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CHECK report for OLIN on malbec2

This page was generated on 2019-04-09 11:23:40 -0400 (Tue, 09 Apr 2019).

Package 1103/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OLIN 1.61.0
Matthias Futschik
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/OLIN
Branch: master
Last Commit: 7c69cd3
Last Changed Date: 2018-10-30 11:54:26 -0400 (Tue, 30 Oct 2018)
malbec2 Linux (Ubuntu 18.04.2 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
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

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

Command output

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### 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
###
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* 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.



Installation output

OLIN.Rcheck/00install.out

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

Tests output


Example timings

OLIN.Rcheck/OLIN-Ex.timings

nameusersystemelapsed
anovaint0.1560.0080.164
anovapin0.1060.0120.118
anovaplate0.1070.0040.111
anovaspatial0.350.000.35
backgroundCorrect20.6290.0200.649
bas0.1010.0000.100
colorbar.mxy0.0680.0080.076
fdr.int000
fdr.int2000
fdr.spatial000
fdr.spatial2000
fgbg.visu0.1630.0080.171
ino0.2940.0080.301
lin0.8640.0160.880
m2v0.0920.0000.092
ma.matrix0.3990.0040.402
ma.vector0.4760.0000.476
mxy.abs.plot0.1640.0000.164
mxy.plot0.1010.0040.106
mxy2.plot0.0910.0000.091
oin1.3190.0121.331
olin17.871 0.00817.879
p.int0.0010.0000.000
p.int20.0000.0000.001
p.spatial000
p.spatial2000
sig.mask000
sigint.plot000
sigint.plot20.0000.0000.001
sigxy.plot000
sigxy.plot20.0000.0010.000
v2m0.0540.0040.059