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BioC 3.5: CHECK report for Mergeomics on tokay2

This page was generated on 2017-08-16 13:25:22 -0400 (Wed, 16 Aug 2017).

Package 779/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Mergeomics 1.4.0
Zeyneb Kurt
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/Mergeomics
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Mergeomics
Version: 1.4.0
Command: rm -rf Mergeomics.buildbin-libdir Mergeomics.Rcheck && mkdir Mergeomics.buildbin-libdir Mergeomics.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Mergeomics.buildbin-libdir Mergeomics_1.4.0.tar.gz >Mergeomics.Rcheck\00install.out 2>&1 && cp Mergeomics.Rcheck\00install.out Mergeomics-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=Mergeomics.buildbin-libdir --install="check:Mergeomics-install.out" --force-multiarch --no-vignettes --timings Mergeomics_1.4.0.tar.gz
StartedAt: 2017-08-16 01:03:11 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 01:24:56 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 1304.5 seconds
RetCode: 0
Status:  OK  
CheckDir: Mergeomics.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf Mergeomics.buildbin-libdir Mergeomics.Rcheck && mkdir Mergeomics.buildbin-libdir Mergeomics.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Mergeomics.buildbin-libdir Mergeomics_1.4.0.tar.gz >Mergeomics.Rcheck\00install.out 2>&1 && cp Mergeomics.Rcheck\00install.out Mergeomics-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=Mergeomics.buildbin-libdir --install="check:Mergeomics-install.out" --force-multiarch --no-vignettes --timings Mergeomics_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/Mergeomics.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Mergeomics/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Mergeomics' version '1.4.0'
* 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 whether package 'Mergeomics' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  8.5Mb
  sub-directories of 1Mb or more:
    extdata   7.5Mb
* 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
kda.analyze: no visible global function definition for 'p.adjust'
kda.analyze.exec: no visible global function definition for 'pnorm'
kda.analyze.simulate: no visible global function definition for 'rnorm'
kda.prepare: no visible global function definition for 'quantile'
kda.prepare: no visible global function definition for 'object.size'
kda.prepare.screen: no visible global function definition for
  'quantile'
kda.prepare.screen: no visible global function definition for 'median'
kda.start: no visible global function definition for 'object.size'
kda2cytoscape: no visible global function definition for 'write.table'
kda2cytoscape.colormap: no visible global function definition for
  'rainbow'
kda2cytoscape.colormap: no visible global function definition for
  'col2rgb'
kda2himmeli: no visible global function definition for 'quantile'
kda2himmeli: no visible global function definition for 'write.table'
kda2himmeli.colormap: no visible global function definition for
  'rainbow'
kda2himmeli.colormap: no visible global function definition for
  'col2rgb'
ssea.analyze: no visible global function definition for 'qnorm'
ssea.analyze: no visible global function definition for 'approx'
ssea.analyze: no visible global function definition for 'pnorm'
ssea.analyze.simulate: no visible global function definition for
  'quantile'
ssea.control: no visible global function definition for 'median'
ssea.control: no visible global function definition for 'object.size'
ssea.meta: no visible global function definition for 'qnorm'
ssea.meta: no visible global function definition for 'quantile'
ssea.meta: no visible global function definition for 'pnorm'
ssea.meta: no visible global function definition for 'median'
ssea.meta: no visible global function definition for 'na.omit'
ssea.prepare: no visible global function definition for 'median'
ssea.prepare: no visible global function definition for 'object.size'
ssea.start: no visible global function definition for 'na.omit'
ssea.start: no visible global function definition for 'object.size'
ssea.start.configure: no visible global function definition for
  'write.table'
ssea2kda: no visible global function definition for 'na.omit'
ssea2kda.import: no visible global function definition for 'na.omit'
tool.aggregate: no visible global function definition for 'na.omit'
tool.cluster: no visible global function definition for 'as.dist'
tool.cluster: no visible global function definition for 'hclust'
tool.fdr.bh: no visible global function definition for 'qnorm'
tool.fdr.bh: no visible global function definition for 'p.adjust'
tool.fdr.bh: no visible global function definition for 'approx'
tool.fdr.empirical: no visible global function definition for 'qnorm'
tool.fdr.empirical: no visible global function definition for 'approx'
tool.metap: no visible global function definition for 'qnorm'
tool.metap: no visible global function definition for 'pnorm'
tool.normalize: no visible global function definition for 'sd'
tool.normalize: no visible global function definition for 'median'
tool.normalize: no visible global function definition for 'optim'
tool.normalize: no visible global function definition for 'ks.test'
tool.normalize.quality: no visible global function definition for 'sd'
tool.normalize.quality: no visible global function definition for
  'ks.test'
tool.overlap: no visible global function definition for 'phyper'
tool.read: no visible global function definition for 'read.delim'
tool.read: no visible global function definition for 'na.omit'
tool.save: no visible global function definition for 'write.table'
tool.unify: no visible global function definition for 'sd'
tool.unify: no visible global function definition for 'quantile'
tool.unify: no visible global function definition for 'approx'
Undefined global functions or variables:
  approx as.dist col2rgb hclust ks.test median na.omit object.size
  optim p.adjust phyper pnorm qnorm quantile rainbow read.delim rnorm
  sd write.table
Consider adding
  importFrom("grDevices", "col2rgb", "rainbow")
  importFrom("stats", "approx", "as.dist", "hclust", "ks.test", "median",
             "na.omit", "optim", "p.adjust", "phyper", "pnorm", "qnorm",
             "quantile", "rnorm", "sd")
  importFrom("utils", "object.size", "read.delim", "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
ssea.meta              15.45   0.11   15.57
kda.analyze.simulate   10.22   0.08   10.30
kda.analyze.exec        9.50   0.14    9.64
ssea2kda.analyze        9.45   0.02    9.46
ssea2kda                8.82   0.00    8.82
kda.prepare             8.67   0.06    8.74
kda.analyze.test        8.45   0.03    8.48
ssea.finish.details     6.60   0.01    6.61
ssea.analyze.randloci   6.41   0.06    6.62
ssea.analyze.simulate   6.25   0.04    6.28
ssea.finish.fdr         5.86   0.00    5.86
ssea2kda.import         5.78   0.00    5.80
ssea.finish.genes       5.42   0.03    5.45
ssea.analyze            5.23   0.00    5.23
ssea.analyze.randgenes  5.12   0.00    5.14
ssea.prepare.structure  5.08   0.03    5.11
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
ssea.meta              17.08   0.00   17.07
kda.analyze.exec       13.65   0.08   13.73
kda.analyze.test       12.44   0.01   12.45
kda.analyze.simulate   12.19   0.07   12.25
kda.prepare            11.78   0.06   11.85
ssea2kda                8.46   0.00    8.53
ssea2kda.analyze        8.22   0.02    8.24
ssea.analyze            8.15   0.02    8.23
ssea.finish             8.12   0.02    8.19
ssea.analyze.simulate   8.07   0.05    8.11
ssea.finish.details     7.94   0.01    7.95
ssea2kda.import         7.18   0.03    7.20
ssea.analyze.randgenes  6.89   0.00    6.89
ssea.finish.genes       6.44   0.02    6.45
ssea.finish.fdr         5.64   0.02    5.66
ssea.analyze.observe    5.64   0.00    5.64
ssea.analyze.randloci   5.53   0.03    5.57
ssea.control            5.47   0.01    5.48
ssea.prepare.structure  5.26   0.02    5.33
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.R'
 OK
* 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/Mergeomics.Rcheck/00check.log'
for details.


Mergeomics.Rcheck/00install.out:


install for i386

* installing *source* package 'Mergeomics' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'Mergeomics' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Mergeomics' as Mergeomics_1.4.0.zip
* DONE (Mergeomics)

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

nameusersystemelapsed
MSEA.KDA.onestep000
job.kda0.030.010.05
kda.analyze0.010.000.02
kda.analyze.exec9.500.149.64
kda.analyze.simulate10.22 0.0810.30
kda.analyze.test8.450.038.48
kda.configure000
kda.finish0.140.020.16
kda.finish.estimate0.100.010.11
kda.finish.save0.090.000.09
kda.finish.summarize0.140.020.16
kda.finish.trim0.140.000.14
kda.prepare8.670.068.74
kda.prepare.overlap0.020.000.01
kda.prepare.screen000
kda.start1.440.001.44
kda.start.edges000
kda.start.identify0.010.000.01
kda.start.modules000
kda2cytoscape0.470.000.47
kda2cytoscape.colorize000
kda2cytoscape.colormap0.030.000.03
kda2cytoscape.drivers0.170.000.18
kda2cytoscape.edges0.140.020.15
kda2cytoscape.exec0.140.010.16
kda2cytoscape.identify000
kda2himmeli0.530.020.55
kda2himmeli.colorize000
kda2himmeli.colormap0.020.000.02
kda2himmeli.drivers0.170.030.20
kda2himmeli.edges0.160.000.15
kda2himmeli.exec0.250.000.25
kda2himmeli.identify0.020.000.02
ssea.analyze5.230.005.23
ssea.analyze.observe3.380.033.41
ssea.analyze.randgenes5.120.005.14
ssea.analyze.randloci6.410.066.62
ssea.analyze.simulate6.250.046.28
ssea.analyze.statistic000
ssea.control4.420.034.46
ssea.finish4.840.004.84
ssea.finish.details6.600.016.61
ssea.finish.fdr5.860.005.86
ssea.finish.genes5.420.035.45
ssea.meta15.45 0.1115.57
ssea.prepare3.880.003.89
ssea.prepare.counts4.060.004.06
ssea.prepare.structure5.080.035.11
ssea.start4.260.004.26
ssea.start.configure0.690.020.71
ssea.start.identify000
ssea.start.relabel3.620.033.65
ssea2kda8.820.008.82
ssea2kda.analyze9.450.029.46
ssea2kda.import5.780.005.80
tool.aggregate000
tool.cluster0.030.000.03
tool.cluster.static000
tool.coalesce0.030.000.03
tool.coalesce.exec0.110.000.11
tool.coalesce.find0.110.000.11
tool.coalesce.merge0.110.000.11
tool.fdr000
tool.fdr.bh000
tool.fdr.empirical000
tool.graph1.390.041.46
tool.graph.degree1.280.041.31
tool.graph.list1.210.041.25
tool.metap000
tool.normalize0.010.000.01
tool.normalize.quality000
tool.overlap000
tool.read0.380.000.37
tool.save000
tool.subgraph0.110.000.11
tool.subgraph.find0.090.000.10
tool.subgraph.search0.090.000.10
tool.subgraph.stats0.110.010.12
tool.translate0.050.000.05
tool.unify000

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

nameusersystemelapsed
MSEA.KDA.onestep0.020.000.02
job.kda0.060.000.07
kda.analyze0.040.010.05
kda.analyze.exec13.65 0.0813.73
kda.analyze.simulate12.19 0.0712.25
kda.analyze.test12.44 0.0112.45
kda.configure000
kda.finish0.170.020.19
kda.finish.estimate0.130.010.14
kda.finish.save0.140.000.14
kda.finish.summarize0.140.000.14
kda.finish.trim0.130.020.14
kda.prepare11.78 0.0611.85
kda.prepare.overlap000
kda.prepare.screen000
kda.start1.870.051.92
kda.start.edges0.020.000.01
kda.start.identify000
kda.start.modules000
kda2cytoscape0.670.010.69
kda2cytoscape.colorize000
kda2cytoscape.colormap0.030.000.03
kda2cytoscape.drivers0.200.000.21
kda2cytoscape.edges0.160.000.15
kda2cytoscape.exec0.190.000.19
kda2cytoscape.identify0.010.000.01
kda2himmeli0.520.020.54
kda2himmeli.colorize000
kda2himmeli.colormap0.010.000.01
kda2himmeli.drivers0.180.010.19
kda2himmeli.edges0.340.000.34
kda2himmeli.exec0.390.000.39
kda2himmeli.identify000
ssea.analyze8.150.028.23
ssea.analyze.observe5.640.005.64
ssea.analyze.randgenes6.890.006.89
ssea.analyze.randloci5.530.035.57
ssea.analyze.simulate8.070.058.11
ssea.analyze.statistic000
ssea.control5.470.015.48
ssea.finish8.120.028.19
ssea.finish.details7.940.017.95
ssea.finish.fdr5.640.025.66
ssea.finish.genes6.440.026.45
ssea.meta17.08 0.0017.07
ssea.prepare4.440.014.46
ssea.prepare.counts4.610.024.62
ssea.prepare.structure5.260.025.33
ssea.start4.640.014.65
ssea.start.configure0.580.020.60
ssea.start.identify000
ssea.start.relabel4.740.004.73
ssea2kda8.460.008.53
ssea2kda.analyze8.220.028.24
ssea2kda.import7.180.037.20
tool.aggregate000
tool.cluster0.010.000.02
tool.cluster.static000
tool.coalesce0.050.000.04
tool.coalesce.exec0.140.000.14
tool.coalesce.find0.140.000.14
tool.coalesce.merge0.140.000.14
tool.fdr000
tool.fdr.bh000
tool.fdr.empirical000
tool.graph1.460.071.55
tool.graph.degree1.580.051.62
tool.graph.list1.390.021.41
tool.metap0.020.000.01
tool.normalize0.010.000.02
tool.normalize.quality000
tool.overlap0.020.000.01
tool.read0.390.000.40
tool.save000
tool.subgraph0.060.030.09
tool.subgraph.find0.080.010.09
tool.subgraph.search0.090.020.11
tool.subgraph.stats0.110.000.11
tool.translate0.070.000.06
tool.unify000