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CHECK report for GSCA on merida1

This page was generated on 2019-04-16 11:57:28 -0400 (Tue, 16 Apr 2019).

Package 690/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GSCA 2.12.0
Zhicheng Ji
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/GSCA
Branch: RELEASE_3_8
Last Commit: dc0593b
Last Changed Date: 2018-10-30 11:41:53 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: GSCA
Version: 2.12.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GSCA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GSCA_2.12.0.tar.gz
StartedAt: 2019-04-16 00:27:09 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 00:30:40 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 211.2 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 --install=check:GSCA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GSCA_2.12.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/GSCA.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘2.12.0’
* 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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
GSCA          100.209  3.638 112.761
GSCAplot       27.335  1.836  29.427
annotatePeaks   6.670  1.166   7.927
ConstructTG     6.809  0.899   7.758
GSCAeda         6.139  0.152   6.345
* 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-3.8-bioc/meat/GSCA.Rcheck/00check.log’
for details.



Installation output

GSCA.Rcheck/00install.out

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL GSCA
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘GSCA’ ...
** R
** data
** inst
** byte-compile and prepare 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
ConstructTG6.8090.8997.758
GSCA100.209 3.638112.761
GSCAeda6.1390.1526.345
GSCAplot27.335 1.83629.427
GSCAui0.0000.0000.001
Oct4ESC_TG0.0010.0010.003
STAT1_TG0.0010.0010.002
annotatePeaks6.6701.1667.927
geneIDdata0.0640.0020.068
tabSearch0.3730.0140.389