BioC 3.5: CHECK report for LowMACA on oaxaca

Package: LowMACA

Version: 1.7.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings LowMACA_1.7.0.tar.gz

StartedAt: 2017-03-04 05:00:58 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 05:15:06 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 847.4 seconds

RetCode: 0

Status:  OK

CheckDir: LowMACA.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings LowMACA_1.7.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/LowMACA.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.7.0’
* 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 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
allPfamAnalysis      148.676  3.843 152.913
lfmSingleSequence     81.321  2.179  83.595
LowMACA-class         11.375  0.841  91.326
LowMACA-package        9.578  0.649  54.216
setup                  6.975  0.328 180.697
lmPlotSingleSequence   5.285  0.496   5.906
lmPlot                 5.177  0.561   5.856
alignSequences         4.742  0.209  20.371
getMutations           0.798  0.055  23.336
* 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
  ‘/Users/biocbuild/bbs-3.5-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	0.007	0.002	0.009
LowMACA-class	11.375	0.841	91.326
LowMACA-package	9.578	0.649	54.216
LowMACA_AML	0.025	0.006	0.031
alignSequences	4.742	0.209	20.371
allPfamAnalysis	148.676	3.843	152.913
bpAll	1.181	0.050	1.232
entropy	0.965	0.038	1.004
getMutations	0.798	0.055	23.336
lfm	1.950	0.056	2.006
lfmSingleSequence	81.321	2.179	83.595
lmAlignment	0.061	0.008	0.069
lmEntropy	1.226	0.052	1.278
lmMutations	0.036	0.005	0.042
lmObj	0.130	0.009	0.138
lmParams	0.656	0.022	0.681
lmPlot	5.177	0.561	5.856
lmPlotSingleSequence	5.285	0.496	5.906
mapMutations	0.516	0.013	0.530
newLowMACA	2.793	0.072	2.865
nullProfile	1.341	0.051	1.394
parallelize	0.689	0.020	0.709
protter	1.203	0.045	3.766
setup	6.975	0.328	180.697
showTumorType	0.046	0.008	0.821