Package: StarBioTrek

Version: 1.10.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:StarBioTrek.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings StarBioTrek_1.10.0.tar.gz

StartedAt: 2019-10-16 05:16:55 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 05:19:05 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 130.1 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: StarBioTrek.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:StarBioTrek.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings StarBioTrek_1.10.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/StarBioTrek.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘StarBioTrek/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘StarBioTrek’ version ‘1.10.0’
* 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 ‘StarBioTrek’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
* 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 ... NOTE
Namespace in Imports field not imported from: ‘AnnotationDbi’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
svm_classification: no visible binding for global variable ‘Target’
Undefined global functions or variables:
  Target
* 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 ... WARNING
Documented arguments not in \usage in documentation object 'svm_classification':
  ‘Target’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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 WARNING, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/StarBioTrek.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL StarBioTrek
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘StarBioTrek’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (StarBioTrek)

name	user	system	elapsed
ConvertedIDgenes	3.440	0.028	3.516
GE_matrix	0.039	0.000	0.038
GE_matrix_mean	0.067	0.000	0.067
GetData	0	0	0
GetPathData	0.005	0.000	0.006
GetPathNet	0.004	0.000	0.003
IPPI	0	0	0
SelectedSample	0.110	0.004	0.114
average	1.141	0.016	1.159
circleplot	1.486	0.003	1.491
dsscorecrtlk	0.028	0.000	0.028
eucdistcrtlk	0.035	0.000	0.035
getNETdata	0	0	0
listpathnet	0.459	0.004	0.464
pathnet	0.470	0.004	0.475
plotcrosstalk	0.034	0.000	0.034
stdv	0.035	0.004	0.038
svm_classification	0.000	0.000	0.001