Cristobal Fresno
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/lmdme |
| git_branch: master |
| git_last_commit: 38e2c74 |
| git_last_commit_date: 2021-10-26 12:04:24 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:07:53 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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 | ||||
|
To the developers/maintainers of the lmdme package: - Please 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 How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1010/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| lmdme 1.37.0 (landing page) Cristobal Fresno
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: lmdme |
| Version: 1.37.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:lmdme.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings lmdme_1.37.0.tar.gz |
| StartedAt: 2022-03-17 19:27:00 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 19:28:06 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 65.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: lmdme.Rcheck |
| Warnings: 1 |
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### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:lmdme.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings lmdme_1.37.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/lmdme.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* 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 '1.37.0'
* 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
* 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 ... 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
lmdme-permutation 4.84 0.9 5.75
* 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
'D:/biocbuild/bbs-3.15-bioc/meat/lmdme.Rcheck/00check.log'
for details.
lmdme.Rcheck/00install.out
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### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL lmdme
###
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* installing to library 'D:/biocbuild/bbs-3.15-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
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
* DONE (lmdme)
Making 'packages.html' ... done
lmdme.Rcheck/lmdme-Ex.timings
| name | user | system | elapsed | |
| lmdme-biplot | 2.12 | 0.47 | 2.60 | |
| lmdme-decomposition | 2.19 | 0.46 | 2.64 | |
| lmdme-getters | 2.43 | 0.48 | 2.92 | |
| lmdme-leverage | 2.46 | 0.39 | 2.85 | |
| lmdme-lmdme | 1.83 | 0.39 | 2.22 | |
| lmdme-loadingplot | 2.23 | 0.31 | 2.56 | |
| lmdme-padjust | 1.89 | 0.32 | 2.20 | |
| lmdme-permutation | 4.84 | 0.90 | 5.75 | |
| lmdme-printshow | 2.11 | 0.33 | 2.44 | |
| lmdme-screeplot | 1.94 | 0.22 | 2.15 | |