Back to Multiple platform build/check report for BioC 3.18:   simplified   long
ABCDEFGHIJKLMNOPQR[S]TUVWXYZ

This page was generated on 2024-03-27 11:36:17 -0400 (Wed, 27 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4667
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4403
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4426
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 1958/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SimBindProfiles 1.40.0  (landing page)
Bettina Fischer
Snapshot Date: 2024-03-25 14:05:07 -0400 (Mon, 25 Mar 2024)
git_url: https://git.bioconductor.org/packages/SimBindProfiles
git_branch: RELEASE_3_18
git_last_commit: cea1be0
git_last_commit_date: 2023-10-24 09:56:00 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 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
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for SimBindProfiles on nebbiolo2


To the developers/maintainers of the SimBindProfiles package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SimBindProfiles.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: SimBindProfiles
Version: 1.40.0
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:SimBindProfiles.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings SimBindProfiles_1.40.0.tar.gz
StartedAt: 2024-03-26 02:32:18 -0400 (Tue, 26 Mar 2024)
EndedAt: 2024-03-26 02:35:23 -0400 (Tue, 26 Mar 2024)
EllapsedTime: 185.3 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: SimBindProfiles.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:SimBindProfiles.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings SimBindProfiles_1.40.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/SimBindProfiles.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* 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 ‘SimBindProfiles/DESCRIPTION’ ... OK
* this is package ‘SimBindProfiles’ version ‘1.40.0’
* 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 ‘SimBindProfiles’ can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'Ringo' is deprecated and will be removed from Bioconductor
See ‘/home/biocbuild/bbs-3.18-bioc/meat/SimBindProfiles.Rcheck/00install.out’ for details.
* 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
compensationRegions: no visible global function definition for
  ‘write.table’
eSetScatterPlot : upPan: no visible global function definition for
  ‘par’
eSetScatterPlot : upPan: no visible global function definition for
  ‘smoothScatter’
eSetScatterPlot : lowPan: no visible global function definition for
  ‘text’
eSetScatterPlot : lowPan: no visible global function definition for
  ‘par’
eSetScatterPlot : lowPan: no visible global function definition for
  ‘cor’
eSetScatterPlot: no visible global function definition for ‘pairs’
filterRegionsPairwise: no visible global function definition for ‘tail’
filterRegionsThreeway: no visible global function definition for ‘tail’
findBoundCutoff: no visible global function definition for ‘hist’
findBoundCutoff: no visible global function definition for ‘p.adjust’
increasedBindingRegions: no visible global function definition for
  ‘write.table’
normalNull: no visible global function definition for ‘na.omit’
normalNull: no visible global function definition for ‘density’
normalNull: no visible global function definition for ‘sd’
normalNull: no visible global function definition for ‘pnorm’
pairwiseRegions: no visible global function definition for
  ‘write.table’
plotBoundProbes: no visible global function definition for ‘points’
probeLengthPlot: no visible global function definition for ‘tail’
readSgrFiles: no visible global function definition for ‘read.delim’
threewayRegions: no visible global function definition for
  ‘write.table’
twoGaussiansNull.BF: no visible global function definition for
  ‘na.omit’
twoGaussiansNull.BF: no visible global function definition for ‘dnorm’
twoGaussiansNull.BF: no visible global function definition for ‘lines’
twoGaussiansNull.BF: no visible global function definition for ‘legend’
twoGaussiansNull.BF: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  cor density dnorm hist legend lines na.omit p.adjust pairs par pnorm
  points read.delim sd smoothScatter tail text write.table
Consider adding
  importFrom("graphics", "hist", "legend", "lines", "pairs", "par",
             "points", "smoothScatter", "text")
  importFrom("stats", "cor", "density", "dnorm", "na.omit", "p.adjust",
             "pnorm", "sd")
  importFrom("utils", "read.delim", "tail", "write.table")
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 ... 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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘SimBindProfiles.Rnw’... OK
 OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/SimBindProfiles.Rcheck/00check.log’
for details.



Installation output

SimBindProfiles.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL SimBindProfiles
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’
* installing *source* package ‘SimBindProfiles’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning message:
Package 'Ringo' is deprecated and will be removed from Bioconductor
  version 3.19 
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: Package 'Ringo' is deprecated and will be removed from Bioconductor
  version 3.19
** testing if installed package can be loaded from final location
Warning: Package 'Ringo' is deprecated and will be removed from Bioconductor
  version 3.19
** testing if installed package keeps a record of temporary installation path
* DONE (SimBindProfiles)

Tests output


Example timings

SimBindProfiles.Rcheck/SimBindProfiles-Ex.timings

nameusersystemelapsed
SGR0.3550.0000.355
compensationRegions1.0440.0071.052
eSetScatterPlot1.2780.0111.290
findBoundCutoff1.8400.0641.904
increasedBindingRegions0.9860.0471.034
pairwiseRegions0.6750.0080.683
plotBoundProbes0.7390.0080.747
probeAnnoFromESet0.5530.0240.577
probeLengthPlot0.9680.0160.984
readSgrFiles0.0880.0040.093
threewayRegions1.2160.0201.237