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This page was generated on 2023-04-12 11:05:05 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
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

CHECK results for gespeR on nebbiolo2


To the developers/maintainers of the gespeR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/gespeR.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 806/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gespeR 1.30.0  (landing page)
Fabian Schmich
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/gespeR
git_branch: RELEASE_3_16
git_last_commit: 6213cb5
git_last_commit_date: 2022-11-01 11:10:56 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: gespeR
Version: 1.30.0
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:gespeR.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings gespeR_1.30.0.tar.gz
StartedAt: 2023-04-10 20:59:08 -0400 (Mon, 10 Apr 2023)
EndedAt: 2023-04-10 21:03:49 -0400 (Mon, 10 Apr 2023)
EllapsedTime: 280.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: gespeR.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:gespeR.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings gespeR_1.30.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/gespeR.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘gespeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gespeR’ version ‘1.30.0’
* 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 ‘gespeR’ 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.gespeR.cv: no visible global function definition for ‘coef’
.select.model: no visible global function definition for ‘predict’
concordance: no visible global function definition for ‘cor’
lasso.rand: no visible global function definition for ‘runif’
plot.gespeR: no visible global function definition for ‘hist’
stability.selection: no visible global function definition for ‘lm’
Phenotypes,character: no visible global function definition for
  ‘read.delim’
Undefined global functions or variables:
  coef cor hist lm predict read.delim runif
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "coef", "cor", "lm", "predict", "runif")
  importFrom("utils", "read.delim")
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 ... WARNING
Codoc mismatches from documentation object 'c,Phenotypes-method':
\S4method{c}{Phenotypes}
  Code: function(x, ...)
  Docs: function(x, ..., recursive = FALSE)
  Argument names in docs not in code:
    recursive

* 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 (user + system) or elapsed time > 5s
                   user system elapsed
gespeR-package    5.995  0.304  54.647
gespeR-class      0.322  0.047  12.938
stability-methods 0.167  0.018  12.441
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘gespeR.Rnw’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.16-bioc/meat/gespeR.Rcheck/00check.log’
for details.



Installation output

gespeR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL gespeR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-library’
* installing *source* package ‘gespeR’ ...
** 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 (gespeR)

Tests output


Example timings

gespeR.Rcheck/gespeR-Ex.timings

nameusersystemelapsed
Phenotypes-class0.0070.0030.011
TargetRelations-class0.0070.0000.007
annotate.gsp-methods0.1090.0040.113
as.data.frame-Phenotypes-method0.1440.0040.149
c-Phenotypes-method0.7800.0750.857
concordance0.5680.0800.649
gespeR-class 0.322 0.04712.938
gespeR-package 5.995 0.30454.647
gspssp-methods0.2120.0200.232
join-methods0.0110.0000.011
lasso.rand0.0060.0000.006
na.rem-methods0.0450.0000.046
path-methods0.0050.0000.005
rbo0.0000.0000.001
scores-methods0.1380.0040.142
simData0.0080.0000.008
stability-methods 0.167 0.01812.441
stabilityfits0.1160.0000.116
target-relations-methods0.1370.0060.142
trmatrix-methods0.1400.0060.146
values-methods0.0170.0030.020