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BioC 3.4: CHECK report for SIM on zin1

This page was generated on 2016-09-21 03:36:36 -0700 (Wed, 21 Sep 2016).

Package 1118/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SIM 1.43.0
Renee X. de Menezes
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SIM
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 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: SIM
Version: 1.43.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings SIM_1.43.0.tar.gz
StartedAt: 2016-09-20 12:38:00 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 12:39:44 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 103.7 seconds
RetCode: 0
Status:  OK 
CheckDir: SIM.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings SIM_1.43.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/SIM.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SIM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SIM’ version ‘1.43.0’
* 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 ‘SIM’ 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 ... NOTE
'library' or 'require' call to ‘biomaRt’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘quantreg’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
File ‘SIM/R/zzz.R’:
  .onAttach calls:
    library.dynam("SIM", pkg, lib)

See section ‘Good practice’ in '?.onAttach'.

dependent.heatmap: warning in get(as.character(adjust[[2]]), env =
  attr(adjust, ".Environment")): partial argument match of 'env' to
  'envir'
sim.plot.zoom.in: warning in eval(call, env = attr(call, "env")):
  partial argument match of 'env' to 'envir'
sim.update.chrom.table: warning in factor(table$name, level = c(1:22,
  "X", "Y")): partial argument match of 'level' to 'levels'
assemble.data: no visible global function definition for ‘data’
assemble.data: no visible binding for global variable ‘chrom.table’
convertGenomicRegion: no visible global function definition for ‘data’
convertGenomicRegion: no visible binding for global variable
  ‘chrom.table’
dependent.heatmap: no visible global function definition for ‘strwidth’
getoverlappingregions: no visible global function definition for
  ‘useMart’
getoverlappingregions: no visible global function definition for
  ‘getBM’
impute.nas.by.surrounding: no visible binding for global variable
  ‘median’
impute.nas.by.surrounding: no visible global function definition for
  ‘na.omit’
independent.heatmap: no visible global function definition for
  ‘strwidth’
link.metadata: no visible binding for global variable ‘expr.data’
link.metadata: no visible binding for global variable ‘hgu133plus2CHR’
link.metadata: no visible binding for global variable
  ‘hgu133plus2CHRLOC’
link.metadata: no visible binding for global variable
  ‘hgu133plus2SYMBOL’
link.metadata: no visible global function definition for ‘aggregate’
plotCytobands: no visible global function definition for ‘data’
plotCytobands: no visible binding for global variable ‘chrom.table’
quantsmooth.plot: no visible global function definition for ‘rainbow’
showProgress: no visible global function definition for ‘flush.console’
sim.plot.overlapping.indep.dep.features: no visible global function
  definition for ‘box’
sim.plot.pvals.on.genome: no visible global function definition for
  ‘data’
sim.plot.pvals.on.genome: no visible binding for global variable
  ‘chrom.table’
sim.plot.zoom.in: no visible global function definition for
  ‘flush.console’
sim.plot.zoom.in: no visible global function definition for ‘dev.new’
sim.plot.zscore.heatmap: no visible global function definition for
  ‘colorRampPalette’
sim.update.chrom.table: no visible global function definition for
  ‘dbConnect’
sim.update.chrom.table: no visible global function definition for
  ‘MySQL’
sim.update.chrom.table: no visible global function definition for
  ‘dbGetQuery’
tabulate.top.dep.features: no visible global function definition for
  ‘na.omit’
tabulate.top.dep.features: no visible global function definition for
  ‘write.table’
tabulate.top.indep.features: no visible global function definition for
  ‘na.omit’
tabulate.top.indep.features: no visible global function definition for
  ‘write.table’
validColumn: no visible global function definition for ‘type.convert’
Undefined global functions or variables:
  MySQL aggregate box chrom.table colorRampPalette data dbConnect
  dbGetQuery dev.new expr.data flush.console getBM hgu133plus2CHR
  hgu133plus2CHRLOC hgu133plus2SYMBOL median na.omit rainbow strwidth
  type.convert useMart write.table
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.new", "rainbow")
  importFrom("graphics", "box", "strwidth")
  importFrom("stats", "aggregate", "median", "na.omit")
  importFrom("utils", "data", "flush.console", "type.convert",
             "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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... 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
SIM-package         7.900  0.036   7.949
integrated.analysis 6.056  0.000   6.069
* 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
  ‘/home/biocbuild/bbs-3.4-bioc/meat/SIM.Rcheck/00check.log’
for details.


SIM.Rcheck/00install.out:

* installing *source* package ‘SIM’ ...
** libs
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c withinWindow.c -o withinWindow.o
gcc -shared -L/home/biocbuild/bbs-3.4-bioc/R/lib -L/usr/local/lib -o SIM.so withinWindow.o -L/home/biocbuild/bbs-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-bioc/meat/SIM.Rcheck/SIM/libs
** 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 (SIM)

SIM.Rcheck/SIM-Ex.timings:

nameusersystemelapsed
RESOURCERER.annotation.to.ID000
SIM-package7.9000.0367.949
acgh.data0.0000.0000.002
assemble.data0.0200.0040.025
chrom.table0.0040.0000.002
expr.data0.0000.0000.002
getoverlappingregions0.0000.0000.001
impute.nas.by.surrounding0.0000.0000.001
integrated.analysis6.0560.0006.069
link.metadata0.0000.0000.002
samples0.0000.0000.002
sim.plot.overlapping.indep.dep.features0.0480.0000.048
sim.plot.pvals.on.genome0.1240.0080.134
sim.plot.pvals.on.region0.0080.0000.008
sim.plot.zoom.in0.2400.0000.238
sim.plot.zscore.heatmap0.3560.0040.361
sim.update.chrom.table0.0000.0000.001
tabulate.pvals0.0040.0000.006
tabulate.top.dep.features0.0200.0000.016
tabulate.top.indep.features0.0120.0000.013