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This page was generated on 2024-07-03 11:38 -0400 (Wed, 03 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4693
palomino6Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4413
lconwaymacOS 12.7.1 Montereyx86_644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4407
kjohnson3macOS 13.6.5 Venturaarm644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4356
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 (2024-04-24) -- "Puppy Cup" 4407
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 829/2243HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gespeR 1.37.0  (landing page)
Fabian Schmich
Snapshot Date: 2024-07-02 14:00 -0400 (Tue, 02 Jul 2024)
git_url: https://git.bioconductor.org/packages/gespeR
git_branch: devel
git_last_commit: 44a1e66
git_last_commit_date: 2024-04-30 10:41:08 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  NO, package depends on 'cellHTS2' which is not available
palomino6Windows Server 2022 Datacenter / x64  ERROR    ERROR  skippedskipped
lconwaymacOS 12.7.1 Monterey / x86_64  ERROR    ERROR  skippedskipped
kjohnson3macOS 13.6.5 Ventura / arm64  ERROR    ERROR  skippedskipped
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  ERROR    ERROR  skipped


CHECK results for gespeR on nebbiolo2

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: 1.37.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:gespeR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings gespeR_1.37.0.tar.gz
StartedAt: 2024-07-02 23:28:33 -0400 (Tue, 02 Jul 2024)
EndedAt: 2024-07-02 23:33:25 -0400 (Tue, 02 Jul 2024)
EllapsedTime: 292.6 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: gespeR.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:gespeR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings gespeR_1.37.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/gespeR.Rcheck’
* using R version 4.4.0 RC (2024-04-16 r86468)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘gespeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gespeR’ 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 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 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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
gespeR-package    5.618  0.635  67.314
gespeR-class      0.184  0.006  14.254
stability-methods 0.129  0.019  14.628
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/gespeR.Rcheck/00check.log’
for details.


Installation output

gespeR.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL gespeR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-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-class0.0060.0040.010
TargetRelations-class0.0070.0000.007
annotate.gsp-methods0.1100.0030.115
as.data.frame-Phenotypes-method0.1390.0040.143
c-Phenotypes-method0.0270.0040.030
concordance0.4590.0640.522
gespeR-class 0.184 0.00614.254
gespeR-package 5.618 0.63567.314
gspssp-methods0.1430.0160.159
join-methods0.0100.0050.014
lasso.rand0.0050.0030.008
na.rem-methods0.0260.0000.026
path-methods0.0050.0000.006
rbo0.0010.0000.001
scores-methods0.1370.0000.137
simData0.0090.0000.009
stability-methods 0.129 0.01914.628
stabilityfits0.1410.0070.149
target-relations-methods0.1100.0070.117
trmatrix-methods0.1100.0040.115
values-methods0.0130.0090.021