage per sample per chromosome done at Sat Feb 17 05:40:40 2024.

total coverage start at Sat Feb 17 05:40:40 2024.

total coverage done at Sat Feb 17 05:40:40 2024.

backgroud around 3utr done at Sat Feb 17 05:40:40 2024.

utr3 TotalCov done at Sat Feb 17 05:40:40 2024.

chromsome chr1 coverage merged.

Preparation for CPsite search done at Sat Feb 17 05:40:40 2024.

No readable configuration file found
Created registry in '/private/tmp/RtmpPA6BcX/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 -- Sat Feb 17 05:40:44 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 
 55.041   2.698  71.912 

Example timings

InPAS.Rcheck/InPAS-Ex.timings

nameusersystemelapsed
addInPASTxDb0.6980.0340.822
assemble_allCov0.0070.0020.009
extract_UTR3Anno13.503 0.64416.709
filter_testOut0.2980.0370.402
gcComp0.0000.0010.000
gcContents0.0000.0010.001
getInPASTxDb0.2880.0240.379
get_UTR3eSet0.0290.0040.037
get_chromosomes10.173 0.28012.056
get_seqLen0.3480.0400.451
get_ssRleCov0.0060.0020.008
get_usage4plot35.122 2.11645.685
parse_TxDb4.2450.1825.417
run_coverageQC0.0130.0050.034
run_singleGroupAnalysis0.0200.0020.038
run_singleSampleAnalysis0.0050.0010.012
search_CPs0.0210.0050.051
setup_CPsSearch0.0110.0030.015
setup_GSEA0.0520.0050.071
setup_sqlitedb0.0020.0020.003
test_dPDUI0.0440.0040.066