Thomas J. Hardcastle
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/segmentSeq |
| Branch: RELEASE_3_11 |
| Last Commit: 4bb4854 |
| Last Changed Date: 2020-04-27 14:21:25 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:57:47 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE segmentSeq PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1618/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| segmentSeq 2.22.0 Thomas J. Hardcastle
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | |||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |
| Package: segmentSeq |
| Version: 2.22.0 |
| Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:segmentSeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings segmentSeq_2.22.0.tar.gz |
| StartedAt: 2020-10-17 08:08:13 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 08:18:06 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 593.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: segmentSeq.Rcheck |
| Warnings: 1 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:segmentSeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings segmentSeq_2.22.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/segmentSeq.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'segmentSeq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'segmentSeq' version '2.22.0'
* 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 'segmentSeq' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp8QKcj8/R.INSTALL237854a42ae6/segmentSeq/man/classifySeg.Rd:45: file link 'getPriors.NB' in package 'baySeq' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp8QKcj8/R.INSTALL237854a42ae6/segmentSeq/man/lociLikelihoods.Rd:27: file link 'getLikelihoods.NB' in package 'baySeq' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp8QKcj8/R.INSTALL237854a42ae6/segmentSeq/man/segClass-class.Rd:23: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp8QKcj8/R.INSTALL237854a42ae6/segmentSeq/man/segData-class.Rd:25: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp8QKcj8/R.INSTALL237854a42ae6/segmentSeq/man/segMeth-class.Rd:25: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.11-bioc/meat/segmentSeq.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 ... NOTE
heuristicSeg : <anonymous>: no visible binding for global variable
'sDP'
Undefined global functions or variables:
sDP
* 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 (user + system) or elapsed time > 5s
user system elapsed
classifySeg 36.90 0.75 37.69
lociLikelihoods 15.45 0.00 15.45
heuristicSeg 15.07 0.00 15.08
plotGenome 8.39 0.02 8.41
normaliseNC 5.48 0.39 6.81
getCounts 5.69 0.00 5.68
thresholdFinder 4.81 0.56 5.37
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
classifySeg 36.12 0.04 36.17
heuristicSeg 17.62 0.00 17.63
lociLikelihoods 17.58 0.00 17.58
plotGenome 7.82 0.02 7.84
* 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, 1 NOTE
See
'C:/Users/biocbuild/bbs-3.11-bioc/meat/segmentSeq.Rcheck/00check.log'
for details.
segmentSeq.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/segmentSeq_2.22.0.tar.gz && rm -rf segmentSeq.buildbin-libdir && mkdir segmentSeq.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=segmentSeq.buildbin-libdir segmentSeq_2.22.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL segmentSeq_2.22.0.zip && rm segmentSeq_2.22.0.tar.gz segmentSeq_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 2355k 100 2355k 0 0 30.7M 0 --:--:-- --:--:-- --:--:-- 33.3M
install for i386
* installing *source* package 'segmentSeq' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'segmentSeq'
finding HTML links ... done
SL html
alignmentClass-class html
alignmentData-class html
alignmentMeth-class html
averageMethylationRegions html
finding level-2 HTML links ... done
classifySeg html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp8QKcj8/R.INSTALL237854a42ae6/segmentSeq/man/classifySeg.Rd:45: file link 'getPriors.NB' in package 'baySeq' does not exist and so has been treated as a topic
findChunks html
getCounts html
getOverlaps html
givenExpression html
hSL html
heuristicSeg html
lociData-class html
lociLikelihoods html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp8QKcj8/R.INSTALL237854a42ae6/segmentSeq/man/lociLikelihoods.Rd:27: file link 'getLikelihoods.NB' in package 'baySeq' does not exist and so has been treated as a topic
mergeMethSegs html
methData-class html
normaliseNC html
plotGenome html
plotMeth html
plotMethDistribution html
processAD html
readMethods html
readMeths html
segClass-class html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp8QKcj8/R.INSTALL237854a42ae6/segmentSeq/man/segClass-class.Rd:23: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
segData-class html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp8QKcj8/R.INSTALL237854a42ae6/segmentSeq/man/segData-class.Rd:25: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
segMeth-class html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp8QKcj8/R.INSTALL237854a42ae6/segmentSeq/man/segMeth-class.Rd:25: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
segmentSeq-package html
selectLoci html
summariseLoci html
thresholdFinder 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 'segmentSeq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'segmentSeq' as segmentSeq_2.22.0.zip
* DONE (segmentSeq)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'segmentSeq' successfully unpacked and MD5 sums checked
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segmentSeq.Rcheck/examples_i386/segmentSeq-Ex.timings
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segmentSeq.Rcheck/examples_x64/segmentSeq-Ex.timings
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