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This page was generated on 2021-09-20 15:05:16 -0400 (Mon, 20 Sep 2021).

CHECK results for InPAS on tokay2

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.
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raw results

Package 923/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
InPAS 2.0.0  (landing page)
Jianhong Ou
Snapshot Date: 2021-09-19 04:50:10 -0400 (Sun, 19 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: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:InPAS.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings InPAS_2.0.0.tar.gz
StartedAt: 2021-09-20 00:04:04 -0400 (Mon, 20 Sep 2021)
EndedAt: 2021-09-20 00:13:30 -0400 (Mon, 20 Sep 2021)
EllapsedTime: 565.4 seconds
RetCode: 0
Status:   OK  
CheckDir: InPAS.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:InPAS.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings InPAS_2.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/InPAS.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '2.0.0'
* 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 ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
get_usage4plot   25.52   2.64   44.08
extract_UTR3Anno  7.06   0.66    7.73
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
get_usage4plot   25.30   0.62   25.89
extract_UTR3Anno  7.93   0.25    8.18
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  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


Installation output

InPAS.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/InPAS_2.0.0.tar.gz && rm -rf InPAS.buildbin-libdir && mkdir InPAS.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=InPAS.buildbin-libdir InPAS_2.0.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL InPAS_2.0.0.zip && rm InPAS_2.0.0.tar.gz InPAS_2.0.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  5 1080k    5 56485    0     0   361k      0  0:00:02 --:--:--  0:00:02  360k
100 1080k  100 1080k    0     0  2848k      0 --:--:-- --:--:-- --:--:-- 2849k

install for i386

* 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

install for x64

* installing *source* package 'InPAS' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'InPAS' as InPAS_2.0.0.zip
* DONE (InPAS)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'InPAS' successfully unpacked and MD5 sums checked

Tests output

InPAS.Rcheck/tests_i386/runTests.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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

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 C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpI1V1Hc\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 C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpI1V1Hc\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 -- Mon Sep 20 00:12:50 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 
  26.26    1.84   32.12 

InPAS.Rcheck/tests_x64/runTests.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
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
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

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 C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpS2iumd\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 C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpS2iumd\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 -- Mon Sep 20 00:13:19 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 
  27.62    0.85   28.60 

Example timings

InPAS.Rcheck/examples_i386/InPAS-Ex.timings

nameusersystemelapsed
assemble_allCov000
extract_UTR3Anno7.060.667.73
filter_testOut0.250.000.45
gcComp000
gcContents000
get_UTR3eSet0.020.000.01
get_seqLen0.120.010.14
get_ssRleCov000
get_usage4plot25.52 2.6444.08
parse_TxDb2.160.032.18
run_coverageQC000
run_singleGroupAnalysis0.020.000.02
run_singleSampleAnalysis000
search_CPs0.010.000.02
setup_GSEA000
setup_sqlitedb000
test_dPDUI0.030.000.03

InPAS.Rcheck/examples_x64/InPAS-Ex.timings

nameusersystemelapsed
assemble_allCov000
extract_UTR3Anno7.930.258.18
filter_testOut0.160.000.16
gcComp000
gcContents000
get_UTR3eSet000
get_seqLen0.080.020.10
get_ssRleCov000
get_usage4plot25.30 0.6225.89
parse_TxDb2.390.062.45
run_coverageQC0.010.000.02
run_singleGroupAnalysis000
run_singleSampleAnalysis0.020.000.01
search_CPs000
setup_GSEA000
setup_sqlitedb000
test_dPDUI0.030.000.03