Daniel Castillo Secilla
| Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020) |
| URL: https://git.bioconductor.org/packages/KnowSeq |
| Branch: master |
| Last Commit: f32f60a |
| Last Changed Date: 2019-12-19 08:45:48 -0500 (Thu, 19 Dec 2019) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-01-16 13:54:42 -0500 (Thu, 16 Jan 2020).
| Package 891/1818 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| KnowSeq 1.1.19 Daniel Castillo Secilla
| malbec2 | Linux (Ubuntu 18.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: KnowSeq |
| Version: 1.1.19 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:KnowSeq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings KnowSeq_1.1.19.tar.gz |
| StartedAt: 2020-01-16 05:51:23 -0500 (Thu, 16 Jan 2020) |
| EndedAt: 2020-01-16 06:03:25 -0500 (Thu, 16 Jan 2020) |
| EllapsedTime: 722.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: KnowSeq.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:KnowSeq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings KnowSeq_1.1.19.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/KnowSeq.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘KnowSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘KnowSeq’ version ‘1.1.19’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘KnowSeq’ 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 ... 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
* 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
limmaDEGsExtraction: warning in topTable(fit, number = number, coef =
2, sort.by = "logFC", p.value = pvalue, adjust = "fdr", lfc = lfc):
partial argument match of 'adjust' to 'adjust.method'
dataPlot: no visible binding for global variable ‘Classes’
dataPlot: no visible binding for global variable ‘Value’
Undefined global functions or variables:
Classes Value
* 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
svm_CV 126.113 0.778 126.909
knn_CV 47.659 0.691 48.515
geneOntologyEnrichment 38.916 2.120 51.356
svm_test 26.583 0.220 26.803
rf_CV 15.454 0.209 15.666
knn_test 9.166 0.035 9.208
dataPlot 6.458 0.469 6.783
downloadPublicSeries 1.257 0.278 17.166
* 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
‘/Users/biocbuild/bbs-3.11-bioc/meat/KnowSeq.Rcheck/00check.log’
for details.
KnowSeq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL KnowSeq ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’ * installing *source* package ‘KnowSeq’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built. ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built. ** testing if installed package can be loaded from final location groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built. ** testing if installed package keeps a record of temporary installation path * DONE (KnowSeq)
KnowSeq.Rcheck/KnowSeq-Ex.timings
| name | user | system | elapsed | |
| DEGsPathwayVisualization | 0.001 | 0.000 | 0.000 | |
| DEGsToDiseases | 0.619 | 0.015 | 0.804 | |
| batchEffectRemoval | 1.887 | 0.053 | 1.944 | |
| calculateGeneExpressionValues | 1.376 | 0.088 | 1.469 | |
| countsToMatrix | 0.111 | 0.015 | 0.130 | |
| dataPlot | 6.458 | 0.469 | 6.783 | |
| downloadPublicSeries | 1.257 | 0.278 | 17.166 | |
| featureSelection | 0.573 | 0.406 | 0.207 | |
| fileMove | 0.001 | 0.001 | 0.001 | |
| gdcClientDownload | 0.001 | 0.001 | 0.000 | |
| geneOntologyEnrichment | 38.916 | 2.120 | 51.356 | |
| getAnnotationFromEnsembl | 0.523 | 0.017 | 2.022 | |
| hisatAlignment | 0.002 | 0.000 | 0.004 | |
| kallistoAlignment | 0.002 | 0.000 | 0.003 | |
| knn_CV | 47.659 | 0.691 | 48.515 | |
| knn_test | 9.166 | 0.035 | 9.208 | |
| limmaDEGsExtraction | 1.196 | 0.047 | 1.244 | |
| plotConfMatrix | 0.042 | 0.002 | 0.044 | |
| rawAlignment | 0.003 | 0.001 | 0.004 | |
| rf_CV | 15.454 | 0.209 | 15.666 | |
| rf_test | 0.212 | 0.002 | 0.214 | |
| salmonAlignment | 0.002 | 0.001 | 0.003 | |
| sraToFastq | 0.001 | 0.001 | 0.000 | |
| svm_CV | 126.113 | 0.778 | 126.909 | |
| svm_test | 26.583 | 0.220 | 26.803 | |
| tophatAlignment | 0.004 | 0.000 | 0.004 | |