Back to the "Multiple platform build/check report" A  B  C  D  E  F  G  H  I  J  K  L  M [N] O  P  Q  R  S  T  U  V  W  X  Y  Z 

BioC 3.5: CHECK report for netbiov on malbec2

This page was generated on 2017-08-16 13:15:53 -0400 (Wed, 16 Aug 2017).

Package 890/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
netbiov 1.10.0
Shailesh tripathi
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/netbiov
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: netbiov
Version: 1.10.0
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings netbiov_1.10.0.tar.gz
StartedAt: 2017-08-16 00:57:27 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 01:00:22 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 175.0 seconds
RetCode: 0
Status:  OK 
CheckDir: netbiov.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings netbiov_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/netbiov.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘netbiov/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘netbiov’ version ‘1.10.0’
* 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 ‘netbiov’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc   6.7Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
.edgeCol: no visible global function definition for ‘colors’
.get.coord.abstract : dst: no visible global function definition for
  ‘dist’
.get.coord.mod : dst: no visible global function definition for ‘dist’
.get.coord.mod_abs : dst: no visible global function definition for
  ‘dist’
.getalllevels: no visible global function definition for ‘pdf’
.getalllevels: no visible global function definition for ‘dev.off’
.getcrd.mod : dst: no visible global function definition for ‘dist’
.getcrd.mod: no visible global function definition for ‘rnorm’
.getcrd.mod.nodes : dst: no visible global function definition for
  ‘dist’
.getcrd.mod_abs : dst: no visible global function definition for ‘dist’
.getcrd.mod_abs: no visible global function definition for ‘rnorm’
.getcrd.mod_mst : dst: no visible global function definition for ‘dist’
.getcrd.mod_mst: no visible global function definition for ‘rnorm’
.ploteachstep: no visible global function definition for ‘plot’
.set.mst.node.col: no visible global function definition for
  ‘heat.colors’
.set.mst.node.col_mod: no visible global function definition for
  ‘heat.colors’
.set.rank.abstract: no visible global function definition for ‘colors’
.set.rank.abstract: no visible global function definition for ‘hist’
.set.rank.abstract: no visible global function definition for
  ‘heat.colors’
.set.rank.mod: no visible global function definition for ‘hist’
.set.rank.mod: no visible global function definition for ‘colors’
.set.rank.mod: no visible global function definition for ‘heat.colors’
.set.rank.mod_abs: no visible global function definition for ‘hist’
.set.rank.mod_abs: no visible global function definition for ‘colors’
.set.rank.mod_abs: no visible global function definition for
  ‘heat.colors’
.set.rank.nodes: no visible global function definition for ‘hist’
.set.rank.nodes: no visible global function definition for ‘colors’
.set.rank.nodes: no visible global function definition for
  ‘heat.colors’
.set.rank.spiral: no visible global function definition for ‘hist’
.set.rank.spiral: no visible global function definition for ‘colors’
.set.rank.spiral: no visible global function definition for
  ‘heat.colors’
.set.split.vertex.color: no visible global function definition for
  ‘colors’
level.plot: no visible global function definition for ‘colors’
plot.NetworkSperical: no visible global function definition for
  ‘colors’
plot.NetworkSperical: no visible global function definition for
  ‘palette’
plot.NetworkSperical.startSet: no visible global function definition
  for ‘colors’
plot.NetworkSperical.startSet: no visible global function definition
  for ‘palette’
plot.netbiov: no visible global function definition for ‘par’
plot.netbiov: no visible global function definition for ‘plot’
plot.spiral.graph : dst: no visible global function definition for
  ‘dist’
tkplot.netbiov: no visible global function definition for ‘par’
Undefined global functions or variables:
  colors dev.off dist heat.colors hist palette par pdf plot rnorm
Consider adding
  importFrom("grDevices", "colors", "dev.off", "heat.colors", "palette",
             "pdf")
  importFrom("graphics", "hist", "par", "plot")
  importFrom("stats", "dist", "rnorm")
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’ ... NOTE
The following files are already in R: ‘Sweave.sty’
Please remove them from your package.
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
level.plot           52.196  0.240  52.495
plot.abstract.module 35.772  0.064  35.927
plot.modules         26.860  0.016  26.913
mst.plot              8.796  0.036   8.836
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.5-bioc/meat/netbiov.Rcheck/00check.log’
for details.


netbiov.Rcheck/00install.out:

* installing *source* package ‘netbiov’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (netbiov)

netbiov.Rcheck/netbiov-Ex.timings:

nameusersystemelapsed
PPI_Athalina0.0280.0000.026
level.plot52.196 0.24052.495
mst.plot8.7960.0368.836
mst.plot.mod3.8320.0163.871
plot.NetworkSperical0.8120.0040.816
plot.NetworkSperical.startSet0.5760.0120.586
plot.abstract.module35.772 0.06435.927
plot.abstract.nodes0.4560.0000.457
plot.modules26.860 0.01626.913
plot.netbiov0.4360.0000.436
plot.spiral.graph0.3480.0080.354
split.mst0.5440.0000.544