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This page was generated on 2024-12-23 11:42 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4372
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1107/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
lmdme 1.49.0  (landing page)
Cristobal Fresno
Snapshot Date: 2024-12-22 13:40 -0500 (Sun, 22 Dec 2024)
git_url: https://git.bioconductor.org/packages/lmdme
git_branch: devel
git_last_commit: 2d18be3
git_last_commit_date: 2024-10-29 09:42:26 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  


CHECK results for lmdme on palomino7

To the developers/maintainers of the lmdme package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/lmdme.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: lmdme
Version: 1.49.0
Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:lmdme.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings lmdme_1.49.0.tar.gz
StartedAt: 2024-12-23 02:01:15 -0500 (Mon, 23 Dec 2024)
EndedAt: 2024-12-23 02:02:28 -0500 (Mon, 23 Dec 2024)
EllapsedTime: 72.9 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: lmdme.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:lmdme.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings lmdme_1.49.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/lmdme.Rcheck'
* using R Under development (unstable) (2024-10-26 r87273 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'lmdme/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'lmdme' version '1.49.0'
* 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 code 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 '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 : <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 plsr prcomp pt pvalues quantile terms
Consider adding
  importFrom("grDevices", "X11")
  importFrom("graphics", "abline", "axis", "box", "legend", "lines",
             "matplot", "par")
  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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  lmdme-Class.Rd: lmFit
  lmdme-biplot.Rd: biplot.mvr, plsr
  lmdme-decomposition.Rd: plsr
  lmdme-lmdme.Rd: lmFit
  lmdme-permutation.Rd: lmFit
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Documented arguments not in \usage in Rd file 'lmdme-padjust.Rd':
  '...'

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 sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
lmdme-permutation 5.78   0.59    6.37
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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, 3 NOTEs
See
  'E:/biocbuild/bbs-3.21-bioc/meat/lmdme.Rcheck/00check.log'
for details.


Installation output

lmdme.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL lmdme
###
##############################################################################
##############################################################################


* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library'
* 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
** 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 (lmdme)

Tests output


Example timings

lmdme.Rcheck/lmdme-Ex.timings

nameusersystemelapsed
lmdme-biplot2.180.292.89
lmdme-decomposition1.830.222.04
lmdme-getters2.020.142.15
lmdme-leverage2.030.302.33
lmdme-lmdme2.360.332.69
lmdme-loadingplot2.140.192.33
lmdme-padjust2.080.172.25
lmdme-permutation5.780.596.37
lmdme-printshow2.000.172.17
lmdme-screeplot1.860.192.05