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BioC 3.3: CHECK report for LowMACA on morelia

This page was generated on 2016-04-21 13:26:26 -0700 (Thu, 21 Apr 2016).

Package 637/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
LowMACA 1.3.2
Stefano de Pretis , Giorgio Melloni
Snapshot Date: 2016-04-20 17:20:35 -0700 (Wed, 20 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/LowMACA
Last Changed Rev: 116542 / Revision: 116626
Last Changed Date: 2016-04-19 03:33:49 -0700 (Tue, 19 Apr 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  ERROR  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: LowMACA
Version: 1.3.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings LowMACA_1.3.2.tar.gz
StartedAt: 2016-04-21 04:26:17 -0700 (Thu, 21 Apr 2016)
EndedAt: 2016-04-21 04:40:37 -0700 (Thu, 21 Apr 2016)
EllapsedTime: 859.6 seconds
RetCode: 0
Status:  OK 
CheckDir: LowMACA.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings LowMACA_1.3.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/LowMACA.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* 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 ‘1.3.2’
* 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 ... [17s/18s] 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 ... [7m/11m] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
allPfamAnalysis      187.362 28.627 186.881
lfmSingleSequence    104.242 16.689 104.905
LowMACA-class         10.037  0.866  85.182
LowMACA-package        9.123  1.556  47.921
lmPlotSingleSequence   6.969  1.265   7.420
setup                  7.327  0.398 164.484
lmPlot                 5.925  1.158   6.476
alignSequences         5.381  0.226  19.072
protter                1.922  0.617   5.226
getMutations           0.756  0.055  23.045
* 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-3.3-bioc/meat/LowMACA.Rcheck/00check.log’
for details.

LowMACA.Rcheck/00install.out:

* 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)

LowMACA.Rcheck/LowMACA-Ex.timings:

nameusersystemelapsed
BLOSUM620.0110.0030.014
LowMACA-class10.037 0.86685.182
LowMACA-package 9.123 1.55647.921
LowMACA_AML0.0240.0110.034
alignSequences 5.381 0.22619.072
allPfamAnalysis187.362 28.627186.881
bpAll1.5380.5051.470
entropy1.0180.3241.326
getMutations 0.756 0.05523.045
lfm2.5030.6282.311
lfmSingleSequence104.242 16.689104.905
lmAlignment0.0550.0120.067
lmEntropy1.3060.4831.408
lmMutations0.0410.0070.047
lmObj0.1060.0160.122
lmParams0.6630.0370.707
lmPlot5.9251.1586.476
lmPlotSingleSequence6.9691.2657.420
mapMutations0.7060.0300.758
newLowMACA3.6470.1143.806
nullProfile1.6040.6721.685
parallelize0.6990.0300.731
protter1.9220.6175.226
setup 7.327 0.398164.484
showTumorType0.0400.0110.880