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BioC 3.2: CHECK report for Rnits on zin1

This page was generated on 2016-04-23 10:14:04 -0700 (Sat, 23 Apr 2016).

Package 901/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rnits 1.4.0
Dipen P. Sangurdekar
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/Rnits
Last Changed Rev: 109589 / Revision: 116712
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  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 UNNEEDED, same version exists in internal repository

Summary

Package: Rnits
Version: 1.4.0
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings Rnits_1.4.0.tar.gz
StartedAt: 2016-04-23 04:57:43 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 04:58:31 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 48.1 seconds
RetCode: 0
Status:  OK 
CheckDir: Rnits.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings Rnits_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/Rnits.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rnits/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Rnits’ version ‘1.4.0’
* 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 ‘Rnits’ can be installed ... [3s/3s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plotResults,Rnits: no visible global function definition for ‘aes’
plotResults,Rnits: no visible binding for global variable ‘Time’
plotResults,Rnits: no visible binding for global variable ‘value’
plotResults,Rnits: no visible global function definition for
  ‘geom_point’
plotResults,Rnits: no visible binding for global variable ‘Sample’
plotResults,Rnits: no visible global function definition for
  ‘geom_smooth’
plotResults,Rnits: no visible global function definition for ‘ylab’
plotResults,Rnits: no visible global function definition for ‘theme_bw’
plotResults,Rnits: no visible global function definition for ‘theme’
plotResults,Rnits: no visible global function definition for
  ‘scale_color_brewer’
plotResults,Rnits: no visible global function definition for
  ‘facet_wrap’
* 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 ... [13s/13s] 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.2-bioc/meat/Rnits.Rcheck/00check.log’
for details.


Rnits.Rcheck/00install.out:

* installing *source* package ‘Rnits’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Creating a generic function for ‘summary’ from package ‘base’ in package ‘Rnits’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Rnits)

Rnits.Rcheck/Rnits-Ex.timings:

nameusersystemelapsed
build.Rnits0.5310.0160.546
calculateGCV-methods4.9120.0274.942
fit-methods0.3020.0000.302
getCID-methods0.3550.0000.354
getFitModel-methods0.3490.0040.354
getLR-methods0.3090.0000.309
getPval-methods0.360.000.36
getStat-methods0.3630.0040.367
plotResults-methods0.3660.0000.366
summarizeProbes-methods0.3670.0000.367
summary-methods0.3650.0040.369
timeAlign-methods2.3950.0042.400
topData-methods0.3460.0000.345