Package: EBcoexpress

Version: 1.28.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:EBcoexpress.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings EBcoexpress_1.28.0.tar.gz

StartedAt: 2019-10-16 02:28:34 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 02:29:36 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 62.6 seconds

RetCode: 0

Status:  OK

CheckDir: EBcoexpress.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:EBcoexpress.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings EBcoexpress_1.28.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/EBcoexpress.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 ‘EBcoexpress/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘EBcoexpress’ version ‘1.28.0’
* 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 ‘EBcoexpress’ can be installed ... OK
* checking installed package size ... OK
* 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 dependencies in R code ... NOTE
'library' or 'require' calls in package code:
  ‘colorspace’ ‘graph’ ‘igraph’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘EBarrays’ ‘mclust’ ‘minqa’
  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
rankMyGenes: warning in sort(table(allNames), decr = TRUE): partial
  argument match of 'decr' to 'decreasing'
bwmc: no visible binding for global variable ‘median’
bwmc: no visible binding for global variable ‘mad’
ebCoexpressFullTCAECM: no visible global function definition for
  ‘bobyqa’
ebCoexpressOneStep: no visible global function definition for ‘bobyqa’
initializeHP : getMclustHPests : devHelper: no visible global function
  definition for ‘density’
initializeHP : getMclustHPests : devHelper : fundDev: no visible global
  function definition for ‘dnorm’
initializeHP : getMclustHPests: no visible global function definition
  for ‘Mclust’
initializeHP : getMclustHPests : checkMyData : funa: no visible global
  function definition for ‘dnorm’
initializeHP : getMclustHPests : checkMyData: no visible global
  function definition for ‘density’
initializeHP : getMclustHPests : checkMyData: no visible global
  function definition for ‘plot’
initializeHP : getMclustHPests : checkMyData: no visible global
  function definition for ‘lines’
initializeHP: no visible global function definition for ‘par’
makeMyD: no visible global function definition for ‘cor’
priorDiagnostic : funa: no visible global function definition for
  ‘dnorm’
priorDiagnostic: no visible global function definition for ‘density’
priorDiagnostic: no visible global function definition for ‘plot’
priorDiagnostic: no visible global function definition for ‘lines’
showNetwork: no visible global function definition for ‘graph.full’
showNetwork: no visible global function definition for ‘hex’
showNetwork: no visible global function definition for ‘RGB’
showNetwork: no visible global function definition for ‘layout.circle’
showNetwork: no visible global function definition for ‘plot’
showPair: no visible global function definition for ‘palette’
showPair : getUsed: no visible global function definition for ‘median’
showPair : getUsed: no visible global function definition for ‘mad’
showPair: no visible binding for global variable ‘plot’
showPair: no visible global function definition for ‘box’
showPair: no visible global function definition for ‘lm’
showPair: no visible binding for global variable ‘segments’
Undefined global functions or variables:
  Mclust RGB bobyqa box cor density dnorm graph.full hex layout.circle
  lines lm mad median palette par plot segments
Consider adding
  importFrom("grDevices", "palette")
  importFrom("graphics", "box", "lines", "par", "plot", "segments")
  importFrom("stats", "cor", "density", "dnorm", "lm", "mad", "median")
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
* 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
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/EBcoexpress.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL EBcoexpress
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘EBcoexpress’ ...
** 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 EBcoexpress.c -o EBcoexpress.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 EBcoexpress.so EBcoexpress.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-EBcoexpress/00new/EBcoexpress/libs
** R
** data
** demo
** 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 (EBcoexpress)

name	user	system	elapsed
ebCoexpressMeta	1.174	0.035	1.208
ebCoexpressSeries	0.650	0.012	0.662
fiftyGenes	0.003	0.004	0.007
initializeHP	0.488	0.015	0.502
makeMyD	0.055	0.006	0.061
priorDiagnostic	1.022	0.026	1.051
rankMyGenes	0.734	0.026	0.760
showNetwork	1.069	0.051	1.131
showPair	0.056	0.007	0.064
utilities	0.008	0.002	0.011