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BioC 3.4: CHECK report for LowMACA on morelia

This page was generated on 2017-04-15 16:26:24 -0400 (Sat, 15 Apr 2017).

Package 684/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
LowMACA 1.6.0
Stefano de Pretis , Giorgio Melloni
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/LowMACA
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
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: 1.6.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings LowMACA_1.6.0.tar.gz
StartedAt: 2017-04-15 04:16:31 -0700 (Sat, 15 Apr 2017)
EndedAt: 2017-04-15 04:31:47 -0700 (Sat, 15 Apr 2017)
EllapsedTime: 915.6 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_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/LowMACA.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.6.0’
* 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 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      164.879  4.396 171.039
lfmSingleSequence     91.062  2.433  95.263
LowMACA-class         10.733  0.913  97.877
LowMACA-package        8.955  0.757  59.339
setup                  8.275  0.412 192.998
lmPlotSingleSequence   5.868  0.640   6.641
lmPlot                 5.030  0.597   8.276
alignSequences         5.292  0.268  21.809
getMutations           0.802  0.047  25.854
* 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-3.4-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
BLOSUM620.0070.0050.012
LowMACA-class10.733 0.91397.877
LowMACA-package 8.955 0.75759.339
LowMACA_AML0.0250.0090.034
alignSequences 5.292 0.26821.809
allPfamAnalysis164.879 4.396171.039
bpAll1.5600.0391.600
entropy1.5670.0311.605
getMutations 0.802 0.04725.854
lfm2.0430.0592.105
lfmSingleSequence91.062 2.43395.263
lmAlignment0.0800.0110.098
lmEntropy1.2930.0471.341
lmMutations0.0470.0100.057
lmObj0.1090.0120.121
lmParams0.5950.0250.625
lmPlot5.0300.5978.276
lmPlotSingleSequence5.8680.6406.641
mapMutations0.6160.0180.635
newLowMACA3.2460.0993.347
nullProfile1.4880.0351.523
parallelize0.6330.0210.655
protter1.3250.0353.818
setup 8.275 0.412192.998
showTumorType0.0400.0100.884