Package: ampliQueso

Version: 1.16.0

Command: rm -rf ampliQueso.buildbin-libdir ampliQueso.Rcheck && mkdir ampliQueso.buildbin-libdir ampliQueso.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ampliQueso.buildbin-libdir ampliQueso_1.16.0.tar.gz >ampliQueso.Rcheck\00install.out 2>&1 && cp ampliQueso.Rcheck\00install.out ampliQueso-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=ampliQueso.buildbin-libdir --install="check:ampliQueso-install.out" --force-multiarch --no-vignettes --timings ampliQueso_1.16.0.tar.gz

StartedAt: 2018-04-11 22:10:52 -0400 (Wed, 11 Apr 2018)

EndedAt: 2018-04-11 22:16:36 -0400 (Wed, 11 Apr 2018)

EllapsedTime: 343.8 seconds

RetCode: 0

Status:  OK

CheckDir: ampliQueso.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf ampliQueso.buildbin-libdir ampliQueso.Rcheck && mkdir ampliQueso.buildbin-libdir ampliQueso.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ampliQueso.buildbin-libdir ampliQueso_1.16.0.tar.gz >ampliQueso.Rcheck\00install.out 2>&1 && cp ampliQueso.Rcheck\00install.out ampliQueso-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=ampliQueso.buildbin-libdir --install="check:ampliQueso-install.out" --force-multiarch --no-vignettes --timings ampliQueso_1.16.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/ampliQueso.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 'ampliQueso/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ampliQueso' version '1.16.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'rnaSeqMap' 'knitr' 'rgl' 'ggplot2' 'gplots' 'parallel' 'doParallel'
  'foreach' 'VariantAnnotation' 'genefilter' 'statmod' 'xtable'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'ampliQueso' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... NOTE
Namespace in Imports field not imported from: 'samr'
  All declared Imports should be used.
Packages in Depends field not imported from:
  'VariantAnnotation' 'doParallel' 'foreach' 'genefilter' 'ggplot2'
  'gplots' 'knitr' 'parallel' 'rgl' 'statmod' 'xtable'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' call which should be '::': 'rnaSeqMap:::newSeqReads'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.callCamelTestReg: no visible global function definition for 'permp'
.callSamPileup: no visible global function definition for 'hasArg'
.callSamPileup: no visible global function definition for 'readVcf'
.callSamPileup: no visible global function definition for 'seqnames'
.callSamPileup: no visible global function definition for 'start'
.callSamPileup: no visible global function definition for 'ranges'
.callSamPileup: no visible global function definition for 'end'
.callSamPileup: no visible global function definition for 'width'
.callSamPileup: no visible global function definition for 'ref'
.callSamPileup: no visible global function definition for 'strand'
.callSamPileup: no visible global function definition for 'qual'
.camelTest: no visible global function definition for 'read.table'
.camelTest: no visible binding for global variable 'str'
.camelTest: no visible global function definition for 'permp'
.camelTestParReg: no visible global function definition for
  'read.table'
.camelTestParReg: no visible global function definition for
  'makeCluster'
.camelTestParReg: no visible global function definition for
  'detectCores'
.camelTestParReg: no visible global function definition for
  'registerDoParallel'
.camelTestParReg: no visible global function definition for '%dopar%'
.camelTestParReg: no visible global function definition for 'foreach'
.camelTestParReg: no visible global function definition for
  'stopCluster'
.compareCoveragesRegApply: no visible global function definition for
  'read.table'
.compareCoveragesRegParM: no visible global function definition for
  'read.table'
.compareCoveragesRegParM: no visible global function definition for
  'makeCluster'
.compareCoveragesRegParM: no visible global function definition for
  'detectCores'
.compareCoveragesRegParM: no visible global function definition for
  'registerDoParallel'
.compareCoveragesRegParM: no visible global function definition for
  '%dopar%'
.compareCoveragesRegParM: no visible global function definition for
  'foreach'
.compareCoveragesRegParM: no visible global function definition for
  'stopCluster'
.compareCoveragesRegParR: no visible global function definition for
  'read.table'
.compareCoveragesRegParR: no visible global function definition for
  'makeCluster'
.compareCoveragesRegParR: no visible global function definition for
  'detectCores'
.compareCoveragesRegParR: no visible global function definition for
  'registerDoParallel'
.compareCoveragesRegParR: no visible global function definition for
  '%dopar%'
.compareCoveragesRegParR: no visible global function definition for
  'foreach'
.compareCoveragesRegParR: no visible global function definition for
  'stopCluster'
.compareCoveragesRegSeq: no visible global function definition for
  'read.table'
.getSNP: no visible global function definition for 'read.table'
.getSNP: no visible global function definition for 'hasArg'
.getSNP: no visible global function definition for 'readVcf'
.getSNP: no visible global function definition for 'seqnames'
.getSNP: no visible global function definition for 'start'
.getSNP: no visible global function definition for 'ranges'
.getSNP: no visible global function definition for 'end'
.getSNP: no visible global function definition for 'width'
.getSNP: no visible global function definition for 'ref'
.getSNP: no visible global function definition for 'strand'
.getSNP: no visible global function definition for 'qual'
.getSNPPar: no visible global function definition for 'makeCluster'
.getSNPPar: no visible global function definition for 'detectCores'
.getSNPPar: no visible global function definition for
  'registerDoParallel'
.getSNPPar: no visible global function definition for 'read.table'
.getSNPPar: no visible global function definition for '%dopar%'
.getSNPPar: no visible global function definition for 'foreach'
.getSNPPar: no visible global function definition for 'stopCluster'
.perm.samples: no visible global function definition for 'combn'
compareCoverages: no visible global function definition for
  'read.table'
getCountTable: no visible global function definition for 'read.table'
runAQReport: no visible global function definition for 'read.table'
runAQReport: no visible global function definition for 'rowttests'
runAQReport: no visible global function definition for 'p.adjust'
runAQReport: no visible global function definition for '%do%'
runAQReport: no visible global function definition for 'foreach'
runAQReport: no visible global function definition for 'aggregate'
runAQReport: no visible global function definition for 'knit'
Undefined global functions or variables:
  %do% %dopar% aggregate combn detectCores end foreach hasArg knit
  makeCluster p.adjust permp qual ranges read.table readVcf ref
  registerDoParallel rowttests seqnames start stopCluster str strand
  width
Consider adding
  importFrom("methods", "hasArg")
  importFrom("stats", "aggregate", "end", "p.adjust", "start")
  importFrom("utils", "combn", "read.table", "str")
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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: 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/ampliQueso.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'ampliQueso' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'ampliQueso'
    finding HTML links ... done
    camelSampleTable                        html  
    camelTest                               html  
    compareCoverages                        html  
    compareCoveragesReg                     html  
    getCountTable                           html  
    getSNP                                  html  
    ndMax                                   html  
    ndMin                                   html  
    runAQReport                             html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'ampliQueso' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ampliQueso' as ampliQueso_1.16.0.zip
* DONE (ampliQueso)
In R CMD INSTALL
In R CMD INSTALL