Thomas J. Hardcastle
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/segmentSeq |
| Branch: RELEASE_3_12 |
| Last Commit: 1c3ee51 |
| Last Changed Date: 2020-10-27 10:37:38 -0400 (Tue, 27 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
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This page was generated on 2021-05-06 12:33:32 -0400 (Thu, 06 May 2021).
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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 1668/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| segmentSeq 2.24.0 (landing page) Thomas J. Hardcastle
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: segmentSeq |
| Version: 2.24.0 |
| Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:segmentSeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings segmentSeq_2.24.0.tar.gz |
| StartedAt: 2021-05-06 06:49:14 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 06:59:35 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 621.2 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: segmentSeq.Rcheck |
| Warnings: 1 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:segmentSeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings segmentSeq_2.24.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/segmentSeq.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 'segmentSeq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'segmentSeq' version '2.24.0'
* 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-3.12-bioc/tmpdir/Rtmp6f5Jxm/R.INSTALL16ac6d891a68/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-3.12-bioc/tmpdir/Rtmp6f5Jxm/R.INSTALL16ac6d891a68/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-3.12-bioc/tmpdir/Rtmp6f5Jxm/R.INSTALL16ac6d891a68/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-3.12-bioc/tmpdir/Rtmp6f5Jxm/R.INSTALL16ac6d891a68/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-3.12-bioc/tmpdir/Rtmp6f5Jxm/R.INSTALL16ac6d891a68/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-3.12-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 36.64 0.78 37.43
lociLikelihoods 18.86 0.00 18.87
heuristicSeg 16.70 0.00 16.78
plotGenome 8.81 0.04 8.84
normaliseNC 5.78 0.40 6.41
getCounts 5.78 0.00 5.78
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
classifySeg 44.36 0.14 44.55
lociLikelihoods 21.39 0.00 22.10
heuristicSeg 19.00 0.00 19.00
plotGenome 10.56 0.01 11.79
getCounts 7.45 0.00 7.46
segmentSeq-package 6.47 0.00 6.80
processAD 6.33 0.02 7.25
normaliseNC 5.61 0.49 6.10
segData-class 6.09 0.01 6.30
readMeths 5.32 0.27 5.90
getOverlaps 5.00 0.01 5.01
thresholdFinder 4.37 0.36 5.92
* 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-3.12-bioc/meat/segmentSeq.Rcheck/00check.log'
for details.
segmentSeq.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/segmentSeq_2.24.0.tar.gz && rm -rf segmentSeq.buildbin-libdir && mkdir segmentSeq.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=segmentSeq.buildbin-libdir segmentSeq_2.24.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL segmentSeq_2.24.0.zip && rm segmentSeq_2.24.0.tar.gz segmentSeq_2.24.0.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 2357k 100 2357k 0 0 8268k 0 --:--:-- --:--:-- --:--:-- 8299k
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-3.12-bioc/tmpdir/Rtmp6f5Jxm/R.INSTALL16ac6d891a68/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-3.12-bioc/tmpdir/Rtmp6f5Jxm/R.INSTALL16ac6d891a68/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-3.12-bioc/tmpdir/Rtmp6f5Jxm/R.INSTALL16ac6d891a68/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-3.12-bioc/tmpdir/Rtmp6f5Jxm/R.INSTALL16ac6d891a68/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-3.12-bioc/tmpdir/Rtmp6f5Jxm/R.INSTALL16ac6d891a68/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_2.24.0.zip
* DONE (segmentSeq)
* installing to library 'C:/Users/biocbuild/bbs-3.12-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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