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This page was generated on 2021-10-18 12:03:45 -0400 (Mon, 18 Oct 2021).

CHECK results for KnowSeq on nebbiolo2

To the developers/maintainers of the KnowSeq package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/KnowSeq.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.

raw results

Package 975/2060HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
KnowSeq 1.7.3  (landing page)
Daniel Castillo-Secilla
Snapshot Date: 2021-10-17 14:50:03 -0400 (Sun, 17 Oct 2021)
git_url: https://git.bioconductor.org/packages/KnowSeq
git_branch: master
git_last_commit: 6fcdd68
git_last_commit_date: 2021-10-09 08:02:34 -0400 (Sat, 09 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    NA  

Summary

Package: KnowSeq
Version: 1.7.3
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:KnowSeq.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings KnowSeq_1.7.3.tar.gz
StartedAt: 2021-10-17 20:33:17 -0400 (Sun, 17 Oct 2021)
EndedAt: 2021-10-17 20:38:27 -0400 (Sun, 17 Oct 2021)
EllapsedTime: 310.1 seconds
RetCode: 0
Status:   OK  
CheckDir: KnowSeq.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:KnowSeq.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings KnowSeq_1.7.3.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/KnowSeq.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.7.3’
* 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 ... NOTE
  installed size is  5.9Mb
  sub-directories of 1Mb or more:
    extdata   5.6Mb
* 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
DEGsExtraction: 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'
RNAseqQA : outlierBarPlot: no visible binding for global variable ‘x’
RNAseqQA : outlierBarPlot: no visible binding for global variable ‘y’
RNAseqQA: no visible binding for global variable ‘Var1’
RNAseqQA: no visible binding for global variable ‘Var2’
RNAseqQA: no visible binding for global variable ‘value’
RNAseqQA: no visible binding for global variable ‘Expression’
RNAseqQA: no visible binding for global variable ‘Samples’
dataPlot: no visible binding for global variable ‘Var1’
dataPlot: no visible binding for global variable ‘Var2’
dataPlot: no visible binding for global variable ‘value’
dataPlot: no visible binding for global variable ‘Classes’
dataPlot: no visible binding for global variable ‘Value’
knn_trn: no visible global function definition for ‘knn.cv’
knowseqReport: no visible binding for global variable ‘target’
Undefined global functions or variables:
  Classes Expression Samples Value Var1 Var2 knn.cv target value x y
* 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_test             33.035  0.279  33.315
svm_trn              28.204  0.182  28.387
rf_trn               26.559  0.548  27.107
dataPlot             18.107  0.748  18.857
rf_test              10.398  0.520  10.918
downloadPublicSeries  0.854  0.070  13.563
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.14-bioc/meat/KnowSeq.Rcheck/00check.log’
for details.



Installation output

KnowSeq.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL KnowSeq
###
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* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘KnowSeq’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 (KnowSeq)

Tests output


Example timings

KnowSeq.Rcheck/KnowSeq-Ex.timings

nameusersystemelapsed
DEGsEvidences0.2980.0121.135
DEGsExtraction1.4230.0361.459
DEGsToDiseases0.2420.0041.119
DEGsToPathways0.4170.0012.648
RNAseqQA1.3260.0201.347
batchEffectRemoval1.6180.0151.628
calculateGeneExpressionValues0.6030.0160.619
countsToMatrix0.0480.0000.050
dataPlot18.107 0.74818.857
downloadPublicSeries 0.854 0.07013.563
featureSelection0.0170.0000.014
fileMove000
gdcClientDownload000
geneOntologyEnrichment0.0010.0000.000
getGenesAnnotation0.1700.0040.164
hisatAlignment0.0020.0000.001
knn_test0.040.000.04
knn_trn2.0840.1242.209
knowseqReport0.0050.0000.006
plotConfMatrix0.0170.0000.018
rawAlignment0.0010.0000.001
rf_test10.398 0.52010.918
rf_trn26.559 0.54827.107
sraToFastq000
svm_test33.035 0.27933.315
svm_trn28.204 0.18228.387