BioC 3.3: CHECK report for OLIN on oaxaca

Package: OLIN

Version: 1.50.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings OLIN_1.50.0.tar.gz

StartedAt: 2016-10-13 04:17:02 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 04:18:31 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 88.8 seconds

RetCode: 0

Status:  OK

CheckDir: OLIN.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings OLIN_1.50.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/OLIN.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OLIN/DESCRIPTION’ ... OK
* this is package ‘OLIN’ version ‘1.50.0’
* 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 ‘OLIN’ 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.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘marray’ ‘methods’
A package should be listed in only one of these fields.
* 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 ‘convert’ 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: ‘locfit’
  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
ino: no visible global function definition for ‘locfit’
ino: no visible global function definition for ‘predict’
lin: no visible global function definition for ‘locfit’
lin: no visible global function definition for ‘predict’
oin: no visible global function definition for ‘gcvplot’
oin: no visible global function definition for ‘locfit’
oin: no visible global function definition for ‘predict’
olin: no visible global function definition for ‘gcv’
olin: no visible global function definition for ‘locfit’
olin: no visible global function definition for ‘predict’
Undefined global functions or variables:
  gcv gcvplot locfit predict
Consider adding
  importFrom("stats", "predict")
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 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
olin 18.431  0.048   19.07
* 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-3.3-bioc/meat/OLIN.Rcheck/00check.log’
for details.

* installing *source* package ‘OLIN’ ...
** 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 (OLIN)

name	user	system	elapsed
anovaint	0.191	0.026	0.232
anovapin	0.104	0.019	0.129
anovaplate	0.145	0.021	0.170
anovaspatial	0.315	0.028	1.278
backgroundCorrect2	0.563	0.029	0.719
bas	0.075	0.010	0.949
colorbar.mxy	0.068	0.010	0.094
fdr.int	0.001	0.000	0.001
fdr.int2	0.000	0.000	0.001
fdr.spatial	0.001	0.001	0.001
fdr.spatial2	0.001	0.000	0.001
fgbg.visu	0.178	0.014	0.251
ino	0.282	0.015	1.300
lin	0.847	0.020	1.562
m2v	0.079	0.007	0.110
ma.matrix	0.306	0.010	0.340
ma.vector	0.282	0.013	0.295
mxy.abs.plot	0.122	0.010	0.277
mxy.plot	0.069	0.005	0.117
mxy2.plot	0.063	0.005	0.088
oin	0.819	0.021	1.297
olin	18.431	0.048	19.070
p.int	0.001	0.000	0.000
p.int2	0.001	0.000	0.001
p.spatial	0.001	0.000	0.001
p.spatial2	0.001	0.000	0.000
sig.mask	0.001	0.001	0.001
sigint.plot	0.001	0.000	0.001
sigint.plot2	0.001	0.000	0.000
sigxy.plot	0.000	0.000	0.005
sigxy.plot2	0.001	0.001	0.001
v2m	0.116	0.006	0.146