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BioC 3.5: CHECK report for GSCA on oaxaca

This page was generated on 2017-03-04 16:46:53 -0500 (Sat, 04 Mar 2017).

Package 580/1339HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GSCA 2.5.0
Zhicheng Ji
Snapshot Date: 2017-03-03 17:15:47 -0500 (Fri, 03 Mar 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GSCA
Last Changed Rev: 122712 / Revision: 127142
Last Changed Date: 2016-10-17 15:10:43 -0400 (Mon, 17 Oct 2016)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK 

Summary

Package: GSCA
Version: 2.5.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GSCA_2.5.0.tar.gz
StartedAt: 2017-03-04 04:08:21 -0800 (Sat, 04 Mar 2017)
EndedAt: 2017-03-04 04:14:17 -0800 (Sat, 04 Mar 2017)
EllapsedTime: 355.3 seconds
RetCode: 0
Status:  OK 
CheckDir: GSCA.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GSCA_2.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/GSCA.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘2.5.0’
* 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          112.580  3.226 120.125
GSCAplot       24.679  1.595  26.364
ConstructTG    24.027  0.092  24.131
annotatePeaks  20.139  1.446  21.592
GSCAeda         5.289  0.093   5.814
* 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-3.5-bioc/meat/GSCA.Rcheck/00check.log’
for details.


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)

GSCA.Rcheck/GSCA-Ex.timings:

nameusersystemelapsed
ConstructTG24.027 0.09224.131
GSCA112.580 3.226120.125
GSCAeda5.2890.0935.814
GSCAplot24.679 1.59526.364
GSCAui000
Oct4ESC_TG0.0020.0010.004
STAT1_TG0.0010.0010.001
annotatePeaks20.139 1.44621.592
geneIDdata0.0630.0080.071
tabSearch0.3820.0300.412