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This page was generated on 2024-06-11 14:43 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4757
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4491
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4522
kjohnson3macOS 13.6.5 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4468
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 854/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gespeR 1.36.0  (landing page)
Fabian Schmich
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/gespeR
git_branch: RELEASE_3_19
git_last_commit: a1e0cc3
git_last_commit_date: 2024-04-30 10:41:08 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows 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 13.6.5 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published


CHECK results for gespeR on kjohnson3

To the developers/maintainers of the gespeR package:
- 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 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: gespeR
Version: 1.36.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:gespeR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings gespeR_1.36.0.tar.gz
StartedAt: 2024-06-10 17:06:29 -0400 (Mon, 10 Jun 2024)
EndedAt: 2024-06-10 17:14:20 -0400 (Mon, 10 Jun 2024)
EllapsedTime: 471.2 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: gespeR.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:gespeR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings gespeR_1.36.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/gespeR.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gespeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gespeR’ version ‘1.36.0’
* 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 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 ... 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 Rd file 'c-Phenotypes-method.Rd':
\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 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
gespeR-package    5.463  0.423  88.673
gespeR-class      1.236  0.051  22.669
stability-methods 0.106  0.044  18.875
* 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, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/gespeR.Rcheck/00check.log’
for details.


Installation output

gespeR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL gespeR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/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-class0.0130.0010.028
TargetRelations-class0.0080.0020.016
annotate.gsp-methods0.1310.0070.235
as.data.frame-Phenotypes-method0.1560.0060.268
c-Phenotypes-method0.0350.0030.057
concordance0.7010.0291.183
gespeR-class 1.236 0.05122.669
gespeR-package 5.463 0.42388.673
gspssp-methods0.1460.0050.232
join-methods0.0120.0020.017
lasso.rand0.0070.0010.008
na.rem-methods0.0280.0010.028
path-methods0.0050.0010.005
rbo0.0010.0000.001
scores-methods0.1170.0040.121
simData0.0090.0010.011
stability-methods 0.106 0.04418.875
stabilityfits0.0960.0040.171
target-relations-methods0.0990.0050.183
trmatrix-methods0.0950.0040.164
values-methods0.0160.0090.044