Package: sRAP

Version: 1.18.0

Command: rm -rf sRAP.buildbin-libdir sRAP.Rcheck && mkdir sRAP.buildbin-libdir sRAP.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=sRAP.buildbin-libdir sRAP_1.18.0.tar.gz >sRAP.Rcheck\00install.out 2>&1 && cp sRAP.Rcheck\00install.out sRAP-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=sRAP.buildbin-libdir --install="check:sRAP-install.out" --force-multiarch --no-vignettes --timings sRAP_1.18.0.tar.gz

StartedAt: 2018-04-12 03:23:47 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 03:28:37 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 289.5 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: sRAP.Rcheck

Warnings: 1

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### Running command:
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###   rm -rf sRAP.buildbin-libdir sRAP.Rcheck && mkdir sRAP.buildbin-libdir sRAP.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=sRAP.buildbin-libdir sRAP_1.18.0.tar.gz >sRAP.Rcheck\00install.out 2>&1 && cp sRAP.Rcheck\00install.out sRAP-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=sRAP.buildbin-libdir --install="check:sRAP-install.out" --force-multiarch --no-vignettes --timings sRAP_1.18.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/sRAP.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'sRAP/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'sRAP' version '1.18.0'
* 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 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
* loading checks for arch 'i386'
** 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 loading without being on the library search path ... OK
* loading checks for arch 'x64'
** 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 loading without being on the library search path ... 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
RNA.bdfunc.signal 64.64   0.10   68.20
RNA.bdfunc.fc     10.37   0.03   19.70
RNA.deg            8.54   0.00   13.03
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
RNA.bdfunc.signal 93.12   0.05   97.18
RNA.bdfunc.fc     12.41   0.04   16.31
RNA.deg           12.11   0.06   16.17
* 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
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/sRAP.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'sRAP' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'sRAP'
    finding HTML links ... done
    RNA.bdfunc.fc                           html  
    RNA.bdfunc.signal                       html  
    RNA.deg                                 html  
    RNA.norm                                html  
    RNA.prepare.input                       html  
    RNA.qc                                  html  
    bdfunc.enrichment.human                 html  
    bdfunc.enrichment.mouse                 html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'sRAP' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'sRAP' as sRAP_1.18.0.zip
* DONE (sRAP)
In R CMD INSTALL
In R CMD INSTALL