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CHECK report for lmdme on tokay1

This page was generated on 2020-04-15 12:20:56 -0400 (Wed, 15 Apr 2020).

Package 912/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
lmdme 1.28.0
Cristobal Fresno
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/lmdme
Branch: RELEASE_3_10
Last Commit: 6b4ac61
Last Changed Date: 2019-10-29 13:08:34 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: lmdme
Version: 1.28.0
Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:lmdme.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings lmdme_1.28.0.tar.gz
StartedAt: 2020-04-15 04:19:23 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 04:21:02 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 99.2 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: lmdme.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:lmdme.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings lmdme_1.28.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/lmdme.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'lmdme/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'lmdme' version '1.28.0'
* 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 'lmdme' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 'parallel' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
biplot,lmdme : <anonymous>: no visible global function definition for
  'X11'
biplot,lmdme : <anonymous>: no visible global function definition for
  'par'
biplot,lmdme : <anonymous>: no visible global function definition for
  'abline'
decomposition,lmdme : <anonymous>: no visible global function
  definition for 'prcomp'
decomposition,lmdme : <anonymous>: no visible global function
  definition for 'model.matrix'
decomposition,lmdme : <anonymous>: no visible global function
  definition for 'plsr'
fitted.values,lmdme : <anonymous>: no visible global function
  definition for 'model.matrix'
fitted.values,lmdme : <anonymous>: no visible global function
  definition for 'as.formula'
leverage,lmdme: no visible global function definition for 'prcomp'
leverage,lmdme: no visible global function definition for 'quantile'
lmdme,formula-ANY-data.frame : printnow: no visible global function
  definition for 'flush.console'
lmdme,formula-ANY-data.frame: no visible global function definition for
  'terms'
lmdme,formula-ANY-data.frame: no visible binding for global variable
  'as.formula'
lmdme,formula-ANY-data.frame : <anonymous>: no visible global function
  definition for 'model.matrix'
lmdme,formula-ANY-data.frame : <anonymous>: no visible global function
  definition for 'as.formula'
lmdme,formula-ANY-data.frame : <anonymous>: no visible global function
  definition for 'pt'
lmdme,formula-ANY-data.frame : <anonymous>: no visible global function
  definition for 'pchisq'
lmdme,formula-ANY-data.frame : <anonymous>: no visible global function
  definition for 'pf'
lmdme,formula-ANY-data.frame : <anonymous>: no visible global function
  definition for 'terms'
loadingplot,lmdme: no visible global function definition for 'loadings'
loadingplot,lmdme: no visible global function definition for 'matplot'
loadingplot,lmdme: no visible global function definition for 'box'
loadingplot,lmdme: no visible global function definition for 'axis'
loadingplot,lmdme: no visible global function definition for 'legend'
p.adjust,lmdme: no visible binding for global variable
  'p.adjust.methods'
permutation,formula-data.frame-data.frame : printnow: no visible global
  function definition for 'flush.console'
permutation,formula-data.frame-data.frame: no visible binding for
  global variable 'mclapply'
permutation,formula-data.frame-data.frame: no visible global function
  definition for 'detectCores'
print,lmdme: no visible global function definition for 'head'
print,lmdme: no visible global function definition for 'pvalues'
print,lmdme: no visible binding for global variable 'head'
screeplot,lmdme : <anonymous>: no visible global function definition
  for 'X11'
screeplot,lmdme : <anonymous>: no visible global function definition
  for 'par'
screeplot,lmdme: no visible global function definition for 'plot'
screeplot,lmdme : <anonymous>: no visible global function definition
  for 'lines'
screeplot,lmdme: no visible global function definition for 'legend'
show,lmdme: no visible global function definition for 'head'
Undefined global functions or variables:
  X11 abline as.formula axis box detectCores flush.console head legend
  lines loadings matplot mclapply model.matrix p.adjust.methods par
  pchisq pf plot plsr prcomp pt pvalues quantile terms
Consider adding
  importFrom("grDevices", "X11")
  importFrom("graphics", "abline", "axis", "box", "legend", "lines",
             "matplot", "par", "plot")
  importFrom("stats", "as.formula", "loadings", "model.matrix",
             "p.adjust.methods", "pchisq", "pf", "prcomp", "pt",
             "quantile", "terms")
  importFrom("utils", "flush.console", "head")
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 ... WARNING
Documented arguments not in \usage in documentation object 'p.adjust':
  '...'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
lmdme-permutation 7.48   0.63    8.11
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
lmdme-permutation 5.19   0.53    5.72
* 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: 1 WARNING, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.10-bioc/meat/lmdme.Rcheck/00check.log'
for details.



Installation output

lmdme.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/lmdme_1.28.0.tar.gz && rm -rf lmdme.buildbin-libdir && mkdir lmdme.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=lmdme.buildbin-libdir lmdme_1.28.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL lmdme_1.28.0.zip && rm lmdme_1.28.0.tar.gz lmdme_1.28.0.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  109k  100  109k    0     0  2482k      0 --:--:-- --:--:-- --:--:-- 2731k

install for i386

* installing *source* package 'lmdme' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for 'p.adjust' in package 'lmdme'
** help
*** installing help indices
  converting help for package 'lmdme'
    finding HTML links ... done
    lmdme-Class                             html  
    finding level-2 HTML links ... done

    lmdme-biplot                            html  
    lmdme-decomposition                     html  
    lmdme-getters                           html  
    lmdme-leverage                          html  
    lmdme-lmdme                             html  
    lmdme-loadingplot                       html  
    lmdme-padjust                           html  
    lmdme-permutation                       html  
    lmdme-printshow                         html  
    lmdme-screeplot                         html  
** 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

install for x64

* installing *source* package 'lmdme' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'lmdme' as lmdme_1.28.0.zip
* DONE (lmdme)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'lmdme' successfully unpacked and MD5 sums checked

Tests output


Example timings

lmdme.Rcheck/examples_i386/lmdme-Ex.timings

nameusersystemelapsed
lmdme-biplot3.500.273.99
lmdme-decomposition2.750.253.00
lmdme-getters2.460.112.57
lmdme-leverage3.210.173.38
lmdme-lmdme2.810.142.95
lmdme-loadingplot2.280.142.42
lmdme-padjust2.700.122.85
lmdme-permutation7.480.638.11
lmdme-printshow2.930.203.12
lmdme-screeplot3.200.163.36

lmdme.Rcheck/examples_x64/lmdme-Ex.timings

nameusersystemelapsed
lmdme-biplot2.170.222.39
lmdme-decomposition1.910.172.08
lmdme-getters2.230.222.45
lmdme-leverage2.210.192.39
lmdme-lmdme1.970.092.06
lmdme-loadingplot1.930.142.08
lmdme-padjust2.110.192.30
lmdme-permutation5.190.535.72
lmdme-printshow1.880.192.06
lmdme-screeplot1.870.272.14