Package: OLIN

Version: 1.61.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:OLIN.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings OLIN_1.61.0.tar.gz

StartedAt: 2019-04-09 02:25:19 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 02:26:19 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 59.8 seconds

RetCode: 0

Status:  OK

CheckDir: OLIN.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:OLIN.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings OLIN_1.61.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/OLIN.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OLIN/DESCRIPTION’ ... OK
* this is package ‘OLIN’ version ‘1.61.0’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
       user system elapsed
olin 17.871  0.008  17.879
* 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
  ‘/home/biocbuild/bbs-3.9-bioc/meat/OLIN.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL OLIN
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘OLIN’ ...
** using staged installation
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (OLIN)

name	user	system	elapsed
anovaint	0.156	0.008	0.164
anovapin	0.106	0.012	0.118
anovaplate	0.107	0.004	0.111
anovaspatial	0.35	0.00	0.35
backgroundCorrect2	0.629	0.020	0.649
bas	0.101	0.000	0.100
colorbar.mxy	0.068	0.008	0.076
fdr.int	0	0	0
fdr.int2	0	0	0
fdr.spatial	0	0	0
fdr.spatial2	0	0	0
fgbg.visu	0.163	0.008	0.171
ino	0.294	0.008	0.301
lin	0.864	0.016	0.880
m2v	0.092	0.000	0.092
ma.matrix	0.399	0.004	0.402
ma.vector	0.476	0.000	0.476
mxy.abs.plot	0.164	0.000	0.164
mxy.plot	0.101	0.004	0.106
mxy2.plot	0.091	0.000	0.091
oin	1.319	0.012	1.331
olin	17.871	0.008	17.879
p.int	0.001	0.000	0.000
p.int2	0.000	0.000	0.001
p.spatial	0	0	0
p.spatial2	0	0	0
sig.mask	0	0	0
sigint.plot	0	0	0
sigint.plot2	0.000	0.000	0.001
sigxy.plot	0	0	0
sigxy.plot2	0.000	0.001	0.000
v2m	0.054	0.004	0.059