Package: AffiXcan

Version: 1.4.0

Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:AffiXcan.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings AffiXcan_1.4.0.tar.gz

StartedAt: 2020-04-15 06:03:12 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 06:06:00 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 167.7 seconds

RetCode: 0

Status:  OK

CheckDir: AffiXcan.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:AffiXcan.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings AffiXcan_1.4.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/AffiXcan.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 ‘AffiXcan/DESCRIPTION’ ... OK
* this is package ‘AffiXcan’ version ‘1.4.0’
* 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 ‘AffiXcan’ 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
affiXcanBs: no visible global function definition for ‘p.adjust’
affiXcanPcs: no visible global function definition for ‘setNames’
computeBs: no visible binding for global variable ‘V1’
computeBs: no visible global function definition for ‘lm’
computeBs: no visible global function definition for ‘anova’
computeBs: no visible global function definition for ‘pf’
computeCorrelation: no visible global function definition for ‘cor’
computeCorrelation: no visible global function definition for
  ‘cor.test’
computePca: no visible global function definition for ‘var’
computePca: no visible global function definition for ‘prcomp’
computeRSquared: no visible binding for global variable ‘exprMatrix’
Undefined global functions or variables:
  V1 anova cor cor.test exprMatrix lm p.adjust pf prcomp setNames var
Consider adding
  importFrom("stats", "anova", "cor", "cor.test", "lm", "p.adjust", "pf",
             "prcomp", "setNames", "var")
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 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 NOTE
See
  ‘/home/biocbuild/bbs-3.10-bioc/meat/AffiXcan.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL AffiXcan
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘AffiXcan’ ...
** using staged installation
** R
** data
** 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 (AffiXcan)

name	user	system	elapsed
AffiXcan-package	4.020	0.864	3.696
affiXcanBs	0.000	0.000	0.002
affiXcanGReX	0.004	0.000	0.001
affiXcanImpute	2.164	0.760	1.588
affiXcanPca	0.000	0.000	0.002
affiXcanPcs	0.000	0.000	0.001
affiXcanTrain	0.000	0.000	0.001
assoc2list	0.000	0.000	0.001
computeBs	0.008	0.000	0.006
computeCorrelation	0.000	0.000	0.002
computeExpr	0.000	0.000	0.002
computePca	0.000	0.000	0.003
computePcs	0.000	0.000	0.002
computeRSquared	0.004	0.000	0.002
exprMatrix	0.016	0.000	0.014
overlookRegions	0.000	0.000	0.001
regionAssoc	0.008	0.000	0.008
subsetKFold	0	0	0
trainingCovariates	0.004	0.000	0.004