Felix G.M. Ernst
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/RNAmodR |
| Branch: RELEASE_3_10 |
| Last Commit: 73dfc12 |
| Last Changed Date: 2020-01-12 15:48:43 -0400 (Sun, 12 Jan 2020) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:49:33 -0400 (Wed, 15 Apr 2020).
| Package 1452/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| RNAmodR 1.0.2 Felix G.M. Ernst
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: RNAmodR |
| Version: 1.0.2 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:RNAmodR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings RNAmodR_1.0.2.tar.gz |
| StartedAt: 2020-04-15 05:14:49 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 05:24:46 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 597.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: RNAmodR.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:RNAmodR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings RNAmodR_1.0.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/RNAmodR.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RNAmodR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RNAmodR’ version ‘1.0.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘RNAmodR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* 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 ... NOTE
Unexported objects imported by ':::' calls:
'BiocGenerics:::replaceSlots' 'IRanges:::.valid.CompressedList'
'IRanges:::coerceToCompressedList' 'S4Vectors:::.valid.DataFrame'
'S4Vectors:::labeledLine' 'S4Vectors:::make_zero_col_DataFrame'
'S4Vectors:::prepare_objects_to_bind'
See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
'.get_inosine_score'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
CoverageSequenceData-class 19.730 0.800 21.911
ModInosine 15.242 0.307 16.459
ProtectedEndSequenceData-class 12.047 0.217 13.062
PileupSequenceData-class 11.420 0.204 12.480
EndSequenceData-class 10.695 0.226 12.090
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.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 NOTE
See
‘/Users/biocbuild/bbs-3.10-bioc/meat/RNAmodR.Rcheck/00check.log’
for details.
RNAmodR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL RNAmodR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘RNAmodR’ ... ** using staged installation ** R ** data ** 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 (RNAmodR)
RNAmodR.Rcheck/tests/testthat.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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.
> library(testthat)
> library(RNAmodR)
Loading required package: IRanges
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
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: Modstrings
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Attaching package: 'RNAmodR'
The following object is masked from 'package:testthat':
compare
>
> test_check("RNAmodR")
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 182 | SKIPPED: 9 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
63.286 1.956 66.795
RNAmodR.Rcheck/RNAmodR-Ex.timings
| name | user | system | elapsed | |
| CoverageSequenceData-class | 19.730 | 0.800 | 21.911 | |
| EndSequenceData-class | 10.695 | 0.226 | 12.090 | |
| ModDNASequenceTrack | 0.368 | 0.005 | 0.375 | |
| ModInosine-functions | 0.794 | 0.018 | 0.818 | |
| ModInosine | 15.242 | 0.307 | 16.459 | |
| ModRNASequenceTrack | 0.274 | 0.006 | 0.282 | |
| Modifier-functions | 0.332 | 0.008 | 0.342 | |
| NormEndSequenceData-class | 0.000 | 0.000 | 0.001 | |
| PileupSequenceData-class | 11.420 | 0.204 | 12.480 | |
| ProtectedEndSequenceData-class | 12.047 | 0.217 | 13.062 | |
| RNASequenceTrack | 0.170 | 0.002 | 0.174 | |
| RNAmodR-development | 0.112 | 0.002 | 0.116 | |
| SequenceData-functions | 0.114 | 0.003 | 0.117 | |
| SequenceDataFrame-class | 0.102 | 0.001 | 0.103 | |
| SequenceDataList-class | 0.223 | 0.012 | 0.239 | |
| SequenceDataSet-class | 0.131 | 0.003 | 0.136 | |
| aggregate | 0.777 | 0.004 | 0.790 | |
| compareByCoord | 2.910 | 0.021 | 2.964 | |
| modify | 0.785 | 0.004 | 0.798 | |
| plotData | 2.292 | 0.010 | 2.319 | |
| plotROC | 1.960 | 0.021 | 2.000 | |
| settings | 0.170 | 0.001 | 0.172 | |
| subsetByCoord | 0.856 | 0.005 | 0.863 | |