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CHECK report for NanoStringDiff on malbec2

This page was generated on 2018-10-17 08:27:54 -0400 (Wed, 17 Oct 2018).

Package 978/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
NanoStringDiff 1.10.0
tingting zhai ,hong wang
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/NanoStringDiff
Branch: RELEASE_3_7
Last Commit: baf4179
Last Changed Date: 2018-04-30 10:35:37 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: NanoStringDiff
Version: 1.10.0
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:NanoStringDiff.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings NanoStringDiff_1.10.0.tar.gz
StartedAt: 2018-10-16 02:18:10 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 02:20:10 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 119.8 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: NanoStringDiff.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:NanoStringDiff.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings NanoStringDiff_1.10.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/NanoStringDiff.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.10.0’
* 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 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
PlotsPositiveHousekeeping: no visible global function definition for
  ‘read.table’
PlotsPositiveHousekeeping: no visible global function definition for
  ‘glm’
PlotsPositiveHousekeeping: no visible global function definition for
  ‘poisson’
PlotsPositiveHousekeeping: no visible global function definition for
  ‘rowVars’
PlotsPositiveHousekeeping: no visible global function definition for
  ‘par’
PlotsPositiveHousekeeping: no visible global function definition for
  ‘plot’
PlotsPositiveHousekeeping: no visible global function definition for
  ‘abline’
PlotsPositiveHousekeeping: no visible global function definition for
  ‘lm’
PlotsPositiveHousekeeping: no visible global function definition for
  ‘title’
PlotsPositiveHousekeeping: no visible global function definition for
  ‘textxy’
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 abline glm lm median optim optimize p.adjust par pchisq plot
  poisson read.table rgamma rowVars rpois textxy title
Consider adding
  importFrom("graphics", "abline", "par", "plot", "title")
  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 ... WARNING
Undocumented code objects:
  ‘compute.baseSigma’ ‘est.dispersion’ ‘fun5’ ‘glmfit.OneGroup’
  ‘glmfit.full’ ‘glmfit.reduce’ ‘rnegbinom’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking installed files from ‘inst/doc’ ... NOTE
The following files look like leftovers/mistakes:
  ‘NanoStringDiff.log’
Please remove them from your package.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
          user system elapsed
glm.LRT 91.112  0.084  91.248
* 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 WARNING, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.7-bioc/meat/NanoStringDiff.Rcheck/00check.log’
for details.



Installation output

NanoStringDiff.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL NanoStringDiff
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘NanoStringDiff’ ...
** libs
g++  -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++  -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c fun5.cpp -o fun5.o
g++ -shared -L/home/biocbuild/bbs-3.7-bioc/R/lib -L/usr/local/lib -o NanoStringDiff.so RcppExports.o fun5.o -L/home/biocbuild/bbs-3.7-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.7-bioc/R/library/NanoStringDiff/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (NanoStringDiff)

Tests output

NanoStringDiff.Rcheck/tests/testthat.Rout


R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(NanoStringDiff)
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

> 
> test_check("NanoStringDiff")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 13 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  1.912   0.044   1.954 

Example timings

NanoStringDiff.Rcheck/NanoStringDiff-Ex.timings

nameusersystemelapsed
NanoStringData0.0080.0120.018
NanoStringDataNormalization000
NanoStringDiff-class0.1560.0000.155
NanoStringDiff-package0.0000.0000.001
PlotsPositiveHousekeeping000
estNormalizationFactors0.0120.0000.013
glm.LRT91.112 0.08491.248
housekeepingControl0.0000.0000.003
housekeepingFactor0.0000.0000.003
negativeControl0.0000.0040.002
negativeFactor0.0040.0000.003
positiveControl0.0040.0000.003
positiveFactor0.0040.0000.003