CHECK report for NOISeq on malbec1
This page was generated on 2018-04-12 13:10:42 -0400 (Thu, 12 Apr 2018).
NOISeq 2.22.1
Sonia Tarazona
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/NOISeq |
| Branch: RELEASE_3_6 |
| Last Commit: 14fa533 |
| Last Changed Date: 2018-02-08 09:24:09 -0400 (Thu, 08 Feb 2018) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ WARNINGS ] | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
Summary
Command output
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### Running command:
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### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings NOISeq_2.22.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/NOISeq.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘2.22.1’
* 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 ... WARNING
Invalid citation information in ‘inst/CITATION’:
Error in bibentry(bibtype = entry, textVersion = textVersion, header = header, footer = footer, ...): object 'e140' not found
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
noiseqbio 13.664 0.012 13.684
noiseq 13.412 0.024 13.442
QCreport 6.376 0.028 6.409
* 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, 1 NOTE
See
‘/home/biocbuild/bbs-3.6-bioc/meat/NOISeq.Rcheck/00check.log’
for details.
Installation output
NOISeq.Rcheck/00install.out
Tests output
Example timings
NOISeq.Rcheck/NOISeq-Ex.timings