Diego Gallego
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/nucleR |
| Branch: RELEASE_3_11 |
| Last Commit: ce1b2d0 |
| Last Changed Date: 2020-04-27 14:26:22 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:55:17 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE nucleR PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1208/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| nucleR 2.20.0 Diego Gallego
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ WARNINGS ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | ERROR | skipped | skipped | |||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | ERROR | skipped | skipped |
| Package: nucleR |
| Version: 2.20.0 |
| Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:nucleR.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings nucleR_2.20.0.tar.gz |
| StartedAt: 2020-10-17 03:43:27 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 03:48:05 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 278.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: nucleR.Rcheck |
| Warnings: 1 |
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### Running command:
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### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:nucleR.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings nucleR_2.20.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/nucleR.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘nucleR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘nucleR’ version ‘2.20.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘nucleR’ 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 ... OK
* 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 ... WARNING
Undocumented arguments in documentation object '.fftRegion'
‘data2’ ‘pcKeepComp’
Undocumented arguments in documentation object '.loadFiles'
‘singleLoad’ ‘pairedLoad’
Undocumented arguments in documentation object '.loadPairedBam'
‘file’
Undocumented arguments in documentation object '.loadSingleBam'
‘exp’
Undocumented arguments in documentation object '.mid'
‘x’
Undocumented arguments in documentation object '.unlist_as_integer'
‘x’
Undocumented arguments in documentation object '.xlapply'
‘X’ ‘FUN’ ‘...’ ‘mc.cores’
Documented arguments not in \usage in documentation object 'pcKeepCompDetect':
‘...’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 (user + system) or elapsed time > 5s
user system elapsed
syntheticNucMap 42.028 0.084 42.126
* 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 WARNING
See
‘/home/biocbuild/bbs-3.11-bioc/meat/nucleR.Rcheck/00check.log’
for details.
nucleR.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL nucleR
###
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘nucleR’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Loading required package: usethis
Loading required package: BiocGenerics
Loading required package: utils
Loading required package: graphics
Loading required package: stats
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: IRanges
Loading required package: XVector
Attaching package: ‘Biostrings’
The following object is masked from ‘package:base’:
strsplit
Welcome at Fri Oct 16 16:50:29 2020
Goodbye at Fri Oct 16 16:50:37 2020
** help
*** installing help indices
** building package indices
Loading required package: usethis
Loading required package: BiocGenerics
Loading required package: utils
Loading required package: graphics
Loading required package: stats
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: IRanges
Loading required package: XVector
Attaching package: ‘Biostrings’
The following object is masked from ‘package:base’:
strsplit
Welcome at Fri Oct 16 16:50:41 2020
Goodbye at Fri Oct 16 16:50:41 2020
** installing vignettes
** testing if installed package can be loaded from temporary location
Loading required package: usethis
Loading required package: BiocGenerics
Loading required package: utils
Loading required package: graphics
Loading required package: stats
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: IRanges
Loading required package: XVector
Attaching package: ‘Biostrings’
The following object is masked from ‘package:base’:
strsplit
Welcome at Fri Oct 16 16:50:45 2020
Goodbye at Fri Oct 16 16:50:51 2020
** testing if installed package can be loaded from final location
Loading required package: usethis
Loading required package: BiocGenerics
Loading required package: utils
Loading required package: graphics
Loading required package: stats
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: IRanges
Loading required package: XVector
Attaching package: ‘Biostrings’
The following object is masked from ‘package:base’:
strsplit
Welcome at Fri Oct 16 16:50:55 2020
Goodbye at Fri Oct 16 16:51:02 2020
** testing if installed package keeps a record of temporary installation path
* DONE (nucleR)
nucleR.Rcheck/tests/testthat.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-pc-linux-gnu (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(nucleR)
>
> test_check("nucleR")
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 2 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
10.004 0.357 10.347
nucleR.Rcheck/nucleR-Ex.timings
| name | user | system | elapsed | |
| controlCorrection | 0.107 | 0.020 | 0.127 | |
| coverage.rpm | 0.495 | 0.030 | 0.525 | |
| export.bed | 0.249 | 0.004 | 0.252 | |
| export.wig | 0.098 | 0.012 | 0.111 | |
| filterFFT | 0.909 | 0.003 | 0.913 | |
| fragmentLenDetect | 0.788 | 0.008 | 0.796 | |
| mergeCalls | 0.729 | 0.000 | 0.729 | |
| nucleR-package | 2.485 | 0.016 | 2.501 | |
| pcKeepCompDetect | 0.336 | 0.004 | 0.341 | |
| peakDetection | 2.100 | 0.092 | 2.192 | |
| peakScoring | 0.482 | 0.008 | 0.489 | |
| plotPeaks | 1.588 | 0.012 | 1.601 | |
| processReads | 0.336 | 0.004 | 0.340 | |
| processTilingArray | 0.001 | 0.000 | 0.000 | |
| readBAM | 0.316 | 0.004 | 0.469 | |
| syntheticNucMap | 42.028 | 0.084 | 42.126 | |