Diego Gallego
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/nucleR |
| Branch: RELEASE_3_12 |
| Last Commit: 4f0d071 |
| Last Changed Date: 2020-11-15 11:56:00 -0400 (Sun, 15 Nov 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:32:34 -0400 (Thu, 06 May 2021).
|
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 1239/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| nucleR 2.22.0 (landing page) Diego Gallego
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: nucleR |
| Version: 2.22.0 |
| Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:nucleR.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings nucleR_2.22.0.tar.gz |
| StartedAt: 2021-05-06 05:09:38 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 05:16:25 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 407.2 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: nucleR.Rcheck |
| Warnings: 2 |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:nucleR.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings nucleR_2.22.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/nucleR.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'nucleR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'nucleR' version '2.22.0'
* 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 whether package 'nucleR' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpayfBjr/R.INSTALL1f7c4acb42de/nucleR/man/coverage.rpm.Rd:31: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpayfBjr/R.INSTALL1f7c4acb42de/nucleR/man/coverage.rpm.Rd:32: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpayfBjr/R.INSTALL1f7c4acb42de/nucleR/man/coverage.rpm.Rd:19: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpayfBjr/R.INSTALL1f7c4acb42de/nucleR/man/coverage.rpm.Rd:19: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpayfBjr/R.INSTALL1f7c4acb42de/nucleR/man/coverage.rpm.Rd:48: file link 'coverage' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpayfBjr/R.INSTALL1f7c4acb42de/nucleR/man/dot-processStrand.Rd:16: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpayfBjr/R.INSTALL1f7c4acb42de/nucleR/man/export.bed.Rd:41: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpayfBjr/R.INSTALL1f7c4acb42de/nucleR/man/export.bed.Rd:42: file link 'IRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpayfBjr/R.INSTALL1f7c4acb42de/nucleR/man/export.bed.Rd:42: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpayfBjr/R.INSTALL1f7c4acb42de/nucleR/man/fragmentLenDetect.Rd:41: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpayfBjr/R.INSTALL1f7c4acb42de/nucleR/man/mergeCalls.Rd:19: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpayfBjr/R.INSTALL1f7c4acb42de/nucleR/man/mergeCalls.Rd:31: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpayfBjr/R.INSTALL1f7c4acb42de/nucleR/man/peakScoring.Rd:74: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpayfBjr/R.INSTALL1f7c4acb42de/nucleR/man/plotPeaks.Rd:95: file link 'geom_rect' in package 'ggplot2' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpayfBjr/R.INSTALL1f7c4acb42de/nucleR/man/processReads.Rd:21: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpayfBjr/R.INSTALL1f7c4acb42de/nucleR/man/processReads.Rd:46: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpayfBjr/R.INSTALL1f7c4acb42de/nucleR/man/processReads.Rd:36: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpayfBjr/R.INSTALL1f7c4acb42de/nucleR/man/processReads.Rd:106: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpayfBjr/R.INSTALL1f7c4acb42de/nucleR/man/processTilingArray.Rd:129: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpayfBjr/R.INSTALL1f7c4acb42de/nucleR/man/readBAM.Rd:16: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpayfBjr/R.INSTALL1f7c4acb42de/nucleR/man/readBowtie.Rd:16: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.12-bioc/meat/nucleR.Rcheck/00install.out' for details.
* 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
* 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 ... 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
syntheticNucMap 37.35 0.21 37.55
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
syntheticNucMap 36.07 0.06 36.63
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
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: 2 WARNINGs
See
'C:/Users/biocbuild/bbs-3.12-bioc/meat/nucleR.Rcheck/00check.log'
for details.
nucleR.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/nucleR_2.22.0.tar.gz && rm -rf nucleR.buildbin-libdir && mkdir nucleR.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=nucleR.buildbin-libdir nucleR_2.22.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL nucleR_2.22.0.zip && rm nucleR_2.22.0.tar.gz nucleR_2.22.0.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
100 803k 100 803k 0 0 24.5M 0 --:--:-- --:--:-- --:--:-- 25.3M
install for i386
* installing *source* package 'nucleR' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'nucleR'
finding HTML links ... done
controlCorrection html
coverage.rpm html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpayfBjr/R.INSTALL1f7c4acb42de/nucleR/man/coverage.rpm.Rd:31: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpayfBjr/R.INSTALL1f7c4acb42de/nucleR/man/coverage.rpm.Rd:32: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpayfBjr/R.INSTALL1f7c4acb42de/nucleR/man/coverage.rpm.Rd:19: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpayfBjr/R.INSTALL1f7c4acb42de/nucleR/man/coverage.rpm.Rd:19: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpayfBjr/R.INSTALL1f7c4acb42de/nucleR/man/coverage.rpm.Rd:48: file link 'coverage' in package 'IRanges' does not exist and so has been treated as a topic
dot-fftRegion html
dot-getThreshold html
dot-loadFiles html
dot-loadPairedBam html
dot-loadSingleBam html
dot-mid html
dot-processStrand html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpayfBjr/R.INSTALL1f7c4acb42de/nucleR/man/dot-processStrand.Rd:16: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
dot-unlist_as_integer html
dot-vectorizedAll html
dot-xlapply html
export.bed html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpayfBjr/R.INSTALL1f7c4acb42de/nucleR/man/export.bed.Rd:41: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpayfBjr/R.INSTALL1f7c4acb42de/nucleR/man/export.bed.Rd:42: file link 'IRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpayfBjr/R.INSTALL1f7c4acb42de/nucleR/man/export.bed.Rd:42: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
export.wig html
filterFFT html
fragmentLenDetect html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpayfBjr/R.INSTALL1f7c4acb42de/nucleR/man/fragmentLenDetect.Rd:41: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
mergeCalls html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpayfBjr/R.INSTALL1f7c4acb42de/nucleR/man/mergeCalls.Rd:19: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpayfBjr/R.INSTALL1f7c4acb42de/nucleR/man/mergeCalls.Rd:31: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
nucleR-package html
nucleosome_htseq html
nucleosome_tiling html
pcKeepCompDetect html
peakDetection html
peakScoring html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpayfBjr/R.INSTALL1f7c4acb42de/nucleR/man/peakScoring.Rd:74: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
plotPeaks html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpayfBjr/R.INSTALL1f7c4acb42de/nucleR/man/plotPeaks.Rd:95: file link 'geom_rect' in package 'ggplot2' does not exist and so has been treated as a topic
processReads html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpayfBjr/R.INSTALL1f7c4acb42de/nucleR/man/processReads.Rd:21: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpayfBjr/R.INSTALL1f7c4acb42de/nucleR/man/processReads.Rd:46: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpayfBjr/R.INSTALL1f7c4acb42de/nucleR/man/processReads.Rd:36: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpayfBjr/R.INSTALL1f7c4acb42de/nucleR/man/processReads.Rd:106: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
processTilingArray html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpayfBjr/R.INSTALL1f7c4acb42de/nucleR/man/processTilingArray.Rd:129: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
readBAM html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpayfBjr/R.INSTALL1f7c4acb42de/nucleR/man/readBAM.Rd:16: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
readBowtie html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpayfBjr/R.INSTALL1f7c4acb42de/nucleR/man/readBowtie.Rd:16: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
syntheticNucMap 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 'nucleR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'nucleR' as nucleR_2.22.0.zip
* DONE (nucleR)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'nucleR' successfully unpacked and MD5 sums checked
|
nucleR.Rcheck/tests_i386/testthat.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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.
> library(testthat)
> library(nucleR)
>
> test_check("nucleR")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 2 ]
>
> proc.time()
user system elapsed
8.28 0.62 8.90
|
nucleR.Rcheck/tests_x64/testthat.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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.
> library(testthat)
> library(nucleR)
>
> test_check("nucleR")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 2 ]
>
> proc.time()
user system elapsed
9.29 0.40 10.12
|
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nucleR.Rcheck/examples_i386/nucleR-Ex.timings
|
nucleR.Rcheck/examples_x64/nucleR-Ex.timings
|