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BioC 3.4: CHECK report for NOISeq on zin1

This page was generated on 2016-09-21 03:38:03 -0700 (Wed, 21 Sep 2016).

Package 821/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
NOISeq 2.17.1
Sonia Tarazona
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/NOISeq
Last Changed Rev: 120528 / Revision: 121152
Last Changed Date: 2016-08-26 13:37:20 -0700 (Fri, 26 Aug 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: NOISeq
Version: 2.17.1
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings NOISeq_2.17.1.tar.gz
StartedAt: 2016-09-20 09:58:36 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 10:00:01 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 85.1 seconds
RetCode: 0
Status:  OK 
CheckDir: NOISeq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings NOISeq_2.17.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/NOISeq.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 ‘NOISeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘NOISeq’ version ‘2.17.1’
* 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 ‘NOISeq’ 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
.calcFactorQuantile : <anonymous>: no visible global function
  definition for ‘quantile’
CV: no visible global function definition for ‘sd’
DE.plot: no visible global function definition for ‘par’
DE.plot: no visible global function definition for ‘plot’
DE.plot: no visible global function definition for ‘points’
DE.plot: no visible global function definition for ‘axis’
DE.plot: no visible global function definition for ‘na.omit’
DE.plot: no visible global function definition for ‘aggregate’
DE.plot: no visible global function definition for ‘abline’
DE.plot: no visible global function definition for ‘rect’
DE.plot: no visible global function definition for ‘segments’
DE.plot: no visible global function definition for ‘text’
DE.plot: no visible global function definition for ‘layout’
DE.plot: no visible global function definition for ‘barplot’
DE.plot: no visible global function definition for ‘legend’
GC.dat: no visible global function definition for ‘quantile’
GC.dat: no visible global function definition for ‘aggregate’
GC.dat: no visible global function definition for ‘lm’
GC.plot: no visible global function definition for ‘par’
GC.plot: no visible global function definition for ‘matplot’
GC.plot: no visible global function definition for ‘text’
GC.plot: no visible global function definition for ‘pf’
GC.plot: no visible global function definition for ‘legend’
GC.plot: no visible global function definition for ‘layout’
MD: no visible global function definition for ‘combn’
MD.plot: no visible global function definition for ‘quantile’
MD.plot: no visible global function definition for ‘plot’
MD.plot: no visible global function definition for ‘points’
MD.plot: no visible global function definition for ‘legend’
MDbio: no visible global function definition for ‘combn’
MDbio: no visible global function definition for ‘quantile’
PCA.plot: no visible global function definition for ‘plot’
PCA.plot: no visible global function definition for ‘colors’
PCA.plot: no visible global function definition for ‘points’
PCA.plot: no visible global function definition for ‘legend’
QCreport: no visible global function definition for ‘pdf’
QCreport: no visible global function definition for ‘layout’
QCreport: no visible global function definition for ‘par’
QCreport: no visible global function definition for ‘plot’
QCreport: no visible global function definition for ‘text’
QCreport: no visible global function definition for ‘abline’
QCreport : <anonymous>: no visible global function definition for ‘pf’
QCreport: no visible global function definition for ‘dev.off’
allMDbio: no visible binding for global variable ‘sd’
biodetection.plot: no visible global function definition for ‘par’
biodetection.plot: no visible global function definition for ‘barplot’
biodetection.plot: no visible global function definition for ‘axis’
biodetection.plot: no visible global function definition for ‘abline’
biodetection.plot: no visible global function definition for ‘legend’
biodetection.plot: no visible global function definition for
  ‘prop.test’
biodetection.plot: no visible global function definition for ‘lines’
cd.dat : <anonymous>: no visible binding for global variable ‘median’
cd.dat: no visible binding for global variable ‘quantile’
cd.plot: no visible binding for global variable ‘density’
cd.plot: no visible global function definition for ‘plot’
cd.plot: no visible global function definition for ‘abline’
cd.plot: no visible global function definition for ‘median’
cd.plot: no visible global function definition for ‘lines’
cd.plot: no visible global function definition for ‘legend’
countsbio.plot: no visible global function definition for ‘par’
countsbio.plot: no visible global function definition for ‘barplot’
countsbio.plot: no visible global function definition for ‘abline’
countsbio.plot: no visible global function definition for ‘mtext’
countsbio.plot: no visible global function definition for ‘legend’
countsbio.plot: no visible global function definition for ‘boxplot’
countsbio.plot: no visible global function definition for ‘axis’
degenes: no visible global function definition for ‘na.omit’
filtered.data : <anonymous>: no visible global function definition for
  ‘wilcox.test’
filtered.data: no visible global function definition for ‘p.adjust’
filtered.data : <anonymous>: no visible global function definition for
  ‘prop.test’
length.dat: no visible global function definition for ‘quantile’
length.dat: no visible global function definition for ‘aggregate’
length.dat: no visible global function definition for ‘lm’
length.plot: no visible global function definition for ‘par’
length.plot: no visible global function definition for ‘matplot’
length.plot: no visible global function definition for ‘text’
length.plot: no visible global function definition for ‘pf’
length.plot: no visible global function definition for ‘legend’
length.plot: no visible global function definition for ‘layout’
noiseqbio: no visible global function definition for ‘density’
noiseqbio: no visible global function definition for ‘approxfun’
noiseqbio: no visible global function definition for ‘lines’
noiseqbio: no visible global function definition for ‘legend’
plot.y2: no visible global function definition for ‘plot’
plot.y2: no visible global function definition for ‘axis’
plot.y2: no visible global function definition for ‘points’
plot.y2: no visible global function definition for ‘lines’
plot.y2: no visible global function definition for ‘supsmu’
plot.y2: no visible global function definition for ‘mtext’
plot.y2: no visible global function definition for ‘par’
plot.y2: no visible global function definition for ‘box’
probdeg: no visible global function definition for ‘na.omit’
rpkm: no visible global function definition for ‘na.omit’
saturation.dat: no visible global function definition for ‘rmultinom’
saturation.plot: no visible global function definition for ‘par’
saturation.plot: no visible global function definition for ‘colors’
saturation.plot: no visible global function definition for ‘plot’
saturation.plot: no visible global function definition for ‘lines’
saturation.plot: no visible global function definition for ‘points’
saturation.plot: no visible global function definition for ‘na.omit’
saturation.plot: no visible global function definition for ‘layout’
saturation.plot: no visible global function definition for ‘rect’
saturation.plot: no visible global function definition for ‘text’
share.info: no visible global function definition for ‘kmeans’
share.info : <anonymous>: no visible global function definition for
  ‘sd’
share.info: no visible global function definition for ‘quantile’
sim.samples: no visible global function definition for ‘runif’
sim.samples: no visible global function definition for ‘rmultinom’
tmm: no visible global function definition for ‘na.omit’
uqua: no visible binding for global variable ‘quantile’
uqua: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  abline aggregate approxfun axis barplot box boxplot colors combn
  density dev.off kmeans layout legend lines lm matplot median mtext
  na.omit p.adjust par pdf pf plot points prop.test quantile rect
  rmultinom runif sd segments supsmu text wilcox.test
Consider adding
  importFrom("grDevices", "colors", "dev.off", "pdf")
  importFrom("graphics", "abline", "axis", "barplot", "box", "boxplot",
             "layout", "legend", "lines", "matplot", "mtext", "par",
             "plot", "points", "rect", "segments", "text")
  importFrom("stats", "aggregate", "approxfun", "density", "kmeans",
             "lm", "median", "na.omit", "p.adjust", "pf", "prop.test",
             "quantile", "rmultinom", "runif", "sd", "supsmu",
             "wilcox.test")
  importFrom("utils", "combn")
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
noiseq    15.012  0.016  15.030
noiseqbio 11.192  0.016  11.222
QCreport   6.304  0.024   6.327
* 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/NOISeq.Rcheck/00check.log’
for details.


NOISeq.Rcheck/00install.out:

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

NOISeq.Rcheck/NOISeq-Ex.timings:

nameusersystemelapsed
ARSyNSeq2.4440.0282.471
DE.plot0.2320.0080.240
PCA.GENES0.0080.0000.008
QCreport6.3040.0246.327
dat0.1400.0200.159
dat2save0.1120.0000.111
degenes0.0600.0040.062
explo.plot0.1360.0200.157
filter.low.counts0.5280.0000.525
noiseq15.012 0.01615.030
noiseqbio11.192 0.01611.222
normalization0.0040.0040.007
readData0.1160.0000.118