Multiple platform build/check report for BioC 3.9 - CHECK report for MEDME on celaya2

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MEDME.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MEDME_1.43.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/MEDME.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MEDME/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MEDME’ 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 ‘MEDME’ 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 ... NOTE
Warning: no function found corresponding to methods exports from ‘MEDME’ for: ‘initialize’, ‘show’

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Package in Depends field not imported from: ‘methods’
  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
CGcount: no visible binding for global variable ‘Hsapiens’
CGcount: no visible binding for global variable ‘Mmusculus’
CGcount: no visible global function definition for ‘start’
CGcount: no visible global function definition for ‘new’
MEDME: no visible global function definition for ‘quantile’
MEDME: no visible global function definition for ‘median’
MEDME: no visible global function definition for ‘png’
MEDME: no visible global function definition for ‘contour’
MEDME: no visible global function definition for ‘colors’
MEDME: no visible global function definition for ‘points’
MEDME: no visible global function definition for ‘lines’
MEDME: no visible global function definition for ‘fitted’
MEDME: no visible global function definition for ‘dev.off’
MEDME.predict: no visible global function definition for ‘coef’
MEDME.predict: no visible global function definition for ‘new’
MEDME.readFiles: no visible global function definition for ‘read.table’
MEDME.readFiles: no visible global function definition for ‘new’
MEDME.writeFiles: no visible global function definition for
  ‘write.table’
smooth: no visible global function definition for ‘new’
initialize,MEDMEset: no visible global function definition for
  ‘callNextMethod’
show,MEDMEset: no visible global function definition for ‘show’
Undefined global functions or variables:
  Hsapiens Mmusculus callNextMethod coef colors contour dev.off fitted
  lines median new png points quantile read.table show start
  write.table
Consider adding
  importFrom("grDevices", "colors", "dev.off", "png")
  importFrom("graphics", "contour", "lines", "points")
  importFrom("methods", "callNextMethod", "new", "show")
  importFrom("stats", "coef", "fitted", "median", "quantile", "start")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic '[' and siglist 'MEDMEset,ANY,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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
CGcount       14.520  1.944  16.476
MEDME          5.700  1.288   6.989
MEDME.predict  5.156  1.164   6.322
* 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: 1 WARNING, 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/MEDME.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 MEDME
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘MEDME’ ...
** using staged installation
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -fPIC  -Wall -g -O2  -c MEDMEweight.c -o MEDMEweight.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 MEDME.so MEDMEweight.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-MEDME/00new/MEDME/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 (MEDME)

CHECK report for MEDME on celaya2

Summary

Command output

Installation output

Tests output

Example timings

name	user	system	elapsed
CGcount	14.520	1.944	16.476
MEDME	5.700	1.288	6.989
MEDME.predict	5.156	1.164	6.322
MEDMEset-class	0.001	0.000	0.002
smooth	0.172	0.015	0.187