Back to Multiple platform build/check report for BioC 3.17:   simplified   long
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This page was generated on 2023-09-27 11:37:13 -0400 (Wed, 27 Sep 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4625
palomino3Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4378
merida1macOS 12.6.4 Montereyx86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4394
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 433/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Cormotif 1.46.0  (landing page)
Yingying Wei
Snapshot Date: 2023-09-26 14:00:14 -0400 (Tue, 26 Sep 2023)
git_url: https://git.bioconductor.org/packages/Cormotif
git_branch: RELEASE_3_17
git_last_commit: 65cf1c5
git_last_commit_date: 2023-04-25 10:20:15 -0400 (Tue, 25 Apr 2023)
nebbiolo1Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.6.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for Cormotif on merida1


To the developers/maintainers of the Cormotif package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Cormotif.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: Cormotif
Version: 1.46.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Cormotif.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Cormotif_1.46.0.tar.gz
StartedAt: 2023-09-27 00:15:57 -0400 (Wed, 27 Sep 2023)
EndedAt: 2023-09-27 00:17:32 -0400 (Wed, 27 Sep 2023)
EllapsedTime: 95.3 seconds
RetCode: 0
Status:   OK  
CheckDir: Cormotif.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Cormotif.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Cormotif_1.46.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/Cormotif.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Cormotif/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Cormotif’ version ‘1.46.0’
* 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 ‘Cormotif’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘affy’
A package should be listed in only one of these fields.
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
cmfit: no visible global function definition for ‘runif’
limmafit: no visible global function definition for ‘new’
modt.f0.loglike: no visible global function definition for ‘dt’
modt.f1.loglike: no visible global function definition for ‘dt’
Undefined global functions or variables:
  dt new runif
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "dt", "runif")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 sizes of PDF files under ‘inst/doc’ ... 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.17-bioc/meat/Cormotif.Rcheck/00check.log’
for details.



Installation output

Cormotif.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Cormotif
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’
* installing *source* package ‘Cormotif’ ...
** 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 (Cormotif)

Tests output


Example timings

Cormotif.Rcheck/Cormotif-Ex.timings

nameusersystemelapsed
cormotiffit1.7140.0952.331
cormotiffitall0.5350.0160.719
cormotiffitfull1.4990.0462.112
cormotiffitsep1.4510.0171.966
generank1.5850.2272.274
plotIC1.5420.0352.004
plotMotif1.5470.0302.035