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BioC 3.5: CHECK report for Category on oaxaca

This page was generated on 2017-03-04 16:34:24 -0500 (Sat, 04 Mar 2017).

Package 165/1339HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Category 2.41.0
Bioconductor Package Maintainer
Snapshot Date: 2017-03-03 17:15:47 -0500 (Fri, 03 Mar 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Category
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  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK 

Summary

Package: Category
Version: 2.41.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Category_2.41.0.tar.gz
StartedAt: 2017-03-04 00:07:43 -0800 (Sat, 04 Mar 2017)
EndedAt: 2017-03-04 00:10:57 -0800 (Sat, 04 Mar 2017)
EllapsedTime: 194.2 seconds
RetCode: 0
Status:  OK 
CheckDir: Category.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Category_2.41.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/Category.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 ‘Category/DESCRIPTION’ ... OK
* this is package ‘Category’ version ‘2.41.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ‘Category’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.linearMTestInternal: no visible global function definition for
  ‘setNames’
Undefined global functions or variables:
  setNames
Consider adding
  importFrom("stats", "setNames")
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 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
ChrBandTree-class 4.884  0.173   5.113
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/Category.Rcheck/00check.log’
for details.


Category.Rcheck/00install.out:

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

Category.Rcheck/Category-Ex.timings:

nameusersystemelapsed
ChrBandTree-class4.8840.1735.113
ChrMapHyperGParams-class0.0020.0000.001
ChrMapHyperGResult-class0.0000.0000.001
ChrMapLinearMParams-class0.0010.0010.001
ChrMapLinearMResult-class0.0010.0000.001
DatPkg-class0.0390.0010.040
HyperGResult-accessors1.0010.0501.310
LinearMResult-class0.0010.0000.001
MAPAmat3.0800.1603.242
applyByCategory0.0030.0010.004
cateGOryMatrix0.2980.0481.003
cb_parse_band_Hs000
cb_parse_band_Mm0.0010.0000.001
findAMstats0.0010.0000.001
getPathNames0.0410.0010.043
gseattperm1.0920.0381.286
hyperg0.5020.0540.556
makeChrBandGraph2.0560.0492.106
makeEBcontr0.1250.0030.184
probes2MAP0.1600.0030.163
probes2Path0.0480.0010.049
ttperm0.0160.0010.016