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CHECK report for SIM on merida1

This page was generated on 2019-04-16 11:54:52 -0400 (Tue, 16 Apr 2019).

Package 1448/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SIM 1.52.0
Renee X. de Menezes
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/SIM
Branch: RELEASE_3_8
Last Commit: 0d16b7e
Last Changed Date: 2018-10-30 11:41:44 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: SIM
Version: 1.52.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SIM.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SIM_1.52.0.tar.gz
StartedAt: 2019-04-16 02:49:28 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 02:52:00 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 151.4 seconds
RetCode: 0
Status:  OK 
CheckDir: SIM.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SIM.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SIM_1.52.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/SIM.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.52.0’
* 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 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 ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
SIM-package         9.414  0.142   9.643
integrated.analysis 8.262  0.087   8.416
* 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
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/SIM.Rcheck/00check.log’
for details.



Installation output

SIM.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL SIM
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘SIM’ ...
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c withinWindow.c -o withinWindow.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o SIM.so withinWindow.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/SIM/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (SIM)

Tests output


Example timings

SIM.Rcheck/SIM-Ex.timings

nameusersystemelapsed
RESOURCERER.annotation.to.ID000
SIM-package9.4140.1429.643
acgh.data0.0030.0010.004
assemble.data0.0400.0060.048
chrom.table0.0020.0020.003
expr.data0.0030.0010.003
getoverlappingregions0.0010.0000.000
impute.nas.by.surrounding0.0010.0000.001
integrated.analysis8.2620.0878.416
link.metadata0.0000.0010.000
samples0.0020.0010.003
sim.plot.overlapping.indep.dep.features0.0630.0040.069
sim.plot.pvals.on.genome0.1670.0160.187
sim.plot.pvals.on.region0.0060.0020.007
sim.plot.zoom.in0.2620.0250.290
sim.plot.zscore.heatmap0.3840.0300.420
sim.update.chrom.table000
tabulate.pvals0.0070.0000.007
tabulate.top.dep.features0.0180.0020.020
tabulate.top.indep.features0.0160.0020.018