Ruijia Wang
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/APAlyzer |
| Branch: RELEASE_3_11 |
| Last Commit: 8c1a739 |
| Last Changed Date: 2020-04-27 15:29:12 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:56:05 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE APAlyzer PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 73/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| APAlyzer 1.2.0 Ruijia Wang
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |
| Package: APAlyzer |
| Version: 1.2.0 |
| Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:APAlyzer.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings APAlyzer_1.2.0.tar.gz |
| StartedAt: 2020-10-17 01:34:22 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 01:49:45 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 923.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: APAlyzer.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:APAlyzer.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings APAlyzer_1.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/APAlyzer.Rcheck'
* using R version 4.0.3 (2020-10-10)
* 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 '1.2.0'
* 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
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'
download_testbam: no visible global function definition for
'download.file'
Undefined global functions or variables:
APAreg GENEID 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 ... OK
* 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 47.23 10.64 107.01
PASEXP_IPA 31.13 1.28 33.64
PASEXP_3UTR 21.11 1.05 22.89
GENEXP_CDS 14.62 0.73 15.96
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
download_testbam 39.71 12.67 87.99
PASEXP_IPA 27.17 0.84 28.78
PASEXP_3UTR 19.42 1.17 21.06
GENEXP_CDS 12.69 0.56 13.25
PAS2GEF 0.18 0.24 5.16
* 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: 4 NOTEs
See
'C:/Users/biocbuild/bbs-3.11-bioc/meat/APAlyzer.Rcheck/00check.log'
for details.
APAlyzer.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/APAlyzer_1.2.0.tar.gz && rm -rf APAlyzer.buildbin-libdir && mkdir APAlyzer.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=APAlyzer.buildbin-libdir APAlyzer_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL APAlyzer_1.2.0.zip && rm APAlyzer_1.2.0.tar.gz APAlyzer_1.2.0.zip
###
##############################################################################
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
0 3221k 0 16384 0 0 48633 0 0:01:07 --:--:-- 0:01:07 49349
100 3221k 100 3221k 0 0 8570k 0 --:--:-- --:--:-- --:--:-- 8683k
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
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_1.2.0.zip
* DONE (APAlyzer)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'APAlyzer' successfully unpacked and MD5 sums checked
|
APAlyzer.Rcheck/tests_i386/runTests.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
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("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
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, which.max, which.min
Loading required package: S4Vectors
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
[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: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from 'package:base':
aperm, apply, rowsum
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("DESeq") || stop("unable to load Package:DESeq")
Loading required package: DESeq
Loading required package: locfit
locfit 1.5-9.4 2020-03-24
Loading required package: lattice
[1] TRUE
Warning message:
Package 'DESeq' is deprecated and will be removed from Bioconductor
version 3.13. Please use DESeq2
> 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 2.2.6
//========================== featureCounts setting ===========================\\
|| ||
|| Input files : 1 BAM file ||
|| o SRR316184.bam ||
|| ||
|| Annotation : R data.frame ||
|| Dir for temp files : . ||
|| Threads : 1 ||
|| Level : meta-feature level ||
|| Paired-end : no ||
|| Multimapping reads : counted ||
|| Multi-overlapping reads : counted ||
|| Min overlapping bases : 1 ||
|| ||
\\============================================================================//
//================================= Running ==================================\\
|| ||
|| Load annotation file .Rsubread_UserProvidedAnnotation_pid5560 ... ||
|| 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 2.2.6
//========================== featureCounts setting ===========================\\
|| ||
|| Input files : 1 BAM file ||
|| o SRR316184.bam ||
|| ||
|| Annotation : R data.frame ||
|| Dir for temp files : . ||
|| Threads : 1 ||
|| Level : meta-feature level ||
|| Paired-end : no ||
|| Multimapping reads : counted ||
|| Multi-overlapping reads : counted ||
|| Min overlapping bases : 1 ||
|| ||
\\============================================================================//
//================================= Running ==================================\\
|| ||
|| Load annotation file .Rsubread_UserProvidedAnnotation_pid5560 ... ||
|| 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 2.2.6
//========================== featureCounts setting ===========================\\
|| ||
|| Input files : 1 BAM file ||
|| o SRR316184.bam ||
|| ||
|| Annotation : R data.frame ||
|| Dir for temp files : . ||
|| Threads : 1 ||
|| Level : meta-feature level ||
|| Paired-end : no ||
|| Multimapping reads : counted ||
|| Multi-overlapping reads : counted ||
|| Min overlapping bases : 1 ||
|| ||
\\============================================================================//
//================================= Running ==================================\\
|| ||
|| Load annotation file .Rsubread_UserProvidedAnnotation_pid5560 ... ||
|| 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 2.2.6
//========================== featureCounts setting ===========================\\
|| ||
|| Input files : 1 BAM file ||
|| o SRR316185.bam ||
|| ||
|| Annotation : R data.frame ||
|| Dir for temp files : . ||
|| Threads : 1 ||
|| Level : meta-feature level ||
|| Paired-end : no ||
|| Multimapping reads : counted ||
|| Multi-overlapping reads : counted ||
|| Min overlapping bases : 1 ||
|| ||
\\============================================================================//
//================================= Running ==================================\\
|| ||
|| Load annotation file .Rsubread_UserProvidedAnnotation_pid5560 ... ||
|| 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 2.2.6
//========================== featureCounts setting ===========================\\
|| ||
|| Input files : 1 BAM file ||
|| o SRR316185.bam ||
|| ||
|| Annotation : R data.frame ||
|| Dir for temp files : . ||
|| Threads : 1 ||
|| Level : meta-feature level ||
|| Paired-end : no ||
|| Multimapping reads : counted ||
|| Multi-overlapping reads : counted ||
|| Min overlapping bases : 1 ||
|| ||
\\============================================================================//
//================================= Running ==================================\\
|| ||
|| Load annotation file .Rsubread_UserProvidedAnnotation_pid5560 ... ||
|| 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 2.2.6
//========================== featureCounts setting ===========================\\
|| ||
|| Input files : 1 BAM file ||
|| o SRR316185.bam ||
|| ||
|| Annotation : R data.frame ||
|| Dir for temp files : . ||
|| Threads : 1 ||
|| Level : meta-feature level ||
|| Paired-end : no ||
|| Multimapping reads : counted ||
|| Multi-overlapping reads : counted ||
|| Min overlapping bases : 1 ||
|| ||
\\============================================================================//
//================================= Running ==================================\\
|| ||
|| Load annotation file .Rsubread_UserProvidedAnnotation_pid5560 ... ||
|| 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"
== testthat results ===========================================================
[ OK: 7 | SKIPPED: 0 | WARNINGS: 6 | FAILED: 0 ]
>
> proc.time()
user system elapsed
44.57 3.18 52.45
|
APAlyzer.Rcheck/tests_x64/runTests.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
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("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
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, which.max, which.min
Loading required package: S4Vectors
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
[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: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from 'package:base':
aperm, apply, rowsum
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("DESeq") || stop("unable to load Package:DESeq")
Loading required package: DESeq
Loading required package: locfit
locfit 1.5-9.4 2020-03-24
Loading required package: lattice
[1] TRUE
Warning message:
Package 'DESeq' is deprecated and will be removed from Bioconductor
version 3.13. Please use DESeq2
> 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 2.2.6
//========================== featureCounts setting ===========================\\
|| ||
|| Input files : 1 BAM file ||
|| o SRR316184.bam ||
|| ||
|| Annotation : R data.frame ||
|| Dir for temp files : . ||
|| Threads : 1 ||
|| Level : meta-feature level ||
|| Paired-end : no ||
|| Multimapping reads : counted ||
|| Multi-overlapping reads : counted ||
|| Min overlapping bases : 1 ||
|| ||
\\============================================================================//
//================================= Running ==================================\\
|| ||
|| Load annotation file .Rsubread_UserProvidedAnnotation_pid4908 ... ||
|| 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 2.2.6
//========================== featureCounts setting ===========================\\
|| ||
|| Input files : 1 BAM file ||
|| o SRR316184.bam ||
|| ||
|| Annotation : R data.frame ||
|| Dir for temp files : . ||
|| Threads : 1 ||
|| Level : meta-feature level ||
|| Paired-end : no ||
|| Multimapping reads : counted ||
|| Multi-overlapping reads : counted ||
|| Min overlapping bases : 1 ||
|| ||
\\============================================================================//
//================================= Running ==================================\\
|| ||
|| Load annotation file .Rsubread_UserProvidedAnnotation_pid4908 ... ||
|| 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 2.2.6
//========================== featureCounts setting ===========================\\
|| ||
|| Input files : 1 BAM file ||
|| o SRR316184.bam ||
|| ||
|| Annotation : R data.frame ||
|| Dir for temp files : . ||
|| Threads : 1 ||
|| Level : meta-feature level ||
|| Paired-end : no ||
|| Multimapping reads : counted ||
|| Multi-overlapping reads : counted ||
|| Min overlapping bases : 1 ||
|| ||
\\============================================================================//
//================================= Running ==================================\\
|| ||
|| Load annotation file .Rsubread_UserProvidedAnnotation_pid4908 ... ||
|| 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 2.2.6
//========================== featureCounts setting ===========================\\
|| ||
|| Input files : 1 BAM file ||
|| o SRR316185.bam ||
|| ||
|| Annotation : R data.frame ||
|| Dir for temp files : . ||
|| Threads : 1 ||
|| Level : meta-feature level ||
|| Paired-end : no ||
|| Multimapping reads : counted ||
|| Multi-overlapping reads : counted ||
|| Min overlapping bases : 1 ||
|| ||
\\============================================================================//
//================================= Running ==================================\\
|| ||
|| Load annotation file .Rsubread_UserProvidedAnnotation_pid4908 ... ||
|| 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 2.2.6
//========================== featureCounts setting ===========================\\
|| ||
|| Input files : 1 BAM file ||
|| o SRR316185.bam ||
|| ||
|| Annotation : R data.frame ||
|| Dir for temp files : . ||
|| Threads : 1 ||
|| Level : meta-feature level ||
|| Paired-end : no ||
|| Multimapping reads : counted ||
|| Multi-overlapping reads : counted ||
|| Min overlapping bases : 1 ||
|| ||
\\============================================================================//
//================================= Running ==================================\\
|| ||
|| Load annotation file .Rsubread_UserProvidedAnnotation_pid4908 ... ||
|| 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 2.2.6
//========================== featureCounts setting ===========================\\
|| ||
|| Input files : 1 BAM file ||
|| o SRR316185.bam ||
|| ||
|| Annotation : R data.frame ||
|| Dir for temp files : . ||
|| Threads : 1 ||
|| Level : meta-feature level ||
|| Paired-end : no ||
|| Multimapping reads : counted ||
|| Multi-overlapping reads : counted ||
|| Min overlapping bases : 1 ||
|| ||
\\============================================================================//
//================================= Running ==================================\\
|| ||
|| Load annotation file .Rsubread_UserProvidedAnnotation_pid4908 ... ||
|| 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 : 0.02 minutes ||
|| ||
|| Write the final count table. ||
|| Write the read assignment summary. ||
|| ||
\\============================================================================//
[1] "SRR316185, Strand: forward, finished"
== testthat results ===========================================================
[ OK: 7 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
37.42 2.06 45.54
|
|
APAlyzer.Rcheck/examples_i386/APAlyzer-Ex.timings
|
APAlyzer.Rcheck/examples_x64/APAlyzer-Ex.timings
|