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BioC 3.4: CHECK report for NanoStringDiff on zin1

This page was generated on 2016-09-21 03:40:06 -0700 (Wed, 21 Sep 2016).

Package 804/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
NanoStringDiff 1.3.0
hong wang
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/NanoStringDiff
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 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
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: NanoStringDiff
Version: 1.3.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings NanoStringDiff_1.3.0.tar.gz
StartedAt: 2016-09-20 09:50:20 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 09:53:23 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 182.6 seconds
RetCode: 0
Status:  OK 
CheckDir: NanoStringDiff.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings NanoStringDiff_1.3.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/NanoStringDiff.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘NanoStringDiff/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘NanoStringDiff’ version ‘1.3.0’
* 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 ‘NanoStringDiff’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
compute.baseSigma: no visible global function definition for ‘IQR’
createNanoStringSetFromCsv: no visible global function definition for
  ‘read.table’
est.dispersion : get.phihat: no visible global function definition for
  ‘optimize’
estNormalizationFactors: no visible global function definition for
  ‘glm’
estNormalizationFactors: no visible global function definition for
  ‘poisson’
estNormalizationFactors: no visible binding for global variable
  ‘median’
glm.LRT: no visible global function definition for ‘pchisq’
glm.LRT: no visible global function definition for ‘p.adjust’
glmfit.OneGroup : get.mu: no visible global function definition for
  ‘optimize’
glmfit.full: no visible global function definition for ‘lm’
glmfit.full: no visible global function definition for ‘median’
glmfit.full: no visible global function definition for ‘IQR’
glmfit.full : get.phi: no visible global function definition for
  ‘optimize’
glmfit.full : get.beta.full: no visible global function definition for
  ‘optim’
glmfit.reduce: no visible global function definition for ‘lm’
glmfit.reduce : get.beta.reduce: no visible global function definition
  for ‘optim’
rnegbinom: no visible global function definition for ‘rpois’
rnegbinom: no visible global function definition for ‘rgamma’
Undefined global functions or variables:
  IQR glm lm median optim optimize p.adjust pchisq poisson read.table
  rgamma rpois
Consider adding
  importFrom("stats", "IQR", "glm", "lm", "median", "optim", "optimize",
             "p.adjust", "pchisq", "poisson", "rgamma", "rpois")
  importFrom("utils", "read.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
glm.LRT 155.884  0.104 155.999
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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
  ‘/home/biocbuild/bbs-3.4-bioc/meat/NanoStringDiff.Rcheck/00check.log’
for details.


NanoStringDiff.Rcheck/00install.out:

* installing *source* package ‘NanoStringDiff’ ...
** 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 (NanoStringDiff)

NanoStringDiff.Rcheck/NanoStringDiff-Ex.timings:

nameusersystemelapsed
NanoStringData0.0200.0000.021
NanoStringDiff-class0.1280.0040.129
estNormalizationFactors0.0080.0040.014
glm.LRT155.884 0.104155.999
housekeepingControl0.0040.0000.003
housekeepingFactor0.0040.0000.003
negativeControl0.0040.0000.003
negativeFactor0.0040.0000.002
positiveControl0.0040.0000.003
positiveFactor0.0000.0000.003