Package: SIM

Version: 1.54.0

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_1.54.0.tar.gz

StartedAt: 2019-10-16 06:54:42 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 06:58:12 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 210.5 seconds

RetCode: 0

Status:  OK

CheckDir: SIM.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### 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_1.54.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/SIM.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.54.0’
* 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         12.298  0.353  12.680
integrated.analysis  9.362  0.253   9.616
* 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-3.9-bioc/meat/SIM.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL SIM
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘SIM’ ...
** using staged installation
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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/3.6/Resources/library/00LOCK-SIM/00new/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 from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (SIM)

name	user	system	elapsed
RESOURCERER.annotation.to.ID	0.000	0.000	0.001
SIM-package	12.298	0.353	12.680
acgh.data	0.002	0.003	0.006
assemble.data	0.042	0.011	0.053
chrom.table	0.003	0.002	0.004
expr.data	0.002	0.001	0.003
getoverlappingregions	0.000	0.001	0.000
impute.nas.by.surrounding	0	0	0
integrated.analysis	9.362	0.253	9.616
link.metadata	0.001	0.000	0.001
samples	0.002	0.002	0.004
sim.plot.overlapping.indep.dep.features	0.074	0.007	0.082
sim.plot.pvals.on.genome	0.224	0.040	0.265
sim.plot.pvals.on.region	0.010	0.003	0.014
sim.plot.zoom.in	0.318	0.071	0.390
sim.plot.zscore.heatmap	0.426	0.069	0.498
sim.update.chrom.table	0.001	0.000	0.000
tabulate.pvals	0.007	0.001	0.008
tabulate.top.dep.features	0.027	0.003	0.029
tabulate.top.indep.features	0.018	0.002	0.021