Diego Gallego
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/nucleR |
| Branch: RELEASE_3_9 |
| Last Commit: e5c0efe |
| Last Changed Date: 2019-05-02 11:53:27 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:25:26 -0400 (Wed, 16 Oct 2019).
| Package 1116/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| nucleR 2.16.0 Diego Gallego
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: nucleR |
| Version: 2.16.0 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:nucleR.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings nucleR_2.16.0.tar.gz |
| StartedAt: 2019-10-16 05:38:21 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 05:44:13 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 352.6 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: nucleR.Rcheck |
| Warnings: 1 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:nucleR.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings nucleR_2.16.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/nucleR.Rcheck'
* using R version 3.6.1 (2019-07-05)
* 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 '2.16.0'
* 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-3.9-bioc/tmpdir/RtmpaCSIWz/R.INSTALL204852a0359c/nucleR/man/coverage.rpm.Rd:35: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpaCSIWz/R.INSTALL204852a0359c/nucleR/man/coverage.rpm.Rd:36: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpaCSIWz/R.INSTALL204852a0359c/nucleR/man/coverage.rpm.Rd:23: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpaCSIWz/R.INSTALL204852a0359c/nucleR/man/coverage.rpm.Rd:23: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpaCSIWz/R.INSTALL204852a0359c/nucleR/man/coverage.rpm.Rd:52: file link 'coverage' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpaCSIWz/R.INSTALL204852a0359c/nucleR/man/export.bed.Rd:28: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpaCSIWz/R.INSTALL204852a0359c/nucleR/man/export.bed.Rd:29: file link 'IRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpaCSIWz/R.INSTALL204852a0359c/nucleR/man/export.bed.Rd:29: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpaCSIWz/R.INSTALL204852a0359c/nucleR/man/fragmentLenDetect.Rd:27: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpaCSIWz/R.INSTALL204852a0359c/nucleR/man/mergeCalls.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-3.9-bioc/tmpdir/RtmpaCSIWz/R.INSTALL204852a0359c/nucleR/man/mergeCalls.Rd:28: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpaCSIWz/R.INSTALL204852a0359c/nucleR/man/peakScoring.Rd:63: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpaCSIWz/R.INSTALL204852a0359c/nucleR/man/plotPeaks.Rd:67: file link 'geom_rect' in package 'ggplot2' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpaCSIWz/R.INSTALL204852a0359c/nucleR/man/processReads.Rd:29: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpaCSIWz/R.INSTALL204852a0359c/nucleR/man/processReads.Rd:54: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpaCSIWz/R.INSTALL204852a0359c/nucleR/man/processReads.Rd:44: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpaCSIWz/R.INSTALL204852a0359c/nucleR/man/processReads.Rd:114: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpaCSIWz/R.INSTALL204852a0359c/nucleR/man/processTilingArray.Rd:123: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpaCSIWz/R.INSTALL204852a0359c/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-3.9-bioc/tmpdir/RtmpaCSIWz/R.INSTALL204852a0359c/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-3.9-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 ... 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
syntheticNucMap 30.25 0.11 30.36
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
syntheticNucMap 32.65 0.05 32.71
* 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: 1 WARNING
See
'C:/Users/biocbuild/bbs-3.9-bioc/meat/nucleR.Rcheck/00check.log'
for details.
nucleR.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/nucleR_2.16.0.tar.gz && rm -rf nucleR.buildbin-libdir && mkdir nucleR.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=nucleR.buildbin-libdir nucleR_2.16.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL nucleR_2.16.0.zip && rm nucleR_2.16.0.tar.gz nucleR_2.16.0.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
0 805k 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 805k 100 805k 0 0 11.9M 0 --:--:-- --:--:-- --:--:-- 13.1M
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-3.9-bioc/tmpdir/RtmpaCSIWz/R.INSTALL204852a0359c/nucleR/man/coverage.rpm.Rd:35: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpaCSIWz/R.INSTALL204852a0359c/nucleR/man/coverage.rpm.Rd:36: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpaCSIWz/R.INSTALL204852a0359c/nucleR/man/coverage.rpm.Rd:23: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpaCSIWz/R.INSTALL204852a0359c/nucleR/man/coverage.rpm.Rd:23: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpaCSIWz/R.INSTALL204852a0359c/nucleR/man/coverage.rpm.Rd:52: file link 'coverage' in package 'IRanges' does not exist and so has been treated as a topic
export.bed html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpaCSIWz/R.INSTALL204852a0359c/nucleR/man/export.bed.Rd:28: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpaCSIWz/R.INSTALL204852a0359c/nucleR/man/export.bed.Rd:29: file link 'IRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpaCSIWz/R.INSTALL204852a0359c/nucleR/man/export.bed.Rd:29: 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-3.9-bioc/tmpdir/RtmpaCSIWz/R.INSTALL204852a0359c/nucleR/man/fragmentLenDetect.Rd:27: 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-3.9-bioc/tmpdir/RtmpaCSIWz/R.INSTALL204852a0359c/nucleR/man/mergeCalls.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-3.9-bioc/tmpdir/RtmpaCSIWz/R.INSTALL204852a0359c/nucleR/man/mergeCalls.Rd:28: 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-3.9-bioc/tmpdir/RtmpaCSIWz/R.INSTALL204852a0359c/nucleR/man/peakScoring.Rd:63: 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-3.9-bioc/tmpdir/RtmpaCSIWz/R.INSTALL204852a0359c/nucleR/man/plotPeaks.Rd:67: 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-3.9-bioc/tmpdir/RtmpaCSIWz/R.INSTALL204852a0359c/nucleR/man/processReads.Rd:29: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpaCSIWz/R.INSTALL204852a0359c/nucleR/man/processReads.Rd:54: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpaCSIWz/R.INSTALL204852a0359c/nucleR/man/processReads.Rd:44: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpaCSIWz/R.INSTALL204852a0359c/nucleR/man/processReads.Rd:114: 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-3.9-bioc/tmpdir/RtmpaCSIWz/R.INSTALL204852a0359c/nucleR/man/processTilingArray.Rd:123: 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-3.9-bioc/tmpdir/RtmpaCSIWz/R.INSTALL204852a0359c/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-3.9-bioc/tmpdir/RtmpaCSIWz/R.INSTALL204852a0359c/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_2.16.0.zip
* DONE (nucleR)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'nucleR' successfully unpacked and MD5 sums checked
|
nucleR.Rcheck/tests_i386/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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")
== testthat results ===========================================================
[ OK: 2 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
9.79 0.65 10.43
|
nucleR.Rcheck/tests_x64/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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")
== testthat results ===========================================================
[ OK: 2 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
8.84 0.43 9.26
|
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nucleR.Rcheck/examples_i386/nucleR-Ex.timings
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nucleR.Rcheck/examples_x64/nucleR-Ex.timings
|