BioC 3.1: CHECK report for OLIN on petty

Package: OLIN

Version: 1.46.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings OLIN_1.46.0.tar.gz

StartedAt: 2015-10-09 00:53:23 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 00:55:04 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 100.5 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_1.46.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/OLIN.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OLIN/DESCRIPTION’ ... OK
* this is package ‘OLIN’ version ‘1.46.0’
* 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 ... [4s/4s] 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’
lin: no visible global function definition for ‘locfit’
oin: no visible global function definition for ‘gcvplot’
oin: no visible global function definition for ‘locfit’
olin: no visible global function definition for ‘gcv’
olin: no visible global function definition for ‘locfit’
* 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 ... [44s/45s] OK
Examples with CPU or elapsed time > 5s
       user system elapsed
olin 34.419  0.069  34.517
* 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-3.1-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	0.249	0.020	0.269
anovapin	0.134	0.014	0.148
anovaplate	0.205	0.012	0.217
anovaspatial	0.452	0.019	0.473
backgroundCorrect2	1.088	0.039	1.149
bas	0.106	0.010	0.118
colorbar.mxy	0.103	0.010	0.219
fdr.int	0.001	0.000	0.002
fdr.int2	0.001	0.000	0.001
fdr.spatial	0.002	0.000	0.002
fdr.spatial2	0.001	0.000	0.002
fgbg.visu	0.271	0.016	0.288
ino	0.412	0.021	0.441
lin	1.378	0.019	1.399
m2v	0.112	0.009	0.121
ma.matrix	0.467	0.014	0.480
ma.vector	0.537	0.023	0.561
mxy.abs.plot	0.204	0.014	0.251
mxy.plot	0.237	0.010	0.254
mxy2.plot	0.117	0.013	0.130
oin	1.722	0.025	1.749
olin	34.419	0.069	34.517
p.int	0.002	0.000	0.002
p.int2	0.001	0.000	0.002
p.spatial	0.001	0.000	0.002
p.spatial2	0.001	0.000	0.001
sig.mask	0.003	0.000	0.003
sigint.plot	0.002	0.000	0.002
sigint.plot2	0.001	0.001	0.002
sigxy.plot	0.002	0.000	0.003
sigxy.plot2	0.002	0.000	0.002
v2m	0.098	0.009	0.108