Daniel Castillo Secilla
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/KnowSeq |
| Branch: RELEASE_3_10 |
| Last Commit: 9f19e01 |
| Last Changed Date: 2020-02-13 15:39:36 -0400 (Thu, 13 Feb 2020) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:15:54 -0400 (Wed, 15 Apr 2020).
| Package 894/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| KnowSeq 1.0.0 Daniel Castillo Secilla
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: KnowSeq |
| Version: 1.0.0 |
| Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:KnowSeq.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings KnowSeq_1.0.0.tar.gz |
| StartedAt: 2020-04-15 06:38:00 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 06:47:24 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 564.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: KnowSeq.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:KnowSeq.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings KnowSeq_1.0.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/KnowSeq.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (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 ‘1.0.0’
* 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 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’
dataPlot: no visible global function definition for ‘grid’
Undefined global functions or variables:
Classes Value grid
Consider adding
importFrom("graphics", "grid")
to your NAMESPACE file.
* 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 or elapsed time > 5s
user system elapsed
svm_CV 90.672 0.040 91.799
knn_CV 37.248 0.068 37.487
featureSelection 25.004 0.124 4.599
geneOntologyEnrichment 22.544 0.120 28.315
svm_test 20.836 0.004 21.282
rf_CV 11.344 0.012 11.459
RNAseqQA 7.960 0.132 8.228
knn_test 6.524 0.004 6.568
dataPlot 5.680 0.084 5.775
downloadPublicSeries 2.328 0.832 21.109
* 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
‘/home/biocbuild/bbs-3.10-bioc/meat/KnowSeq.Rcheck/00check.log’
for details.
KnowSeq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL KnowSeq ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/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 | 0 | 0 | |
| DEGsToDiseases | 0.272 | 0.008 | 0.412 | |
| RNAseqQA | 7.960 | 0.132 | 8.228 | |
| batchEffectRemoval | 2.000 | 0.396 | 2.454 | |
| calculateGeneExpressionValues | 1.024 | 0.008 | 1.237 | |
| countsToMatrix | 0.084 | 0.000 | 0.191 | |
| dataPlot | 5.680 | 0.084 | 5.775 | |
| downloadPublicSeries | 2.328 | 0.832 | 21.109 | |
| featureSelection | 25.004 | 0.124 | 4.599 | |
| fileMove | 0 | 0 | 0 | |
| gdcClientDownload | 0.004 | 0.000 | 0.000 | |
| geneOntologyEnrichment | 22.544 | 0.120 | 28.315 | |
| getAnnotationFromEnsembl | 0.460 | 0.012 | 1.774 | |
| hisatAlignment | 0.004 | 0.000 | 0.015 | |
| kallistoAlignment | 0.000 | 0.004 | 0.001 | |
| knn_CV | 37.248 | 0.068 | 37.487 | |
| knn_test | 6.524 | 0.004 | 6.568 | |
| limmaDEGsExtraction | 0.924 | 0.004 | 0.930 | |
| plotConfMatrix | 0.024 | 0.000 | 0.027 | |
| rawAlignment | 0.000 | 0.000 | 0.002 | |
| rf_CV | 11.344 | 0.012 | 11.459 | |
| rf_test | 0.192 | 0.000 | 0.191 | |
| salmonAlignment | 0.004 | 0.000 | 0.002 | |
| sraToFastq | 0 | 0 | 0 | |
| svm_CV | 90.672 | 0.040 | 91.799 | |
| svm_test | 20.836 | 0.004 | 21.282 | |
| tophatAlignment | 0.000 | 0.000 | 0.002 | |