BioC 3.4: CHECK report for LowMACA on malbec1

Package: LowMACA

Version: 1.6.0

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings LowMACA_1.6.0.tar.gz

StartedAt: 2017-04-14 23:30:48 -0400 (Fri, 14 Apr 2017)

EndedAt: 2017-04-14 23:40:02 -0400 (Fri, 14 Apr 2017)

EllapsedTime: 554.0 seconds

RetCode: 0

Status:  OK

CheckDir: LowMACA.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings LowMACA_1.6.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/LowMACA.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 ‘LowMACA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘LowMACA’ version ‘1.6.0’
* 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 ‘LowMACA’ 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
.MAD: no visible global function definition for ‘median’
.Trident_Score: no visible global function definition for ‘data’
.alnWeights: no visible global function definition for ‘aggregate’
.clustalOAlign: no visible global function definition for
  ‘download.file’
.clustalOAlign: no visible global function definition for ‘write.table’
.filterMAlign: no visible binding for global variable ‘median’
.makeNullProfile: no visible binding for global variable ‘median’
.makeNullProfile: no visible binding for global variable ‘sd’
.makeNullProfile: no visible global function definition for ‘qgamma’
.makeNullProfile: no visible global function definition for ‘pgamma’
.makeUniformModel: no visible binding for global variable ‘median’
.makeUniformModel : pn.optim.aic : polyOrderChisq: no visible global
  function definition for ‘lm’
.makeUniformModel : pn.optim.aic : polyOrderChisq: no visible global
  function definition for ‘AIC’
.makeUniformModel: no visible global function definition for ‘par’
.makeUniformModel: no visible global function definition for ‘plot’
.makeUniformModel: no visible global function definition for ‘lines’
.profileDensity: no visible global function definition for ‘density’
.profileEntropy: no visible global function definition for ‘pgamma’
.sampleUnifEntropyL: no visible binding for global variable ‘median’
.sampleUnifEntropyL.old: no visible binding for global variable
  ‘median’
.sampleUnifEntropyL.old : <anonymous>: no visible global function
  definition for ‘density’
.scoreMatrix: no visible global function definition for ‘read.table’
.scoreMatrix : <anonymous>: no visible global function definition for
  ‘median’
allPfamAnalysis: no visible global function definition for ‘read.table’
allPfamAnalysis : <anonymous>: no visible global function definition
  for ‘capture.output’
allPfamAnalysis : <anonymous> : <anonymous> : <anonymous>: no visible
  global function definition for ‘pbinom’
showTumorType: no visible global function definition for ‘aggregate’
bpAll,LowMACA: no visible global function definition for
  ‘colorRampPalette’
bpAll,LowMACA: no visible global function definition for ‘barplot’
bpAll,LowMACA: no visible global function definition for ‘legend’
entropy,LowMACA: no visible global function definition for ‘p.adjust’
lfm,LowMACA: no visible global function definition for ‘p.adjust’
lmPlot,LowMACA: no visible global function definition for ‘par’
lmPlot,LowMACA: no visible global function definition for ‘layout’
lmPlot,LowMACA: no visible global function definition for
  ‘colorRampPalette’
lmPlot,LowMACA: no visible global function definition for ‘barplot’
lmPlot,LowMACA: no visible global function definition for ‘axis’
lmPlot,LowMACA: no visible global function definition for ‘plot.new’
lmPlot,LowMACA: no visible global function definition for ‘plot.window’
lmPlot,LowMACA: no visible global function definition for ‘topo.colors’
lmPlot,LowMACA: no visible global function definition for ‘rect’
lmPlot,LowMACA: no visible global function definition for ‘text’
nullProfile,LowMACA: no visible global function definition for
  ‘p.adjust’
nullProfile,LowMACA: no visible global function definition for
  ‘barplot’
nullProfile,LowMACA: no visible global function definition for ‘axis’
nullProfile,LowMACA: no visible global function definition for ‘lines’
nullProfile,LowMACA: no visible global function definition for ‘text’
protter,LowMACA: no visible global function definition for ‘p.adjust’
protter,LowMACA: no visible global function definition for
  ‘download.file’
protter,LowMACA : <anonymous>: no visible global function definition
  for ‘png’
protter,LowMACA : <anonymous>: no visible global function definition
  for ‘par’
protter,LowMACA : <anonymous>: no visible global function definition
  for ‘plot’
protter,LowMACA : <anonymous>: no visible global function definition
  for ‘text’
protter,LowMACA : <anonymous>: no visible global function definition
  for ‘dev.off’
show,LowMACA: no visible global function definition for ‘head’
Undefined global functions or variables:
  AIC aggregate axis barplot capture.output colorRampPalette data
  density dev.off download.file head layout legend lines lm median
  p.adjust par pbinom pgamma plot plot.new plot.window png qgamma
  read.table rect sd text topo.colors write.table
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.off", "png",
             "topo.colors")
  importFrom("graphics", "axis", "barplot", "layout", "legend", "lines",
             "par", "plot", "plot.new", "plot.window", "rect", "text")
  importFrom("stats", "AIC", "aggregate", "density", "lm", "median",
             "p.adjust", "pbinom", "pgamma", "qgamma", "sd")
  importFrom("utils", "capture.output", "data", "download.file", "head",
             "read.table", "write.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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
allPfamAnalysis      150.568  6.664 157.248
lfmSingleSequence     78.264  3.032  81.659
LowMACA-class          9.572  1.444  26.615
LowMACA-package        7.392  1.276  17.755
setup                  6.916  0.716  44.086
lmPlotSingleSequence   4.616  1.240   6.100
lmPlot                 4.136  1.248   5.631
alignSequences         4.828  0.500  17.066
* 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/LowMACA.Rcheck/00check.log’
for details.

* installing *source* package ‘LowMACA’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Checking if clustalo is in the PATH...
Checking clustalo Version...
Checking perl installation...
Checking perl modules XML::Simple and LWP...
* DONE (LowMACA)

name	user	system	elapsed
BLOSUM62	0.008	0.000	0.009
LowMACA-class	9.572	1.444	26.615
LowMACA-package	7.392	1.276	17.755
LowMACA_AML	0.028	0.000	0.029
alignSequences	4.828	0.500	17.066
allPfamAnalysis	150.568	6.664	157.248
bpAll	1.268	0.008	1.279
entropy	1.204	0.004	1.210
getMutations	0.700	0.128	4.482
lfm	1.792	0.044	1.841
lfmSingleSequence	78.264	3.032	81.659
lmAlignment	0.036	0.004	0.038
lmEntropy	1.024	0.000	1.023
lmMutations	0.020	0.008	0.030
lmObj	0.064	0.000	0.065
lmParams	0.528	0.076	0.623
lmPlot	4.136	1.248	5.631
lmPlotSingleSequence	4.616	1.240	6.100
mapMutations	0.492	0.016	0.511
newLowMACA	2.716	0.020	2.742
nullProfile	1.124	0.028	1.149
parallelize	0.500	0.000	0.501
protter	1.044	0.000	3.254
setup	6.916	0.716	44.086
showTumorType	0.080	0.056	0.261