Package: subSeq

Version: 1.12.1

Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:subSeq.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings subSeq_1.12.1.tar.gz

StartedAt: 2019-04-16 03:19:12 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 03:21:43 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 151.1 seconds

RetCode: 0

Status:  OK

CheckDir: subSeq.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:subSeq.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings subSeq_1.12.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/subSeq.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘subSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘subSeq’ version ‘1.12.1’
* 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 ‘subSeq’ 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
DESeq2: no visible global function definition for ‘selectMethod’
ccc: no visible global function definition for ‘cov’
ccc: no visible global function definition for ‘var’
generateSubsampledMatrix : <anonymous>: no visible global function
  definition for ‘rbinom’
plot.subsamples: no visible global function definition for ‘plot’
plot.summary.subsamples: no visible binding for global variable
  ‘metric’
plot.summary.subsamples: no visible binding for global variable ‘value’
plot.summary.subsamples: no visible binding for global variable
  ‘significant’
plot.summary.subsamples: no visible binding for global variable
  ‘percent’
plot.summary.subsamples: no visible binding for global variable
  ‘method’
plot.summary.subsamples: no visible binding for global variable ‘depth’
plot.summary.subsamples: no visible binding for global variable
  ‘average.depth’
plot.summary.subsamples: no visible binding for global variable
  ‘average.value’
subsample: no visible binding for global variable ‘proportion’
subsample: no visible binding for global variable ‘replication’
subsample: no visible binding for global variable ‘.’
subsample: no visible binding for global variable ‘pvalue’
summary.subsamples: no visible binding for global variable ‘count’
summary.subsamples: no visible binding for global variable ‘method’
summary.subsamples: no visible binding for global variable ‘depth’
summary.subsamples: no visible binding for global variable ‘pvalue’
summary.subsamples: no visible binding for global variable ‘proportion’
summary.subsamples: no visible binding for global variable
  ‘replication’
summary.subsamples: no visible global function definition for
  ‘p.adjust’
summary.subsamples: no visible binding for global variable ‘ID’
summary.subsamples: no visible binding for global variable ‘padj’
summary.subsamples: no visible binding for global variable
  ‘coefficient’
summary.subsamples: no visible binding for global variable
  ‘o.coefficient’
summary.subsamples: no visible global function definition for ‘cor’
summary.subsamples: no visible binding for global variable ‘valid’
summary.subsamples: no visible binding for global variable ‘o.lfdr’
summary.subsamples: no visible binding for global variable ‘o.padj’
summary.subsamples: no visible binding for global variable
  ‘significant’
summary.subsamples: no visible binding for global variable ‘estFDP’
summary.subsamples: no visible binding for global variable ‘rFDP’
summary.subsamples: no visible binding for global variable ‘metric’
summary.subsamples: no visible binding for global variable ‘value’
summary.subsamples: no visible binding for global variable ‘percent’
voomLimma: no visible global function definition for ‘model.matrix’
Undefined global functions or variables:
  . ID average.depth average.value coefficient cor count cov depth
  estFDP method metric model.matrix o.coefficient o.lfdr o.padj
  p.adjust padj percent plot proportion pvalue rFDP rbinom replication
  selectMethod significant valid value var
Consider adding
  importFrom("graphics", "plot")
  importFrom("methods", "selectMethod")
  importFrom("stats", "cor", "cov", "model.matrix", "p.adjust", "rbinom",
             "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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
Examples with CPU or elapsed time > 5s
                           user system elapsed
generateSubsampledMatrix 37.568  0.420  38.114
subsample                33.908  0.032  34.247
getSeed                  31.732  0.036  31.816
* 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-3.8-bioc/meat/subSeq.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL subSeq
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘subSeq’ ...
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (subSeq)

name	user	system	elapsed
combineSubsamples	0.172	0.024	0.213
generateSubsampledMatrix	37.568	0.420	38.114
getSeed	31.732	0.036	31.816
plot.subsamples	0	0	0
plot.summary.subsamples	0	0	0
ss	1.072	0.000	1.076
subsample	33.908	0.032	34.247
summary.subsamples	1.088	0.000	1.150