Felix G.M. Ernst
| Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020) |
| URL: https://git.bioconductor.org/packages/RNAmodR |
| Branch: master |
| Last Commit: 6255229 |
| Last Changed Date: 2020-01-14 14:11:24 -0500 (Tue, 14 Jan 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-01-16 13:54:35 -0500 (Thu, 16 Jan 2020).
| Package 1448/1818 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| RNAmodR 1.1.4 Felix G.M. Ernst
| malbec2 | Linux (Ubuntu 18.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ ERROR ] | OK |
| Package: RNAmodR |
| Version: 1.1.4 |
| 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_1.1.4.tar.gz |
| StartedAt: 2020-01-16 08:18:43 -0500 (Thu, 16 Jan 2020) |
| EndedAt: 2020-01-16 08:31:45 -0500 (Thu, 16 Jan 2020) |
| EllapsedTime: 782.7 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: RNAmodR.Rcheck |
| Warnings: NA |
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### Running 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_1.1.4.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/RNAmodR.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘1.1.4’
* 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 ... WARNING
'::' or ':::' import not declared from: 'SummarizedExperiment'
Unexported objects imported by ':::' calls:
'BiocGenerics:::replaceSlots' 'Biostrings:::XString'
'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 ... ERROR
Running examples in ‘RNAmodR-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ProtectedEndSequenceData-class
> ### Title: ProtectedEndSequenceData
> ### Aliases: ProtectedEndSequenceData-class ProtectedEndSequenceData
> ### ProtectedEndSequenceDataFrame-class ProtectedEndSequenceDataFrame
> ### getData,ProtectedEndSequenceData,BamFileList,GRangesList,XStringSet,ScanBamParam-method
> ### aggregateData,ProtectedEndSequenceData-method
> ### getDataTrack,ProtectedEndSequenceData-method
>
> ### ** Examples
>
> # Construction of a ProtectedEndSequenceData object
> library(RNAmodR.Data)
Loading required package: ExperimentHub
Loading required package: AnnotationHub
Loading required package: BiocFileCache
Loading required package: dbplyr
Loading required package: ExperimentHubData
Loading required package: AnnotationHubData
> library(rtracklayer)
> annotation <- GFF3File(RNAmodR.Data.example.man.gff3())
Error in curl::curl_fetch_memory(url, handle = handle) :
Empty reply from server
Calls: GFF3File ... request_fetch -> request_fetch.write_memory -> <Anonymous>
Execution halted
* 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 ERROR, 1 WARNING
See
‘/Users/biocbuild/bbs-3.11-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/4.0/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 Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 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
81.870 4.058 86.874
RNAmodR.Rcheck/RNAmodR-Ex.timings
| name | user | system | elapsed | |
| CoverageSequenceData-class | 26.068 | 1.737 | 28.957 | |
| EndSequenceData-class | 13.305 | 0.409 | 14.629 | |
| ModDNASequenceTrack | 0.595 | 0.019 | 0.614 | |
| ModInosine-functions | 1.036 | 0.032 | 1.070 | |
| ModInosine | 17.892 | 0.495 | 19.292 | |
| ModRNASequenceTrack | 0.316 | 0.006 | 0.323 | |
| Modifier-functions | 0.320 | 0.008 | 0.329 | |
| NormEndSequenceData-class | 0.000 | 0.000 | 0.001 | |
| PileupSequenceData-class | 13.904 | 0.320 | 14.912 | |