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BioC 3.4: CHECK report for affyILM on malbec1

This page was generated on 2017-04-15 16:10:07 -0400 (Sat, 15 Apr 2017).

Package 22/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
affyILM 1.26.0
Myriam Kroll and Fabrice Berger
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/affyILM
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
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
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: affyILM
Version: 1.26.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings affyILM_1.26.0.tar.gz
StartedAt: 2017-04-14 20:52:15 -0400 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 20:54:11 -0400 (Fri, 14 Apr 2017)
EllapsedTime: 116.2 seconds
RetCode: 0
Status:  OK 
CheckDir: affyILM.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings affyILM_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/affyILM.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘affyILM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘affyILM’ version ‘1.26.0’
* 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 ‘affyILM’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Non-standard license specification:
  GPL version 3
Standardizable: TRUE
Standardized license specification:
  GPL-3
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’
A package should be listed in only one of these fields.
* 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
Package in Depends field not imported from: ‘gcrma’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.affyILM_scale: no visible binding for global variable ‘median’
.affyILM_scale: no visible binding for global variable ‘mad’
.affyILM_scale: no visible global function definition for ‘median’
.getChipInfo: no visible global function definition for
  ‘getProbePackage’
.summarizeConcs: no visible binding for global variable ‘mad’
.summarizeConcs: no visible binding for global variable ‘median’
.summarizeMedpolish: no visible global function definition for
  ‘medpolish’
.summarizeTrMedpolish: no visible global function definition for
  ‘medpolish’
ilm: no visible global function definition for ‘getProbePackage’
plotILM,ILM: no visible global function definition for ‘median’
plotILM,ILM: no visible global function definition for ‘mad’
Undefined global functions or variables:
  getProbePackage mad median medpolish
Consider adding
  importFrom("stats", "mad", "median", "medpolish")
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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
ilm-methods 12.648  0.716  16.693
* 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
  ‘/home/biocbuild/bbs-3.4-bioc/meat/affyILM.Rcheck/00check.log’
for details.


affyILM.Rcheck/00install.out:

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

affyILM.Rcheck/affyILM-Ex.timings:

nameusersystemelapsed
ILM-class0.0000.0040.001
ilm-methods12.648 0.71616.693
ilm4.1160.0004.153
plotILM2.2240.0082.234
plotIntens1.9880.0001.988