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BioC 3.4: CHECK report for EMDomics on tokay1

This page was generated on 2017-04-15 16:20:00 -0400 (Sat, 15 Apr 2017).

Package 375/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
EMDomics 2.4.0
Sadhika Malladi and Daniel Schmolze
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/EMDomics
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: EMDomics
Version: 2.4.0
Command: rm -rf EMDomics.buildbin-libdir EMDomics.Rcheck && mkdir EMDomics.buildbin-libdir EMDomics.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=EMDomics.buildbin-libdir EMDomics_2.4.0.tar.gz >EMDomics.Rcheck\00install.out 2>&1 && cp EMDomics.Rcheck\00install.out EMDomics-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=EMDomics.buildbin-libdir --install="check:EMDomics-install.out" --force-multiarch --no-vignettes --timings EMDomics_2.4.0.tar.gz
StartedAt: 2017-04-14 22:08:44 -0400 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 22:10:39 -0400 (Fri, 14 Apr 2017)
EllapsedTime: 115.2 seconds
RetCode: 0
Status:  OK  
CheckDir: EMDomics.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf EMDomics.buildbin-libdir EMDomics.Rcheck && mkdir EMDomics.buildbin-libdir EMDomics.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=EMDomics.buildbin-libdir EMDomics_2.4.0.tar.gz >EMDomics.Rcheck\00install.out 2>&1 && cp EMDomics.Rcheck\00install.out EMDomics-install.out  && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=EMDomics.buildbin-libdir --install="check:EMDomics-install.out" --force-multiarch --no-vignettes --timings EMDomics_2.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/EMDomics.Rcheck'
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'EMDomics/DESCRIPTION' ... OK
* this is package 'EMDomics' version '2.4.0'
* 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 'EMDomics' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Authors@R field gives more than one person with maintainer role:
  Sadhika Malladi <contact@sadhikamalladi.com> [aut, cre]
  Daniel Schmolze <emd@schmolze.com> [aut, cre]
* 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
.cvm_pairwise_q: no visible global function definition for 'combn'
.cvm_pairwise_q : <anonymous>: no visible global function definition
  for 'median'
.emd_gene_pairwise: no visible global function definition for 'hist'
.emd_pairwise_q: no visible global function definition for 'combn'
.emd_pairwise_q : <anonymous>: no visible global function definition
  for 'median'
.ks_pairwise_table: no visible global function definition for 'ks.test'
calculate_cvm: no visible global function definition for 'combn'
calculate_cvm : <anonymous>: no visible global function definition for
  'median'
calculate_cvm_gene: no visible global function definition for 'combn'
calculate_emd: no visible global function definition for 'combn'
calculate_emd : <anonymous>: no visible global function definition for
  'median'
calculate_emd_gene: no visible global function definition for 'combn'
calculate_ks: no visible global function definition for 'combn'
calculate_ks : <anonymous>: no visible global function definition for
  'p.adjust'
calculate_ks : <anonymous>: no visible global function definition for
  'median'
calculate_ks_gene: no visible global function definition for 'combn'
calculate_ks_gene: no visible global function definition for 'ks.test'
Undefined global functions or variables:
  combn hist ks.test median p.adjust
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "ks.test", "median", "p.adjust")
  importFrom("utils", "combn")
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... NOTE
The following directory looks like a leftover from 'knitr':
  'figure'
Please remove from your package.
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
plot_cvmperms    7.82   0.02    7.83
plot_cvm_density 5.01   0.06    5.08
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
plot_cvm_density 6.00   0.07    6.06
plot_cvmperms    5.77   0.03    5.79
calculate_cvm    5.63   0.01    5.64
* 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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.4-bioc/meat/EMDomics.Rcheck/00check.log'
for details.


EMDomics.Rcheck/00install.out:


install for i386

* installing *source* package 'EMDomics' ...
** R
** 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 'EMDomics' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'EMDomics' as EMDomics_2.4.0.zip
* DONE (EMDomics)

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

nameusersystemelapsed
calculate_cvm4.720.004.72
calculate_cvm_gene0.020.000.02
calculate_emd3.010.023.03
calculate_emd_gene000
calculate_ks0.880.000.88
calculate_ks_gene0.020.000.01
plot_cvm_density5.010.065.08
plot_cvmnull2.060.012.08
plot_cvmperms7.820.027.83
plot_emd_density4.250.004.25
plot_emdnull1.290.011.31
plot_emdperms3.420.003.43
plot_ks_density1.100.021.10
plot_ksnull0.520.010.53
plot_ksperms1.030.001.03

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

nameusersystemelapsed
calculate_cvm5.630.015.64
calculate_cvm_gene0.010.000.02
calculate_emd3.790.033.81
calculate_emd_gene0.010.000.01
calculate_ks1.020.001.02
calculate_ks_gene0.010.000.02
plot_cvm_density6.000.076.06
plot_cvmnull2.110.002.11
plot_cvmperms5.770.035.79
plot_emd_density3.790.013.82
plot_emdnull1.50.01.5
plot_emdperms3.820.043.84
plot_ks_density1.870.001.88
plot_ksnull1.080.011.09
plot_ksperms1.550.021.56