Ruijia Wang
| Snapshot Date: 2024-11-21 13:40 -0500 (Thu, 21 Nov 2024) |
| git_url: https://git.bioconductor.org/packages/APAlyzer |
| git_branch: devel |
| git_last_commit: 7a59a45 |
| git_last_commit_date: 2024-10-29 10:39:10 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-11-22 11:34 -0500 (Fri, 22 Nov 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4742 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4456 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 88/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| APAlyzer 1.21.0 (landing page) Ruijia Wang
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
|
To the developers/maintainers of the APAlyzer package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: APAlyzer |
| Version: 1.21.0 |
| Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:APAlyzer.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings APAlyzer_1.21.0.tar.gz |
| StartedAt: 2024-11-21 22:45:54 -0500 (Thu, 21 Nov 2024) |
| EndedAt: 2024-11-21 23:01:21 -0500 (Thu, 21 Nov 2024) |
| EllapsedTime: 927.2 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: APAlyzer.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:APAlyzer.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings APAlyzer_1.21.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/APAlyzer.Rcheck'
* using R Under development (unstable) (2024-10-26 r87273 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.2.0
GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'APAlyzer/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'APAlyzer' version '1.21.0'
* 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 code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... WARNING
'library' or 'require' call not declared from: 'HybridMTest'
'library' or 'require' call to 'HybridMTest' in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
* 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'
.annotatePASRegion: no visible global function definition for
'queryHits'
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 queryHits
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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
PASEXP_IPA 20.31 0.98 22.98
PASEXP_3UTR 15.24 0.28 160.86
download_testbam 6.11 9.08 55.98
GENEXP_CDS 11.16 0.31 85.65
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'runTests.R'
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 4 NOTEs
See
'E:/biocbuild/bbs-3.21-bioc/meat/APAlyzer.Rcheck/00check.log'
for details.
APAlyzer.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL APAlyzer ### ############################################################################## ############################################################################## * installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library' * installing *source* package 'APAlyzer' ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (APAlyzer)
APAlyzer.Rcheck/tests/runTests.Rout
R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
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: generics
Attaching package: 'generics'
The following objects are masked from 'package:base':
as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
setequal, union
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
unsplit, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
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 2.21.1
//========================== 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_pid8152 ... ||
|| 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 2.21.1
//========================== 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_pid8152 ... ||
|| 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 2.21.1
//========================== 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_pid8152 ... ||
|| 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 2.21.1
//========================== 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_pid8152 ... ||
|| 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 2.21.1
//========================== 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_pid8152 ... ||
|| 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 2.21.1
//========================== 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_pid8152 ... ||
|| 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 1 | SKIP 0 | PASS 8 ]
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 8 ]
>
> proc.time()
user system elapsed
38.76 1.59 275.42
APAlyzer.Rcheck/APAlyzer-Ex.timings
| name | user | system | elapsed | |
| APABox | 0.62 | 0.05 | 0.72 | |
| APAVolcano | 0.40 | 0.11 | 0.52 | |
| APAdiff | 2.06 | 0.03 | 2.10 | |
| GENEXP_CDS | 11.16 | 0.31 | 85.65 | |
| PAS2GEF | 0.01 | 0.08 | 2.96 | |
| PASEXP_3UTR | 15.24 | 0.28 | 160.86 | |
| PASEXP_IPA | 20.31 | 0.98 | 22.98 | |
| REF3UTR | 1.28 | 0.02 | 1.40 | |
| REF4PAS | 0.12 | 0.02 | 0.21 | |
| REFCDS | 0.64 | 0.09 | 0.73 | |
| ThreeMostPairBam | 1.64 | 0.06 | 1.80 | |
| download_testbam | 6.11 | 9.08 | 55.98 | |