Package: sRAP

Version: 1.23.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:sRAP.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings sRAP_1.23.0.tar.gz

StartedAt: 2019-04-09 03:51:26 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 03:54:12 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 165.5 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: sRAP.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:sRAP.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings sRAP_1.23.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/sRAP.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sRAP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sRAP’ version ‘1.23.0’
* 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 ‘sRAP’ 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
RNA.bdfunc.fc: no visible global function definition for ‘data’
RNA.bdfunc.fc: no visible binding for global variable
  ‘bdfunc.enrichment.human’
RNA.bdfunc.fc: no visible binding for global variable
  ‘bdfunc.enrichment.mouse’
RNA.bdfunc.fc: no visible global function definition for ‘read.table’
RNA.bdfunc.fc: no visible global function definition for ‘pdf’
RNA.bdfunc.fc: no visible global function definition for ‘density’
RNA.bdfunc.fc: no visible global function definition for ‘lines’
RNA.bdfunc.fc: no visible global function definition for ‘legend’
RNA.bdfunc.fc: no visible global function definition for ‘dev.off’
RNA.bdfunc.fc: no visible global function definition for ‘p.adjust’
RNA.bdfunc.fc: no visible global function definition for ‘write.table’
RNA.bdfunc.signal: no visible global function definition for ‘colors’
RNA.bdfunc.signal: no visible global function definition for
  ‘read.table’
RNA.bdfunc.signal: no visible global function definition for ‘data’
RNA.bdfunc.signal: no visible binding for global variable
  ‘bdfunc.enrichment.human’
RNA.bdfunc.signal: no visible binding for global variable
  ‘bdfunc.enrichment.mouse’
RNA.bdfunc.signal: no visible global function definition for ‘aov’
RNA.bdfunc.signal: no visible global function definition for ‘median’
RNA.bdfunc.signal: no visible global function definition for ‘pdf’
RNA.bdfunc.signal: no visible global function definition for ‘boxplot’
RNA.bdfunc.signal: no visible global function definition for ‘dev.off’
RNA.bdfunc.signal: no visible global function definition for ‘slot’
RNA.bdfunc.signal: no visible global function definition for ‘p.adjust’
RNA.bdfunc.signal: no visible global function definition for
  ‘write.table’
RNA.deg: no visible global function definition for ‘colors’
RNA.deg: no visible global function definition for ‘read.table’
RNA.deg: no visible global function definition for ‘p.adjust’
RNA.deg: no visible global function definition for ‘na.omit’
RNA.deg: no visible global function definition for ‘pdf’
RNA.deg: no visible global function definition for ‘boxplot’
RNA.deg: no visible global function definition for ‘dev.off’
RNA.norm: no visible global function definition for ‘read.table’
RNA.qc: no visible global function definition for ‘colors’
RNA.qc: no visible global function definition for ‘read.table’
RNA.qc: no visible global function definition for ‘pdf’
RNA.qc: no visible global function definition for ‘quantile’
RNA.qc: no visible global function definition for ‘density’
RNA.qc: no visible global function definition for ‘legend’
RNA.qc: no visible global function definition for ‘lines’
RNA.qc: no visible global function definition for ‘dev.off’
RNA.qc: no visible global function definition for ‘write.table’
RNA.qc: no visible global function definition for ‘dist’
RNA.qc: no visible global function definition for ‘hclust’
RNA.qc: no visible global function definition for ‘as.dendrogram’
RNA.qc: no visible global function definition for ‘dendrapply’
RNA.qc: no visible global function definition for ‘par’
RNA.qc: no visible global function definition for ‘boxplot’
RNA.qc: no visible global function definition for ‘prcomp’
RNA.qc: no visible global function definition for ‘na.omit’
annova.pvalue: no visible global function definition for ‘aov’
colLab: no visible global function definition for ‘is.leaf’
ks.est: no visible global function definition for ‘ks.test’
ks.pvalue: no visible global function definition for ‘ks.test’
lm.annova.pvalue: no visible global function definition for ‘lm’
lm.annova.pvalue: no visible global function definition for ‘anova’
mwu.est: no visible global function definition for ‘wilcox.test’
mwu.pvalue: no visible global function definition for ‘wilcox.test’
ttest.est: no visible global function definition for ‘t.test’
ttest.pvalue: no visible global function definition for ‘t.test’
Undefined global functions or variables:
  anova aov as.dendrogram bdfunc.enrichment.human
  bdfunc.enrichment.mouse boxplot colors data dendrapply density
  dev.off dist hclust is.leaf ks.test legend lines lm median na.omit
  p.adjust par pdf prcomp quantile read.table slot t.test wilcox.test
  write.table
Consider adding
  importFrom("grDevices", "colors", "dev.off", "pdf")
  importFrom("graphics", "boxplot", "legend", "lines", "par")
  importFrom("methods", "slot")
  importFrom("stats", "anova", "aov", "as.dendrogram", "dendrapply",
             "density", "dist", "hclust", "is.leaf", "ks.test", "lm",
             "median", "na.omit", "p.adjust", "prcomp", "quantile",
             "t.test", "wilcox.test")
  importFrom("utils", "data", "read.table", "write.table")
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 ... WARNING
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                              old_size new_size compress
  bdfunc.enrichment.human.rda    1.3Mb    951Kb    bzip2
  bdfunc.enrichment.mouse.rda     31Kb     26Kb       xz
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
RNA.bdfunc.signal 91.512  0.235  91.886
RNA.deg           14.844  0.185  15.045
RNA.bdfunc.fc     14.256  0.238  15.348
* 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, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/sRAP.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 sRAP
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘sRAP’ ...
** 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 (sRAP)

name	user	system	elapsed
RNA.bdfunc.fc	14.256	0.238	15.348
RNA.bdfunc.signal	91.512	0.235	91.886
RNA.deg	14.844	0.185	15.045
RNA.norm	2.243	0.044	2.286
RNA.prepare.input	0.009	0.016	0.049
RNA.qc	2.238	0.114	2.362