Package: manta

Version: 1.28.1

Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:manta.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings manta_1.28.1.tar.gz

StartedAt: 2019-04-13 03:29:53 -0400 (Sat, 13 Apr 2019)

EndedAt: 2019-04-13 03:32:47 -0400 (Sat, 13 Apr 2019)

EllapsedTime: 174.2 seconds

RetCode: 0

Status:  OK

CheckDir: manta.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:manta.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings manta_1.28.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/manta.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'manta/DESCRIPTION' ... OK
* this is package 'manta' version '1.28.1'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 'manta' 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 ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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
* 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 dependencies in R code ... NOTE
'library' or 'require' calls in package code:
  'RSQLite' 'plotrix'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  '.meta2metasum'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.MTDheatplot: no visible global function definition for 'gray'
.MTDheatplot: no visible global function definition for
  'colorRampPalette'
.MTDheatplot: no visible global function definition for 'abline'
.MTDheatplot: no visible global function definition for 'segments'
.MTDheatplot: no visible global function definition for 'par'
.MTDheatplot: no visible global function definition for 'plot'
.aggBinCounts: no visible global function definition for 'hist'
.aggDESigCumDist: no visible global function definition for 'hist'
.as.DGEList: no visible global function definition for 'new'
.as.manta: no visible global function definition for 'new'
.as.manta: no visible binding for global variable 'samples'
.as.manta: no visible binding for global variable 'counts'
.calcTMMvar: no visible binding for global variable 'x'
.checkMetaLev: no visible binding for global variable 'meta.sum'
.meta2metasum: no visible global function definition for 'aggregate'
.normalize: no visible global function definition for 'var'
.normalize: no visible global function definition for 'calcNormFactors'
.wtd.var: no visible global function definition for 'var'
compbiasPlot: no visible global function definition for 'rainbow'
compbiasPlot: no visible binding for global variable 'RAy'
compbiasPlot: no visible global function definition for 'plot'
compbiasPlot : <anonymous>: no visible global function definition for
  'hist'
compbiasPlot: no visible binding for global variable 'legend'
compbiasPlot: no visible global function definition for 'legend'
compbiasPlot: no visible global function definition for 'boxplot'
compbiasPlot: no visible global function definition for 'violins'
compbiasTest: no visible global function definition for 'anova'
compbiasTest: no visible global function definition for 'lm'
counts2manta: no visible binding for global variable 'agg'
manta: no visible global function definition for 'new'
manta: no visible global function definition for 'calcNormFactors'
manta: no visible global function definition for 'estimateCommonDisp'
manta.ra: no visible global function definition for 'par'
manta.ra: no visible global function definition for 'legend'
manta.ra: no visible global function definition for 'gray'
nf2nr: no visible global function definition for 'calcNormFactors'
nr: no visible binding for global variable 'x'
nr: no visible global function definition for 'calcNormFactors'
outGenes: no visible global function definition for 'p.adjust'
outGenes: no visible binding for global variable 'PValue'
outGenes: no visible binding for global variable 'R'
plot.manta: no visible global function definition for 'par'
plot.manta: no visible global function definition for 'legend'
plot.manta: no visible global function definition for 'gray'
pplacer2manta: no visible global function definition for 'dbDriver'
pplacer2manta: no visible global function definition for 'dbConnect'
pplacer2manta: no visible global function definition for 'dbReadTable'
pplacer2manta: no visible global function definition for 'dbDisconnect'
pplacer2manta: no visible global function definition for 'dbGetQuery'
readSeastar: no visible global function definition for 'read.delim'
Undefined global functions or variables:
  PValue R RAy abline agg aggregate anova boxplot calcNormFactors
  colorRampPalette counts dbConnect dbDisconnect dbDriver dbGetQuery
  dbReadTable estimateCommonDisp gray hist legend lm meta.sum new
  p.adjust par plot rainbow read.delim samples segments var violins x
Consider adding
  importFrom("grDevices", "colorRampPalette", "gray", "rainbow")
  importFrom("graphics", "abline", "boxplot", "hist", "legend", "par",
             "plot", "segments")
  importFrom("methods", "new")
  importFrom("stats", "aggregate", "anova", "lm", "p.adjust", "var")
  importFrom("utils", "read.delim")
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 ... NOTE
S3 methods shown with full name in documentation object 'summary.manta':
  'summary.manta'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
          user system elapsed
in2manta 10.46      0   10.78
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
          user system elapsed
in2manta 12.02   0.03   12.05
* 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: 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/manta.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/manta_1.28.1.tar.gz && rm -rf manta.buildbin-libdir && mkdir manta.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=manta.buildbin-libdir manta_1.28.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL manta_1.28.1.zip && rm manta_1.28.1.tar.gz manta_1.28.1.zip
###
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install for i386

* installing *source* package 'manta' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'manta'
    finding HTML links ... done
    cmdArgsToVariables                      html  
    collapseRepliCounts                     html  
    compbiasPlot                            html  
    compbiasTest                            html  
    generateWeights                         html  
    in2manta                                html  
    makeSampleDF                            html  
    manta-class                             html  
    manta                                   html  
    meta2counts                             html  
    metataxa2subcounts                      html  
    nf2nr                                   html  
    normfact2absTMM                         html  
    nr                                      html  
    outliers                                html  
    plot.manta                              html  
    pplacer2manta                           html  
    readSeastar                             html  
    seastar2counts                          html  
    summary.manta                           html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'manta' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'manta' as manta_1.28.1.zip
* DONE (manta)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'manta' successfully unpacked and MD5 sums checked
In R CMD INSTALL