Package: GSCA

Version: 2.8.0

Command: rm -rf GSCA.buildbin-libdir GSCA.Rcheck && mkdir GSCA.buildbin-libdir GSCA.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GSCA.buildbin-libdir GSCA_2.8.0.tar.gz >GSCA.Rcheck\00install.out 2>&1 && cp GSCA.Rcheck\00install.out GSCA-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=GSCA.buildbin-libdir --install="check:GSCA-install.out" --force-multiarch --no-vignettes --timings GSCA_2.8.0.tar.gz

StartedAt: 2018-04-12 00:35:36 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 00:42:17 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 401.8 seconds

RetCode: 0

Status:  OK

CheckDir: GSCA.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf GSCA.buildbin-libdir GSCA.Rcheck && mkdir GSCA.buildbin-libdir GSCA.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GSCA.buildbin-libdir GSCA_2.8.0.tar.gz >GSCA.Rcheck\00install.out 2>&1 && cp GSCA.Rcheck\00install.out GSCA-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=GSCA.buildbin-libdir --install="check:GSCA-install.out" --force-multiarch --no-vignettes --timings GSCA_2.8.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/GSCA.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 'GSCA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GSCA' version '2.8.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'shiny' 'sp' 'gplots' 'ggplot2' 'reshape2' 'RColorBrewer' 'rhdf5'
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 'GSCA' 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 ... NOTE
'library' or 'require' calls in package code:
  'Affyhgu133A2Expr' 'Affyhgu133Plus2Expr' 'Affyhgu133aExpr'
  'Affymoe4302Expr'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
GSCA: no visible global function definition for 'data'
GSCA: no visible binding for global variable 'Affyhgu133aExprtab'
GSCA: no visible binding for global variable 'Affymoe4302Exprtab'
GSCA: no visible binding for global variable 'Affyhgu133A2Exprtab'
GSCA: no visible binding for global variable 'Affyhgu133Plus2Exprtab'
GSCA: no visible binding for global variable 'geneid'
GSCA: no visible global function definition for 'qnorm'
GSCA: no visible global function definition for 'sd'
GSCA: no visible global function definition for 'quantile'
GSCA: no visible global function definition for 'fisher.test'
GSCAeda: no visible global function definition for 'data'
GSCAeda: no visible binding for global variable 'Affyhgu133aExprtab'
GSCAeda: no visible binding for global variable 'Affymoe4302Exprtab'
GSCAeda: no visible binding for global variable 'Affyhgu133A2Exprtab'
GSCAeda: no visible binding for global variable
  'Affyhgu133Plus2Exprtab'
GSCAeda: no visible binding for global variable 'geneid'
GSCAeda: no visible global function definition for 'qnorm'
GSCAeda: no visible global function definition for 'sd'
GSCAeda: no visible global function definition for 'quantile'
GSCAeda: no visible global function definition for 'pdf'
GSCAeda: no visible global function definition for 'str'
GSCAeda: no visible binding for global variable 'variable'
GSCAeda: no visible binding for global variable 'value'
GSCAeda: no visible binding for global variable 'SampleType'
GSCAeda: no visible global function definition for 'par'
GSCAeda: no visible global function definition for 'colorRampPalette'
GSCAeda: no visible global function definition for 't.test'
GSCAeda: no visible binding for global variable 'Var1'
GSCAeda: no visible binding for global variable 'Var2'
GSCAeda: no visible binding for global variable 't.stat'
GSCAeda: no visible binding for global variable 'P.value'
GSCAeda: no visible global function definition for 'fisher.test'
GSCAeda: no visible global function definition for 'dev.off'
GSCAeda: no visible global function definition for 'write.csv'
GSCAeda: no visible global function definition for 'write.table'
GSCAplot: no visible global function definition for 'data'
GSCAplot: no visible binding for global variable 'Affyhgu133aExprtab'
GSCAplot: no visible binding for global variable 'Affymoe4302Exprtab'
GSCAplot: no visible binding for global variable 'Affyhgu133A2Exprtab'
GSCAplot: no visible binding for global variable
  'Affyhgu133Plus2Exprtab'
GSCAplot: no visible global function definition for 'pdf'
GSCAplot: no visible global function definition for 'par'
GSCAplot: no visible global function definition for 'hist'
GSCAplot: no visible global function definition for 'title'
GSCAplot: no visible global function definition for 'dev.off'
annotatePeaks: no visible binding for global variable 'allreffile'
tabSearch: no visible global function definition for 'data'
tabSearch: no visible binding for global variable 'Affyhgu133aExprtab'
tabSearch: no visible binding for global variable 'Affymoe4302Exprtab'
tabSearch: no visible binding for global variable 'Affyhgu133A2Exprtab'
tabSearch: no visible binding for global variable
  'Affyhgu133Plus2Exprtab'
Undefined global functions or variables:
  Affyhgu133A2Exprtab Affyhgu133Plus2Exprtab Affyhgu133aExprtab
  Affymoe4302Exprtab P.value SampleType Var1 Var2 allreffile
  colorRampPalette data dev.off fisher.test geneid hist par pdf qnorm
  quantile sd str t.stat t.test title value variable write.csv
  write.table
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.off", "pdf")
  importFrom("graphics", "hist", "par", "title")
  importFrom("stats", "fisher.test", "qnorm", "quantile", "sd", "t.test")
  importFrom("utils", "data", "str", "write.csv", "write.table")
to your NAMESPACE file.
* 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
Examples with CPU or elapsed time > 5s
               user system elapsed
GSCA          79.84   3.32   97.38
ConstructTG   31.36   0.04   31.40
annotatePeaks 27.50   0.20   27.70
GSCAplot      18.21   1.06   19.63
GSCAeda        4.04   0.06   13.30
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
GSCA          78.31   3.72   82.17
ConstructTG   25.46   0.01   25.47
annotatePeaks 23.10   0.22   23.32
GSCAplot      19.78   1.01   20.80
* 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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/GSCA.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'GSCA' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'GSCA'
    finding HTML links ... done
    ConstructTG                             html  
    GSCA-package                            html  
    GSCA                                    html  
    GSCAeda                                 html  
    GSCAplot                                html  
    GSCAui                                  html  
    Oct4ESC_TG                              html  
    STAT1_TG                                html  
    annotatePeaks                           html  
    geneIDdata                              html  
    tabSearch                               html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'GSCA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GSCA' as GSCA_2.8.0.zip
* DONE (GSCA)
In R CMD INSTALL
In R CMD INSTALL