Package: KnowSeq

Version: 1.0.0

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_1.0.0.tar.gz

StartedAt: 2020-04-15 03:23:15 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 03:33:18 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 602.6 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_1.0.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/KnowSeq.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.0.0’
* 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                 100.705  0.248 101.894
knn_CV                  38.024  0.199  38.480
geneOntologyEnrichment  25.209  0.903  32.391
svm_test                23.526  0.099  24.240
rf_CV                   12.957  0.046  13.100
RNAseqQA                 8.405  0.534   9.039
knn_test                 7.095  0.030   7.176
dataPlot                 6.307  0.372   6.624
downloadPublicSeries     0.937  0.158  21.470
* 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-3.10-bioc/meat/KnowSeq.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL KnowSeq
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/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)

name	user	system	elapsed
DEGsPathwayVisualization	0.001	0.000	0.000
DEGsToDiseases	0.479	0.011	0.788
RNAseqQA	8.405	0.534	9.039
batchEffectRemoval	1.723	0.036	1.773
calculateGeneExpressionValues	1.145	0.041	1.203
countsToMatrix	0.077	0.003	0.084
dataPlot	6.307	0.372	6.624
downloadPublicSeries	0.937	0.158	21.470
featureSelection	0.536	0.574	0.184
fileMove	0.000	0.001	0.000
gdcClientDownload	0.001	0.002	0.001
geneOntologyEnrichment	25.209	0.903	32.391
getAnnotationFromEnsembl	1.003	0.015	2.816
hisatAlignment	0.002	0.000	0.002
kallistoAlignment	0.001	0.000	0.002
knn_CV	38.024	0.199	38.480
knn_test	7.095	0.030	7.176
limmaDEGsExtraction	0.990	0.018	1.017
plotConfMatrix	0.039	0.001	0.040
rawAlignment	0.003	0.000	0.002
rf_CV	12.957	0.046	13.100
rf_test	0.190	0.002	0.195
salmonAlignment	0.003	0.000	0.003
sraToFastq	0.000	0.000	0.001
svm_CV	100.705	0.248	101.894
svm_test	23.526	0.099	24.240
tophatAlignment	0.002	0.000	0.002