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CHECK report for OLIN on tokay2

This page was generated on 2018-10-17 08:32:13 -0400 (Wed, 17 Oct 2018).

Package 1014/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OLIN 1.58.0
Matthias Futschik
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/OLIN
Branch: RELEASE_3_7
Last Commit: c6e482f
Last Changed Date: 2018-04-30 10:35:00 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: OLIN
Version: 1.58.0
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:OLIN.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings OLIN_1.58.0.tar.gz
StartedAt: 2018-10-17 03:42:42 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 03:44:31 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 109.2 seconds
RetCode: 0
Status:  OK  
CheckDir: OLIN.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:OLIN.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings OLIN_1.58.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/OLIN.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'OLIN/DESCRIPTION' ... OK
* this is package 'OLIN' version '1.58.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
      user system elapsed
olin 25.79   0.05   25.84
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
     user system elapsed
olin 19.9      0   19.91
* 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
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/OLIN.Rcheck/00check.log'
for details.



Installation output

OLIN.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/OLIN_1.58.0.tar.gz && rm -rf OLIN.buildbin-libdir && mkdir OLIN.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=OLIN.buildbin-libdir OLIN_1.58.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL OLIN_1.58.0.zip && rm OLIN_1.58.0.tar.gz OLIN_1.58.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  565k  100  565k    0     0  4075k      0 --:--:-- --:--:-- --:--:-- 4283k

install for i386

* installing *source* package 'OLIN' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'OLIN'
    finding HTML links ... done
    anovaint                                html  
    anovapin                                html  
    anovaplate                              html  
    anovaspatial                            html  
    backgroundCorrect2                      html  
    bas                                     html  
    colorbar.mxy                            html  
    colorbar.mxy.abs                        html  
    colorbar.sig                            html  
    fdr.int                                 html  
    fdr.int2                                html  
    fdr.spatial                             html  
    fdr.spatial2                            html  
    fgbg.visu                               html  
    ino                                     html  
    lin                                     html  
    m2v                                     html  
    ma.matrix                               html  
    ma.vector                               html  
    mxy.abs.plot                            html  
    mxy.plot                                html  
    mxy2.plot                               html  
    oin                                     html  
    olin                                    html  
    p.int                                   html  
    p.int2                                  html  
    p.spatial                               html  
    p.spatial2                              html  
    sig.mask                                html  
    sigint.plot                             html  
    sigint.plot2                            html  
    sigxy.plot                              html  
    sigxy.plot2                             html  
    sw                                      html  
    sw.olin                                 html  
    sw.xy                                   html  
    v2m                                     html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'OLIN' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'OLIN' as OLIN_1.58.0.zip
* DONE (OLIN)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'OLIN' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

OLIN.Rcheck/examples_i386/OLIN-Ex.timings

nameusersystemelapsed
anovaint0.220.000.22
anovapin0.110.010.12
anovaplate0.160.000.15
anovaspatial0.340.030.38
backgroundCorrect20.660.020.67
bas0.140.000.14
colorbar.mxy0.090.020.11
fdr.int000
fdr.int2000
fdr.spatial000
fdr.spatial2000
fgbg.visu0.250.000.25
ino0.370.030.41
lin1.100.011.11
m2v0.120.000.12
ma.matrix0.30.00.3
ma.vector0.560.000.56
mxy.abs.plot0.240.000.24
mxy.plot0.140.020.15
mxy2.plot0.110.030.15
oin1.140.001.14
olin25.79 0.0525.84
p.int000
p.int2000
p.spatial000
p.spatial20.020.000.02
sig.mask000
sigint.plot000
sigint.plot2000
sigxy.plot000
sigxy.plot20.010.000.01
v2m0.110.010.13

OLIN.Rcheck/examples_x64/OLIN-Ex.timings

nameusersystemelapsed
anovaint0.110.020.13
anovapin0.080.010.09
anovaplate0.060.040.10
anovaspatial0.240.030.26
backgroundCorrect20.430.030.47
bas0.080.010.10
colorbar.mxy0.050.000.04
fdr.int000
fdr.int2000
fdr.spatial000
fdr.spatial2000
fgbg.visu0.130.000.12
ino0.200.000.21
lin0.520.000.51
m2v0.060.020.08
ma.matrix0.270.020.28
ma.vector0.290.010.31
mxy.abs.plot0.130.000.13
mxy.plot0.080.000.08
mxy2.plot0.040.020.06
oin0.750.000.75
olin19.90 0.0019.91
p.int000
p.int2000
p.spatial000
p.spatial2000
sig.mask000
sigint.plot000
sigint.plot2000
sigxy.plot0.020.000.01
sigxy.plot2000
v2m0.060.000.06