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CHECK report for GSCA on veracruz1

This page was generated on 2018-04-12 13:38:08 -0400 (Thu, 12 Apr 2018).

Package 624/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GSCA 2.8.0
Zhicheng Ji
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/GSCA
Branch: RELEASE_3_6
Last Commit: e6209a4
Last Changed Date: 2017-10-30 12:40:11 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: GSCA
Version: 2.8.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GSCA_2.8.0.tar.gz
StartedAt: 2018-04-12 04:50:54 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 04:54:20 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 205.1 seconds
RetCode: 0
Status:  OK 
CheckDir: GSCA.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GSCA_2.8.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/GSCA.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... 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
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
GSCA          81.464  2.966  86.347
GSCAplot      23.537  1.675  25.712
annotatePeaks 20.551  1.466  22.516
ConstructTG   21.735  0.092  22.097
* 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
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/GSCA.Rcheck/00check.log’
for details.



Installation output

GSCA.Rcheck/00install.out

* installing *source* package ‘GSCA’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GSCA)

Tests output


Example timings

GSCA.Rcheck/GSCA-Ex.timings

nameusersystemelapsed
ConstructTG21.735 0.09222.097
GSCA81.464 2.96686.347
GSCAeda4.6130.1184.828
GSCAplot23.537 1.67525.712
GSCAui0.0010.0000.000
Oct4ESC_TG0.0010.0010.003
STAT1_TG0.0020.0020.004
annotatePeaks20.551 1.46622.516
geneIDdata0.0470.0030.051
tabSearch0.3200.0350.365