Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-17 13:05:53 -0500 (Mon, 17 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4328
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4077
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4138
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 APAlyzer on tokay2


To the developers/maintainers of the APAlyzer package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/APAlyzer.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 73/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
APAlyzer 1.8.0  (landing page)
Ruijia Wang
Snapshot Date: 2022-01-16 01:55:05 -0500 (Sun, 16 Jan 2022)
git_url: https://git.bioconductor.org/packages/APAlyzer
git_branch: RELEASE_3_14
git_last_commit: 4df8ba6
git_last_commit_date: 2021-10-26 12:53:30 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: APAlyzer
Version: 1.8.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:APAlyzer.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings APAlyzer_1.8.0.tar.gz
StartedAt: 2022-01-16 16:48:57 -0500 (Sun, 16 Jan 2022)
EndedAt: 2022-01-16 17:17:21 -0500 (Sun, 16 Jan 2022)
EllapsedTime: 1704.0 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: APAlyzer.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:APAlyzer.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings APAlyzer_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/APAlyzer.Rcheck'
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'APAlyzer/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'APAlyzer' version '1.8.0'
* 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:
  .BBSoptions
  .travis.yml
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'APAlyzer' 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 ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 ... NOTE
.GTF2LE: no visible binding for global variable 'group_name'
.GTF2refUTRraw: no visible binding for global variable 'GENEID'
APABox: no visible binding for global variable 'APAreg'
APABox: no visible binding for global variable 'RED'
APAVolcano: no visible binding for global variable 'APAreg'
APAVolcano: no visible binding for global variable 'color'
PASEXP_IPA: no visible global function definition for 'Print'
ThreeMostPairBam: no visible global function definition for 'Print'
download_testbam: no visible global function definition for
  'download.file'
Undefined global functions or variables:
  APAreg GENEID Print RED color download.file group_name
Consider adding
  importFrom("utils", "download.file")
to your NAMESPACE file.
* checking Rd files ... NOTE
prepare_Rd: download_testbam.Rd:7-8: Dropping empty section \arguments
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'PASEXP_IPA':
PASEXP_IPA
  Code: function(dfIPAraw, dfLEraw, flS, Strandtype = "NONE", nts = 1,
                 minMQS = 0, SeqType = "SingleEnd")
  Docs: function(dfIPAraw, dfLEraw, flS, Strandtype = "NONE", nts = 1,
                 minMQS = 0)
  Argument names in code not in docs:
    SeqType

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... 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
download_testbam 50.04  10.21  114.59
PASEXP_IPA       30.17   1.17   32.60
PASEXP_3UTR      13.71   0.25  146.61
GENEXP_CDS        8.34   0.18   79.36
PAS2GEF           0.09   0.15    7.75
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
download_testbam 46.31  15.97  152.69
PASEXP_IPA       26.10   0.80   28.09
PASEXP_3UTR      15.67   0.14  152.51
GENEXP_CDS        9.31   0.08   78.69
PAS2GEF           0.07   0.41    7.49
* 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: 1 WARNING, 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/APAlyzer.Rcheck/00check.log'
for details.



Installation output

APAlyzer.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/APAlyzer_1.8.0.tar.gz && rm -rf APAlyzer.buildbin-libdir && mkdir APAlyzer.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=APAlyzer.buildbin-libdir APAlyzer_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL APAlyzer_1.8.0.zip && rm APAlyzer_1.8.0.tar.gz APAlyzer_1.8.0.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
 94 3223k   94 3046k    0     0  4233k      0 --:--:-- --:--:-- --:--:-- 4231k
100 3223k  100 3223k    0     0  1946k      0  0:00:01  0:00:01 --:--:-- 1948k

install for i386

* installing *source* package 'APAlyzer' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'APAlyzer'
    finding HTML links ... done
    APABox                                  html  
    APAVolcano                              html  
    APAdiff                                 html  
    GENEXP_CDS                              html  
    PAS2GEF                                 html  
    PASEXP_3UTR                             html  
    PASEXP_IPA                              html  
    REF3UTR                                 html  
    REF4PAS                                 html  
    REFCDS                                  html  
    ThreeMostPairBam                        html  
    download_testbam                        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 'APAlyzer' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'APAlyzer' as APAlyzer_1.8.0.zip
* DONE (APAlyzer)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'APAlyzer' successfully unpacked and MD5 sums checked

Tests output

APAlyzer.Rcheck/tests_i386/runTests.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
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("APAlyzer") || stop("unable to load Package:APAlyzer")
Loading required package: APAlyzer
[1] TRUE
> require("GenomicRanges") || stop("unable to load Package:GenomicRanges")
Loading required package: GenomicRanges
Loading required package: stats4
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

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
[1] TRUE
> require("GenomicFeatures") || stop("unable to load Package:GenomicFeatures")
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("GenomicAlignments") || stop("unable to load Package:GenomicAlignments")
Loading required package: GenomicAlignments
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'matrixStats'

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

    anyMissing, rowMedians


Attaching package: 'MatrixGenerics'

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

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

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

    rowMedians

Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit

Loading required package: Rsamtools
[1] TRUE
> require("DESeq2") || stop("unable to load Package:DESeq2")
Loading required package: DESeq2
[1] TRUE
> require("SummarizedExperiment") || stop("unable to load Package:SummarizedExperiment")
[1] TRUE
> require("Rsubread") || stop("unable to load Package:Rsubread")
Loading required package: Rsubread
[1] TRUE
> require("stats") || stop("unable to load Package:stats")
[1] TRUE
> require("testthat") || stop("unable to load testthat")
Loading required package: testthat
[1] TRUE
> test_check("APAlyzer")
[1] "SRR316184, Strand: forward, finished"
[1] "SRR316185, Strand: forward, finished"
[1] "SRR316186, Strand: forward, finished"
[1] "SRR316187, Strand: forward, finished"
[1] "SRR316188, Strand: forward, finished"
[1] "SRR316189, Strand: forward, finished"

        ==========     _____ _    _ ____  _____  ______          _____  
        =====         / ____| |  | |  _ \|  __ \|  ____|   /\   |  __ \ 
          =====      | (___ | |  | | |_) | |__) | |__     /  \  | |  | |
            ====      \___ \| |  | |  _ <|  _  /|  __|   / /\ \ | |  | |
              ====    ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
        ==========   |_____/ \____/|____/|_|  \_\______/_/    \_\_____/
       Rsubread 2.8.1

//========================== featureCounts setting ===========================\\
||                                                                            ||
||             Input files : 1 BAM file                                       ||
||                                                                            ||
||                           SRR316184.bam                                    ||
||                                                                            ||
||              Paired-end : no                                               ||
||        Count read pairs : no                                               ||
||              Annotation : R data.frame                                     ||
||      Dir for temp files : .                                                ||
||                 Threads : 1                                                ||
||                   Level : meta-feature level                               ||
||      Multimapping reads : counted                                          ||
|| Multi-overlapping reads : counted                                          ||
||   Min overlapping bases : 1                                                ||
||                                                                            ||
\\============================================================================//

//================================= Running ==================================\\
||                                                                            ||
|| Load annotation file .Rsubread_UserProvidedAnnotation_pid3284 ...          ||
||    Features : 536                                                          ||
||    Meta-features : 536                                                     ||
||    Chromosomes/contigs : 1                                                 ||
||                                                                            ||
|| Process BAM file SRR316184.bam...                                          ||
||    Strand specific : stranded                                              ||
||    Single-end reads are included.                                          ||
||    Total alignments : 422429                                               ||
||    Successfully assigned alignments : 6262 (1.5%)                          ||
||    Running time : 0.02 minutes                                             ||
||                                                                            ||
|| Write the final count table.                                               ||
|| Write the read assignment summary.                                         ||
||                                                                            ||
\\============================================================================//


        ==========     _____ _    _ ____  _____  ______          _____  
        =====         / ____| |  | |  _ \|  __ \|  ____|   /\   |  __ \ 
          =====      | (___ | |  | | |_) | |__) | |__     /  \  | |  | |
            ====      \___ \| |  | |  _ <|  _  /|  __|   / /\ \ | |  | |
              ====    ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
        ==========   |_____/ \____/|____/|_|  \_\______/_/    \_\_____/
       Rsubread 2.8.1

//========================== featureCounts setting ===========================\\
||                                                                            ||
||             Input files : 1 BAM file                                       ||
||                                                                            ||
||                           SRR316184.bam                                    ||
||                                                                            ||
||              Paired-end : no                                               ||
||        Count read pairs : no                                               ||
||              Annotation : R data.frame                                     ||
||      Dir for temp files : .                                                ||
||                 Threads : 1                                                ||
||                   Level : meta-feature level                               ||
||      Multimapping reads : counted                                          ||
|| Multi-overlapping reads : counted                                          ||
||   Min overlapping bases : 1                                                ||
||                                                                            ||
\\============================================================================//

//================================= Running ==================================\\
||                                                                            ||
|| Load annotation file .Rsubread_UserProvidedAnnotation_pid3284 ...          ||
||    Features : 536                                                          ||
||    Meta-features : 536                                                     ||
||    Chromosomes/contigs : 1                                                 ||
||                                                                            ||
|| Process BAM file SRR316184.bam...                                          ||
||    Strand specific : stranded                                              ||
||    Single-end reads are included.                                          ||
||    Total alignments : 422429                                               ||
||    Successfully assigned alignments : 6258 (1.5%)                          ||
||    Running time : 0.02 minutes                                             ||
||                                                                            ||
|| Write the final count table.                                               ||
|| Write the read assignment summary.                                         ||
||                                                                            ||
\\============================================================================//


        ==========     _____ _    _ ____  _____  ______          _____  
        =====         / ____| |  | |  _ \|  __ \|  ____|   /\   |  __ \ 
          =====      | (___ | |  | | |_) | |__) | |__     /  \  | |  | |
            ====      \___ \| |  | |  _ <|  _  /|  __|   / /\ \ | |  | |
              ====    ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
        ==========   |_____/ \____/|____/|_|  \_\______/_/    \_\_____/
       Rsubread 2.8.1

//========================== featureCounts setting ===========================\\
||                                                                            ||
||             Input files : 1 BAM file                                       ||
||                                                                            ||
||                           SRR316184.bam                                    ||
||                                                                            ||
||              Paired-end : no                                               ||
||        Count read pairs : no                                               ||
||              Annotation : R data.frame                                     ||
||      Dir for temp files : .                                                ||
||                 Threads : 1                                                ||
||                   Level : meta-feature level                               ||
||      Multimapping reads : counted                                          ||
|| Multi-overlapping reads : counted                                          ||
||   Min overlapping bases : 1                                                ||
||                                                                            ||
\\============================================================================//

//================================= Running ==================================\\
||                                                                            ||
|| Load annotation file .Rsubread_UserProvidedAnnotation_pid3284 ...          ||
||    Features : 222                                                          ||
||    Meta-features : 222                                                     ||
||    Chromosomes/contigs : 1                                                 ||
||                                                                            ||
|| Process BAM file SRR316184.bam...                                          ||
||    Strand specific : stranded                                              ||
||    Single-end reads are included.                                          ||
||    Total alignments : 422429                                               ||
||    Successfully assigned alignments : 22878 (5.4%)                         ||
||    Running time : 0.02 minutes                                             ||
||                                                                            ||
|| Write the final count table.                                               ||
|| Write the read assignment summary.                                         ||
||                                                                            ||
\\============================================================================//

[1] "SRR316184, Strand: forward, finished"

        ==========     _____ _    _ ____  _____  ______          _____  
        =====         / ____| |  | |  _ \|  __ \|  ____|   /\   |  __ \ 
          =====      | (___ | |  | | |_) | |__) | |__     /  \  | |  | |
            ====      \___ \| |  | |  _ <|  _  /|  __|   / /\ \ | |  | |
              ====    ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
        ==========   |_____/ \____/|____/|_|  \_\______/_/    \_\_____/
       Rsubread 2.8.1

//========================== featureCounts setting ===========================\\
||                                                                            ||
||             Input files : 1 BAM file                                       ||
||                                                                            ||
||                           SRR316185.bam                                    ||
||                                                                            ||
||              Paired-end : no                                               ||
||        Count read pairs : no                                               ||
||              Annotation : R data.frame                                     ||
||      Dir for temp files : .                                                ||
||                 Threads : 1                                                ||
||                   Level : meta-feature level                               ||
||      Multimapping reads : counted                                          ||
|| Multi-overlapping reads : counted                                          ||
||   Min overlapping bases : 1                                                ||
||                                                                            ||
\\============================================================================//

//================================= Running ==================================\\
||                                                                            ||
|| Load annotation file .Rsubread_UserProvidedAnnotation_pid3284 ...          ||
||    Features : 536                                                          ||
||    Meta-features : 536                                                     ||
||    Chromosomes/contigs : 1                                                 ||
||                                                                            ||
|| Process BAM file SRR316185.bam...                                          ||
||    Strand specific : stranded                                              ||
||    Single-end reads are included.                                          ||
||    Total alignments : 437626                                               ||
||    Successfully assigned alignments : 5390 (1.2%)                          ||
||    Running time : 0.01 minutes                                             ||
||                                                                            ||
|| Write the final count table.                                               ||
|| Write the read assignment summary.                                         ||
||                                                                            ||
\\============================================================================//


        ==========     _____ _    _ ____  _____  ______          _____  
        =====         / ____| |  | |  _ \|  __ \|  ____|   /\   |  __ \ 
          =====      | (___ | |  | | |_) | |__) | |__     /  \  | |  | |
            ====      \___ \| |  | |  _ <|  _  /|  __|   / /\ \ | |  | |
              ====    ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
        ==========   |_____/ \____/|____/|_|  \_\______/_/    \_\_____/
       Rsubread 2.8.1

//========================== featureCounts setting ===========================\\
||                                                                            ||
||             Input files : 1 BAM file                                       ||
||                                                                            ||
||                           SRR316185.bam                                    ||
||                                                                            ||
||              Paired-end : no                                               ||
||        Count read pairs : no                                               ||
||              Annotation : R data.frame                                     ||
||      Dir for temp files : .                                                ||
||                 Threads : 1                                                ||
||                   Level : meta-feature level                               ||
||      Multimapping reads : counted                                          ||
|| Multi-overlapping reads : counted                                          ||
||   Min overlapping bases : 1                                                ||
||                                                                            ||
\\============================================================================//

//================================= Running ==================================\\
||                                                                            ||
|| Load annotation file .Rsubread_UserProvidedAnnotation_pid3284 ...          ||
||    Features : 536                                                          ||
||    Meta-features : 536                                                     ||
||    Chromosomes/contigs : 1                                                 ||
||                                                                            ||
|| Process BAM file SRR316185.bam...                                          ||
||    Strand specific : stranded                                              ||
||    Single-end reads are included.                                          ||
||    Total alignments : 437626                                               ||
||    Successfully assigned alignments : 5387 (1.2%)                          ||
||    Running time : 0.02 minutes                                             ||
||                                                                            ||
|| Write the final count table.                                               ||
|| Write the read assignment summary.                                         ||
||                                                                            ||
\\============================================================================//


        ==========     _____ _    _ ____  _____  ______          _____  
        =====         / ____| |  | |  _ \|  __ \|  ____|   /\   |  __ \ 
          =====      | (___ | |  | | |_) | |__) | |__     /  \  | |  | |
            ====      \___ \| |  | |  _ <|  _  /|  __|   / /\ \ | |  | |
              ====    ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
        ==========   |_____/ \____/|____/|_|  \_\______/_/    \_\_____/
       Rsubread 2.8.1

//========================== featureCounts setting ===========================\\
||                                                                            ||
||             Input files : 1 BAM file                                       ||
||                                                                            ||
||                           SRR316185.bam                                    ||
||                                                                            ||
||              Paired-end : no                                               ||
||        Count read pairs : no                                               ||
||              Annotation : R data.frame                                     ||
||      Dir for temp files : .                                                ||
||                 Threads : 1                                                ||
||                   Level : meta-feature level                               ||
||      Multimapping reads : counted                                          ||
|| Multi-overlapping reads : counted                                          ||
||   Min overlapping bases : 1                                                ||
||                                                                            ||
\\============================================================================//

//================================= Running ==================================\\
||                                                                            ||
|| Load annotation file .Rsubread_UserProvidedAnnotation_pid3284 ...          ||
||    Features : 222                                                          ||
||    Meta-features : 222                                                     ||
||    Chromosomes/contigs : 1                                                 ||
||                                                                            ||
|| Process BAM file SRR316185.bam...                                          ||
||    Strand specific : stranded                                              ||
||    Single-end reads are included.                                          ||
||    Total alignments : 437626                                               ||
||    Successfully assigned alignments : 23378 (5.3%)                         ||
||    Running time : 0.03 minutes                                             ||
||                                                                            ||
|| Write the final count table.                                               ||
|| Write the read assignment summary.                                         ||
||                                                                            ||
\\============================================================================//

[1] "SRR316185, Strand: forward, finished"
[1] "Reading and extracting (Strand = forward-reverse):  untreated3_chr4.bam"
[1] "Exporting: untreated3_chr4.3most.bam"
[ FAIL 0 | WARN 6 | SKIP 0 | PASS 8 ]
> 
> proc.time()
   user  system elapsed 
  34.93    2.07  258.96 

APAlyzer.Rcheck/tests_x64/runTests.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
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("APAlyzer") || stop("unable to load Package:APAlyzer")
Loading required package: APAlyzer
[1] TRUE
> require("GenomicRanges") || stop("unable to load Package:GenomicRanges")
Loading required package: GenomicRanges
Loading required package: stats4
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

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
[1] TRUE
> require("GenomicFeatures") || stop("unable to load Package:GenomicFeatures")
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("GenomicAlignments") || stop("unable to load Package:GenomicAlignments")
Loading required package: GenomicAlignments
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'matrixStats'

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

    anyMissing, rowMedians


Attaching package: 'MatrixGenerics'

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

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

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

    rowMedians

Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit

Loading required package: Rsamtools
[1] TRUE
> require("DESeq2") || stop("unable to load Package:DESeq2")
Loading required package: DESeq2
[1] TRUE
> require("SummarizedExperiment") || stop("unable to load Package:SummarizedExperiment")
[1] TRUE
> require("Rsubread") || stop("unable to load Package:Rsubread")
Loading required package: Rsubread
[1] TRUE
> require("stats") || stop("unable to load Package:stats")
[1] TRUE
> require("testthat") || stop("unable to load testthat")
Loading required package: testthat
[1] TRUE
> test_check("APAlyzer")
[1] "SRR316184, Strand: forward, finished"
[1] "SRR316185, Strand: forward, finished"
[1] "SRR316186, Strand: forward, finished"
[1] "SRR316187, Strand: forward, finished"
[1] "SRR316188, Strand: forward, finished"
[1] "SRR316189, Strand: forward, finished"

        ==========     _____ _    _ ____  _____  ______          _____  
        =====         / ____| |  | |  _ \|  __ \|  ____|   /\   |  __ \ 
          =====      | (___ | |  | | |_) | |__) | |__     /  \  | |  | |
            ====      \___ \| |  | |  _ <|  _  /|  __|   / /\ \ | |  | |
              ====    ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
        ==========   |_____/ \____/|____/|_|  \_\______/_/    \_\_____/
       Rsubread 2.8.1

//========================== featureCounts setting ===========================\\
||                                                                            ||
||             Input files : 1 BAM file                                       ||
||                                                                            ||
||                           SRR316184.bam                                    ||
||                                                                            ||
||              Paired-end : no                                               ||
||        Count read pairs : no                                               ||
||              Annotation : R data.frame                                     ||
||      Dir for temp files : .                                                ||
||                 Threads : 1                                                ||
||                   Level : meta-feature level                               ||
||      Multimapping reads : counted                                          ||
|| Multi-overlapping reads : counted                                          ||
||   Min overlapping bases : 1                                                ||
||                                                                            ||
\\============================================================================//

//================================= Running ==================================\\
||                                                                            ||
|| Load annotation file .Rsubread_UserProvidedAnnotation_pid4880 ...          ||
||    Features : 536                                                          ||
||    Meta-features : 536                                                     ||
||    Chromosomes/contigs : 1                                                 ||
||                                                                            ||
|| Process BAM file SRR316184.bam...                                          ||
||    Strand specific : stranded                                              ||
||    Single-end reads are included.                                          ||
||    Total alignments : 422429                                               ||
||    Successfully assigned alignments : 6262 (1.5%)                          ||
||    Running time : 0.01 minutes                                             ||
||                                                                            ||
|| Write the final count table.                                               ||
|| Write the read assignment summary.                                         ||
||                                                                            ||
\\============================================================================//


        ==========     _____ _    _ ____  _____  ______          _____  
        =====         / ____| |  | |  _ \|  __ \|  ____|   /\   |  __ \ 
          =====      | (___ | |  | | |_) | |__) | |__     /  \  | |  | |
            ====      \___ \| |  | |  _ <|  _  /|  __|   / /\ \ | |  | |
              ====    ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
        ==========   |_____/ \____/|____/|_|  \_\______/_/    \_\_____/
       Rsubread 2.8.1

//========================== featureCounts setting ===========================\\
||                                                                            ||
||             Input files : 1 BAM file                                       ||
||                                                                            ||
||                           SRR316184.bam                                    ||
||                                                                            ||
||              Paired-end : no                                               ||
||        Count read pairs : no                                               ||
||              Annotation : R data.frame                                     ||
||      Dir for temp files : .                                                ||
||                 Threads : 1                                                ||
||                   Level : meta-feature level                               ||
||      Multimapping reads : counted                                          ||
|| Multi-overlapping reads : counted                                          ||
||   Min overlapping bases : 1                                                ||
||                                                                            ||
\\============================================================================//

//================================= Running ==================================\\
||                                                                            ||
|| Load annotation file .Rsubread_UserProvidedAnnotation_pid4880 ...          ||
||    Features : 536                                                          ||
||    Meta-features : 536                                                     ||
||    Chromosomes/contigs : 1                                                 ||
||                                                                            ||
|| Process BAM file SRR316184.bam...                                          ||
||    Strand specific : stranded                                              ||
||    Single-end reads are included.                                          ||
||    Total alignments : 422429                                               ||
||    Successfully assigned alignments : 6258 (1.5%)                          ||
||    Running time : 0.01 minutes                                             ||
||                                                                            ||
|| Write the final count table.                                               ||
|| Write the read assignment summary.                                         ||
||                                                                            ||
\\============================================================================//


        ==========     _____ _    _ ____  _____  ______          _____  
        =====         / ____| |  | |  _ \|  __ \|  ____|   /\   |  __ \ 
          =====      | (___ | |  | | |_) | |__) | |__     /  \  | |  | |
            ====      \___ \| |  | |  _ <|  _  /|  __|   / /\ \ | |  | |
              ====    ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
        ==========   |_____/ \____/|____/|_|  \_\______/_/    \_\_____/
       Rsubread 2.8.1

//========================== featureCounts setting ===========================\\
||                                                                            ||
||             Input files : 1 BAM file                                       ||
||                                                                            ||
||                           SRR316184.bam                                    ||
||                                                                            ||
||              Paired-end : no                                               ||
||        Count read pairs : no                                               ||
||              Annotation : R data.frame                                     ||
||      Dir for temp files : .                                                ||
||                 Threads : 1                                                ||
||                   Level : meta-feature level                               ||
||      Multimapping reads : counted                                          ||
|| Multi-overlapping reads : counted                                          ||
||   Min overlapping bases : 1                                                ||
||                                                                            ||
\\============================================================================//

//================================= Running ==================================\\
||                                                                            ||
|| Load annotation file .Rsubread_UserProvidedAnnotation_pid4880 ...          ||
||    Features : 222                                                          ||
||    Meta-features : 222                                                     ||
||    Chromosomes/contigs : 1                                                 ||
||                                                                            ||
|| Process BAM file SRR316184.bam...                                          ||
||    Strand specific : stranded                                              ||
||    Single-end reads are included.                                          ||
||    Total alignments : 422429                                               ||
||    Successfully assigned alignments : 22878 (5.4%)                         ||
||    Running time : 0.01 minutes                                             ||
||                                                                            ||
|| Write the final count table.                                               ||
|| Write the read assignment summary.                                         ||
||                                                                            ||
\\============================================================================//

[1] "SRR316184, Strand: forward, finished"

        ==========     _____ _    _ ____  _____  ______          _____  
        =====         / ____| |  | |  _ \|  __ \|  ____|   /\   |  __ \ 
          =====      | (___ | |  | | |_) | |__) | |__     /  \  | |  | |
            ====      \___ \| |  | |  _ <|  _  /|  __|   / /\ \ | |  | |
              ====    ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
        ==========   |_____/ \____/|____/|_|  \_\______/_/    \_\_____/
       Rsubread 2.8.1

//========================== featureCounts setting ===========================\\
||                                                                            ||
||             Input files : 1 BAM file                                       ||
||                                                                            ||
||                           SRR316185.bam                                    ||
||                                                                            ||
||              Paired-end : no                                               ||
||        Count read pairs : no                                               ||
||              Annotation : R data.frame                                     ||
||      Dir for temp files : .                                                ||
||                 Threads : 1                                                ||
||                   Level : meta-feature level                               ||
||      Multimapping reads : counted                                          ||
|| Multi-overlapping reads : counted                                          ||
||   Min overlapping bases : 1                                                ||
||                                                                            ||
\\============================================================================//

//================================= Running ==================================\\
||                                                                            ||
|| Load annotation file .Rsubread_UserProvidedAnnotation_pid4880 ...          ||
||    Features : 536                                                          ||
||    Meta-features : 536                                                     ||
||    Chromosomes/contigs : 1                                                 ||
||                                                                            ||
|| Process BAM file SRR316185.bam...                                          ||
||    Strand specific : stranded                                              ||
||    Single-end reads are included.                                          ||
||    Total alignments : 437626                                               ||
||    Successfully assigned alignments : 5390 (1.2%)                          ||
||    Running time : 0.01 minutes                                             ||
||                                                                            ||
|| Write the final count table.                                               ||
|| Write the read assignment summary.                                         ||
||                                                                            ||
\\============================================================================//


        ==========     _____ _    _ ____  _____  ______          _____  
        =====         / ____| |  | |  _ \|  __ \|  ____|   /\   |  __ \ 
          =====      | (___ | |  | | |_) | |__) | |__     /  \  | |  | |
            ====      \___ \| |  | |  _ <|  _  /|  __|   / /\ \ | |  | |
              ====    ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
        ==========   |_____/ \____/|____/|_|  \_\______/_/    \_\_____/
       Rsubread 2.8.1

//========================== featureCounts setting ===========================\\
||                                                                            ||
||             Input files : 1 BAM file                                       ||
||                                                                            ||
||                           SRR316185.bam                                    ||
||                                                                            ||
||              Paired-end : no                                               ||
||        Count read pairs : no                                               ||
||              Annotation : R data.frame                                     ||
||      Dir for temp files : .                                                ||
||                 Threads : 1                                                ||
||                   Level : meta-feature level                               ||
||      Multimapping reads : counted                                          ||
|| Multi-overlapping reads : counted                                          ||
||   Min overlapping bases : 1                                                ||
||                                                                            ||
\\============================================================================//

//================================= Running ==================================\\
||                                                                            ||
|| Load annotation file .Rsubread_UserProvidedAnnotation_pid4880 ...          ||
||    Features : 536                                                          ||
||    Meta-features : 536                                                     ||
||    Chromosomes/contigs : 1                                                 ||
||                                                                            ||
|| Process BAM file SRR316185.bam...                                          ||
||    Strand specific : stranded                                              ||
||    Single-end reads are included.                                          ||
||    Total alignments : 437626                                               ||
||    Successfully assigned alignments : 5387 (1.2%)                          ||
||    Running time : 0.01 minutes                                             ||
||                                                                            ||
|| Write the final count table.                                               ||
|| Write the read assignment summary.                                         ||
||                                                                            ||
\\============================================================================//


        ==========     _____ _    _ ____  _____  ______          _____  
        =====         / ____| |  | |  _ \|  __ \|  ____|   /\   |  __ \ 
          =====      | (___ | |  | | |_) | |__) | |__     /  \  | |  | |
            ====      \___ \| |  | |  _ <|  _  /|  __|   / /\ \ | |  | |
              ====    ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
        ==========   |_____/ \____/|____/|_|  \_\______/_/    \_\_____/
       Rsubread 2.8.1

//========================== featureCounts setting ===========================\\
||                                                                            ||
||             Input files : 1 BAM file                                       ||
||                                                                            ||
||                           SRR316185.bam                                    ||
||                                                                            ||
||              Paired-end : no                                               ||
||        Count read pairs : no                                               ||
||              Annotation : R data.frame                                     ||
||      Dir for temp files : .                                                ||
||                 Threads : 1                                                ||
||                   Level : meta-feature level                               ||
||      Multimapping reads : counted                                          ||
|| Multi-overlapping reads : counted                                          ||
||   Min overlapping bases : 1                                                ||
||                                                                            ||
\\============================================================================//

//================================= Running ==================================\\
||                                                                            ||
|| Load annotation file .Rsubread_UserProvidedAnnotation_pid4880 ...          ||
||    Features : 222                                                          ||
||    Meta-features : 222                                                     ||
||    Chromosomes/contigs : 1                                                 ||
||                                                                            ||
|| Process BAM file SRR316185.bam...                                          ||
||    Strand specific : stranded                                              ||
||    Single-end reads are included.                                          ||
||    Total alignments : 437626                                               ||
||    Successfully assigned alignments : 23378 (5.3%)                         ||
||    Running time : 0.01 minutes                                             ||
||                                                                            ||
|| Write the final count table.                                               ||
|| Write the read assignment summary.                                         ||
||                                                                            ||
\\============================================================================//

[1] "SRR316185, Strand: forward, finished"
[1] "Reading and extracting (Strand = forward-reverse):  untreated3_chr4.bam"
[1] "Exporting: untreated3_chr4.3most.bam"
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 8 ]
> 
> proc.time()
   user  system elapsed 
  37.70    1.32  261.11 

Example timings

APAlyzer.Rcheck/examples_i386/APAlyzer-Ex.timings

nameusersystemelapsed
APABox0.670.121.00
APAVolcano0.490.020.50
APAdiff0.880.070.95
GENEXP_CDS 8.34 0.1879.36
PAS2GEF0.090.157.75
PASEXP_3UTR 13.71 0.25146.61
PASEXP_IPA30.17 1.1732.60
REF3UTR0.250.020.45
REF4PAS0.250.030.44
REFCDS0.680.000.69
ThreeMostPairBam1.650.031.67
download_testbam 50.04 10.21114.59

APAlyzer.Rcheck/examples_x64/APAlyzer-Ex.timings

nameusersystemelapsed
APABox0.360.050.41
APAVolcano0.390.040.44
APAdiff0.770.000.77
GENEXP_CDS 9.31 0.0878.69
PAS2GEF0.070.417.49
PASEXP_3UTR 15.67 0.14152.51
PASEXP_IPA26.10 0.8028.09
REF3UTR0.270.000.83
REF4PAS0.250.000.37
REFCDS0.640.040.69
ThreeMostPairBam1.500.031.53
download_testbam 46.31 15.97152.69