Rosario M. Piro
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/decompTumor2Sig |
| git_branch: master |
| git_last_commit: 218491c |
| git_last_commit_date: 2021-10-26 12:48:26 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:07:19 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the decompTumor2Sig package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/decompTumor2Sig.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 470/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| decompTumor2Sig 2.11.0 (landing page) Rosario M. Piro
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: decompTumor2Sig |
| Version: 2.11.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:decompTumor2Sig.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings decompTumor2Sig_2.11.0.tar.gz |
| StartedAt: 2022-03-17 18:53:15 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 18:58:27 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 312.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: decompTumor2Sig.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:decompTumor2Sig.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings decompTumor2Sig_2.11.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/decompTumor2Sig.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'decompTumor2Sig/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'decompTumor2Sig' version '2.11.0'
* 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 'decompTumor2Sig' 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 ... NOTE
File
inst/LICENSE
will install at top-level and is not mentioned in the DESCRIPTION file.
* 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 ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plotExplainedVariance 57.09 0.16 60.61
convertGenomesFromVRanges 5.66 0.52 6.17
* 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 NOTE
See
'D:/biocbuild/bbs-3.15-bioc/meat/decompTumor2Sig.Rcheck/00check.log'
for details.
decompTumor2Sig.Rcheck/00install.out
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL decompTumor2Sig
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'decompTumor2Sig' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'decompTumor2Sig'
finding HTML links ... done
QPforSig html
addBestSignatureToSubset html
adjustAlexandrovSignature html
adjustShiraishiSignature html
adjustSignaturesForRegionSet html
buildGenomesFromMutationData html
buildSortedAlexandrovSignaturePatternList
html
compNucFreq html
composeGenomesFromExposures html
computeExplainedVariance html
computeFrobeniusNorm html
computeRSS html
convAlx2Shi html
convertAlexandrov2Shiraishi html
convertGenomesFromVRanges html
convertSeqFreqToBaseFreq html
decompTumor2Sig-package html
decomposeTumorGenomes html
determineSignatureDistances html
determineTypeNumBasesAndTrDir html
downgradeShiraishiSignatures html
evaluateDecompositionQuality html
getBestDecomp4Ksignatures html
getCountData html
getFeatVectList html
getGenomesFromMutFeatData html
getNumFlankingBases html
getNumSignatures html
getSampleList html
getSigFeatDist html
getSigFromEstParam html
getSigType html
getSignaturesFromEstParam html
haveTrDir html
is.probability.data.frame html
is.probability.data.frame.list html
is.probability.matrix html
is.probability.matrix.list html
is.probability.object html
is.probability.vector html
is.probability.vector.list html
isAlexandrovSet html
isBackGround html
isEstParamObject html
isExposureSet html
isMutFeatDataObject html
isShiraishiSet html
isSignatureSet html
mapSignatureSets html
plotAlexandrovModel html
plotDecomposedContribution html
plotExplainedVariance html
plotMutationDistribution html
plotShiraishiModel html
processMultipleSigSets html
readAlexandrovSignatures html
readGenomesFromMPF html
readGenomesFromVCF html
readShiraishiSignatures html
roundIntegerSum html
sameSignatureFormat html
setNames4ShiraishiTable html
setNumFlankingBases html
setSigFeatDist html
setSigType html
setTrDir 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
* DONE (decompTumor2Sig)
Making 'packages.html' ... done
decompTumor2Sig.Rcheck/decompTumor2Sig-Ex.timings
| name | user | system | elapsed | |
| adjustSignaturesForRegionSet | 2.13 | 0.22 | 3.25 | |
| composeGenomesFromExposures | 0.19 | 0.03 | 1.06 | |
| computeExplainedVariance | 0.20 | 0.02 | 1.06 | |
| convertAlexandrov2Shiraishi | 0.03 | 0.00 | 0.86 | |
| convertGenomesFromVRanges | 5.66 | 0.52 | 6.17 | |
| decomposeTumorGenomes | 2.40 | 0.39 | 3.63 | |
| determineSignatureDistances | 0.05 | 0.00 | 0.89 | |
| downgradeShiraishiSignatures | 0 | 0 | 0 | |
| evaluateDecompositionQuality | 0.17 | 0.02 | 1.02 | |
| getGenomesFromMutFeatData | 0.36 | 0.00 | 0.36 | |
| getSignaturesFromEstParam | 0.11 | 0.00 | 0.11 | |
| isAlexandrovSet | 0.03 | 0.00 | 0.84 | |
| isExposureSet | 2.25 | 0.42 | 3.50 | |
| isShiraishiSet | 0.05 | 0.00 | 0.88 | |
| isSignatureSet | 0.01 | 0.00 | 0.84 | |
| mapSignatureSets | 0.13 | 0.00 | 1.17 | |
| plotDecomposedContribution | 0.52 | 0.03 | 1.67 | |
| plotExplainedVariance | 57.09 | 0.16 | 60.61 | |
| plotMutationDistribution | 1.51 | 0.01 | 2.36 | |
| readAlexandrovSignatures | 0.02 | 0.00 | 0.88 | |
| readGenomesFromMPF | 2.59 | 0.38 | 2.97 | |
| readGenomesFromVCF | 3.05 | 0.26 | 3.31 | |
| readShiraishiSignatures | 0 | 0 | 0 | |
| sameSignatureFormat | 0.06 | 0.00 | 0.89 | |