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CHECK report for InPAS on tokay1

This page was generated on 2020-08-07 12:05:57 -0400 (Fri, 07 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE InPAS PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 866/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
InPAS 1.21.0
Jianhong Ou
Snapshot Date: 2020-08-06 14:50:46 -0400 (Thu, 06 Aug 2020)
URL: https://git.bioconductor.org/packages/InPAS
Branch: master
Last Commit: 54b29cc
Last Changed Date: 2020-04-27 14:47:33 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: InPAS
Version: 1.21.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:InPAS.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings InPAS_1.21.0.tar.gz
StartedAt: 2020-08-07 02:06:05 -0400 (Fri, 07 Aug 2020)
EndedAt: 2020-08-07 02:17:59 -0400 (Fri, 07 Aug 2020)
EllapsedTime: 714.2 seconds
RetCode: 0
Status:  OK  
CheckDir: InPAS.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:InPAS.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings InPAS_1.21.0.tar.gz
###
##############################################################################
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/InPAS.Rcheck'
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'InPAS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'InPAS' version '1.21.0'
* 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 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
testUsage   23.36   0.03   23.40
filterRes   21.95   1.01   23.36
getUTR3eSet 21.39   0.01   21.41
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
filterRes   23.34   0.23   23.57
testUsage   21.84   0.00   21.84
getUTR3eSet 21.35   0.05   21.40
* 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

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/InPAS_1.21.0.tar.gz && rm -rf InPAS.buildbin-libdir && mkdir InPAS.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=InPAS.buildbin-libdir InPAS_1.21.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL InPAS_1.21.0.zip && rm InPAS_1.21.0.tar.gz InPAS_1.21.0.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
 63 2776k   63 1776k    0     0  6479k      0 --:--:-- --:--:-- --:--:-- 6553k
100 2776k  100 2776k    0     0  9819k      0 --:--:-- --:--:-- --:--:-- 9914k

install for i386

* installing *source* package 'InPAS' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'InPAS'
    finding HTML links ... done
    CPsite_estimation                       html  
    CPsites                                 html  
    InPAS-package                           html  
    PAscore                                 html  
    PAscore2                                html  
    UTR3TotalCoverage                       html  
    UTR3eSet                                html  
    UTR3usage                               html  
    covThreshold                            html  
    coverageFromBedGraph                    html  
    coverageRate                            html  
    depthWeight                             html  
    distalAdj                               html  
    filterRes                               html  
    fisher.exact.test                       html  
    get.regions.coverage                    html  
    getCov                                  html  
    getUTR3eSet                             html  
    getUTR3region                           html  
    inPAS                                   html  
    lastCDSusage                            html  
    limmaAnalyze                            html  
    optimalSegmentation                     html  
    polishCPs                               html  
    prepare4GSEA                            html  
    proximalAdj                             html  
    proximalAdjByCleanUpdTSeq               html  
    proximalAdjByPWM                        html  
    removeUTR3__UTR3                        html  
    searchDistalCPs                         html  
    searchProximalCPs                       html  
    seqLen                                  html  
    singleGroupAnalyze                      html  
    singleSampleAnalyze                     html  
    finding level-2 HTML links ... done

    sortGR                                  html  
    testUsage                               html  
    totalCoverage                           html  
    trimSeqnames                            html  
    usage4plot                              html  
    utr3.danRer10                           html  
    utr3.hg19                               html  
    utr3.mm10                               html  
    utr3Annotation                          html  
    utr3UsageEstimation                     html  
    valley                                  html  
    zScoreThrethold                         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_1.21.0.zip
* DONE (InPAS)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'InPAS' successfully unpacked and MD5 sums checked

Tests output

InPAS.Rcheck/tests_i386/runTests.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 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 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 object is masked from 'package:base':

    expand.grid

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("BSgenome.Hsapiens.UCSC.hg19") || stop("can not load BSgenome.")
Loading required package: BSgenome.Hsapiens.UCSC.hg19
[1] TRUE
> require("TxDb.Mmusculus.UCSC.mm10.knownGene") || stop("can not load 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("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")
seqlevelsStyle of genome is different from bedgraph file.


RUNIT TEST PROTOCOL -- Fri Aug 07 02:16:56 2020 
*********************************************** 
Number of test functions: 4 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
InPAS RUnit Tests - 4 test functions, 0 errors, 0 failures
Number of test functions: 4 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  47.35    2.84   50.92 

InPAS.Rcheck/tests_x64/runTests.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 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 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 object is masked from 'package:base':

    expand.grid

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("BSgenome.Hsapiens.UCSC.hg19") || stop("can not load BSgenome.")
Loading required package: BSgenome.Hsapiens.UCSC.hg19
[1] TRUE
> require("TxDb.Mmusculus.UCSC.mm10.knownGene") || stop("can not load 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("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")
seqlevelsStyle of genome is different from bedgraph file.


RUNIT TEST PROTOCOL -- Fri Aug 07 02:17:52 2020 
*********************************************** 
Number of test functions: 4 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
InPAS RUnit Tests - 4 test functions, 0 errors, 0 failures
Number of test functions: 4 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  53.54    1.06   54.98 

Example timings

InPAS.Rcheck/examples_i386/InPAS-Ex.timings

nameusersystemelapsed
CPsites000
coverageFromBedGraph000
coverageRate000
filterRes21.95 1.0123.36
fisher.exact.test0.070.020.08
getUTR3eSet21.39 0.0121.41
inPAS0.010.000.01
limmaAnalyze0.020.020.03
prepare4GSEA0.110.000.14
singleGroupAnalyze0.010.000.02
singleSampleAnalyze0.020.000.01
testUsage23.36 0.0323.40
usage4plot2.090.362.51
utr3.danRer100.290.000.29
utr3.hg190.500.020.52
utr3.mm100.540.010.55
utr3Annotation000
utr3UsageEstimation000

InPAS.Rcheck/examples_x64/InPAS-Ex.timings

nameusersystemelapsed
CPsites000
coverageFromBedGraph000
coverageRate000
filterRes23.34 0.2323.57
fisher.exact.test0.050.000.05
getUTR3eSet21.35 0.0521.40
inPAS000
limmaAnalyze0.040.000.03
prepare4GSEA0.090.020.18
singleGroupAnalyze0.030.000.03
singleSampleAnalyze000
testUsage21.84 0.0021.84
usage4plot2.000.062.06
utr3.danRer100.410.010.43
utr3.hg190.530.000.53
utr3.mm100.770.000.76
utr3Annotation000
utr3UsageEstimation000