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BioC 3.4: CHECK report for LowMACA on moscato1

This page was generated on 2016-09-21 03:46:57 -0700 (Wed, 21 Sep 2016).

Package 666/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
LowMACA 1.5.2
Stefano de Pretis , Giorgio Melloni
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/LowMACA
Last Changed Rev: 117512 / Revision: 121152
Last Changed Date: 2016-05-15 13:14:22 -0700 (Sun, 15 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / 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: 1.5.2
Command: rm -rf LowMACA.buildbin-libdir LowMACA.Rcheck && mkdir LowMACA.buildbin-libdir LowMACA.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=LowMACA.buildbin-libdir LowMACA_1.5.2.tar.gz >LowMACA.Rcheck\00install.out 2>&1 && cp LowMACA.Rcheck\00install.out LowMACA-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=LowMACA.buildbin-libdir --install="check:LowMACA-install.out" --force-multiarch --no-vignettes --timings LowMACA_1.5.2.tar.gz
StartedAt: 2016-09-20 11:15:38 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 11:44:07 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 1708.9 seconds
RetCode: 0
Status:  OK  
CheckDir: LowMACA.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf LowMACA.buildbin-libdir LowMACA.Rcheck && mkdir LowMACA.buildbin-libdir LowMACA.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=LowMACA.buildbin-libdir LowMACA_1.5.2.tar.gz >LowMACA.Rcheck\00install.out 2>&1 && cp LowMACA.Rcheck\00install.out LowMACA-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=LowMACA.buildbin-libdir --install="check:LowMACA-install.out" --force-multiarch --no-vignettes --timings LowMACA_1.5.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/LowMACA.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'LowMACA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'LowMACA' version '1.5.2'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
allPfamAnalysis      180.46   2.17  197.14
lfmSingleSequence     99.76   1.03  107.08
setup                 51.53   4.57  139.00
LowMACA-class         25.41   2.64   71.25
LowMACA-package       20.38   1.42   52.05
lmPlotSingleSequence   3.65   0.09    9.84
alignSequences         3.47   0.03   16.91
lmPlot                 2.73   0.11    8.47
getMutations           2.23   0.28   11.30
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
allPfamAnalysis      172.23   1.64  186.52
lfmSingleSequence     93.04   0.94  102.16
setup                 29.28   8.04  108.27
LowMACA-class         17.29   3.25   58.83
LowMACA-package       14.79   1.72   42.90
lmPlotSingleSequence   3.54   0.17    9.48
lmPlot                 3.33   0.14   11.44
alignSequences         2.87   0.07  219.70
getMutations           1.45   0.40   10.65
* 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
  'D:/biocbld/bbs-3.4-bioc/meat/LowMACA.Rcheck/00check.log'
for details.

LowMACA.Rcheck/00install.out:


install for i386

* 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...

install for x64

* installing *source* package 'LowMACA' ...
** 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...
* MD5 sums
packaged installation of 'LowMACA' as LowMACA_1.5.2.zip
* DONE (LowMACA)

LowMACA.Rcheck/examples_i386/LowMACA-Ex.timings:

nameusersystemelapsed
BLOSUM620.010.000.02
LowMACA-class25.41 2.6471.25
LowMACA-package20.38 1.4252.05
LowMACA_AML0.010.010.03
alignSequences 3.47 0.0316.91
allPfamAnalysis180.46 2.17197.14
bpAll1.650.001.66
entropy1.610.001.60
getMutations 2.23 0.2811.30
lfm3.790.023.80
lfmSingleSequence 99.76 1.03107.08
lmAlignment0.050.000.05
lmEntropy1.510.001.51
lmMutations0.050.000.04
lmObj0.070.000.08
lmParams0.640.031.11
lmPlot2.730.118.47
lmPlotSingleSequence3.650.099.84
mapMutations0.640.000.64
newLowMACA3.590.033.63
nullProfile1.80.01.8
parallelize0.650.020.67
protter1.510.003.93
setup 51.53 4.57139.00
showTumorType0.130.020.67

LowMACA.Rcheck/examples_x64/LowMACA-Ex.timings:

nameusersystemelapsed
BLOSUM62000
LowMACA-class17.29 3.2558.83
LowMACA-package14.79 1.7242.90
LowMACA_AML0.010.000.01
alignSequences 2.87 0.07219.70
allPfamAnalysis172.23 1.64186.52
bpAll2.170.022.18
entropy1.950.001.95
getMutations 1.45 0.4010.65
lfm2.590.002.59
lfmSingleSequence 93.04 0.94102.16
lmAlignment0.050.000.05
lmEntropy1.70.01.7
lmMutations0.050.000.05
lmObj0.090.000.09
lmParams0.600.001.04
lmPlot 3.33 0.1411.44
lmPlotSingleSequence3.540.179.48
mapMutations0.560.020.58
newLowMACA3.100.073.18
nullProfile1.710.001.70
parallelize0.620.000.63
protter1.670.004.30
setup 29.28 8.04108.27
showTumorType0.120.040.68