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CHECK report for OLIN on malbec2

This page was generated on 2020-10-17 11:55:17 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE OLIN PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1217/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OLIN 1.66.0
Matthias Futschik
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/OLIN
Branch: RELEASE_3_11
Last Commit: 5ea9fbe
Last Changed Date: 2020-04-27 14:10:09 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: OLIN
Version: 1.66.0
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:OLIN.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings OLIN_1.66.0.tar.gz
StartedAt: 2020-10-17 03:44:47 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 03:45:50 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 62.4 seconds
RetCode: 0
Status:  OK 
CheckDir: OLIN.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:OLIN.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings OLIN_1.66.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/OLIN.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘1.66.0’
* 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 (user + system) or elapsed time > 5s
       user system elapsed
olin 19.047  0.012  19.062
* 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-3.11-bioc/meat/OLIN.Rcheck/00check.log’
for details.



Installation output

OLIN.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL OLIN
###
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* installing to library ‘/home/biocbuild/bbs-3.11-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)

Tests output


Example timings

OLIN.Rcheck/OLIN-Ex.timings

nameusersystemelapsed
anovaint0.1450.0080.153
anovapin0.0710.0080.080
anovaplate0.0750.0000.076
anovaspatial0.1610.0040.165
backgroundCorrect20.5100.0080.518
bas0.2100.0040.214
colorbar.mxy0.0470.0000.047
fdr.int000
fdr.int2000
fdr.spatial000
fdr.spatial2000
fgbg.visu0.1000.0040.105
ino0.2860.0160.303
lin0.6080.0000.608
m2v0.0600.0000.061
ma.matrix0.2270.0040.231
ma.vector0.3750.0000.375
mxy.abs.plot0.2460.0080.253
mxy.plot0.0670.0000.067
mxy2.plot0.0540.0000.054
oin0.9460.0040.950
olin19.047 0.01219.062
p.int0.0000.0000.001
p.int2000
p.spatial000
p.spatial2000
sig.mask000
sigint.plot000
sigint.plot2000
sigxy.plot0.0000.0000.001
sigxy.plot20.0000.0000.001
v2m0.0750.0080.082