Back to Multiple platform build/check report for BioC 3.21:   simplified   long
ABCDEFGHIJKL[M]NOPQRSTUVWXYZ

This page was generated on 2024-12-24 11:40 -0500 (Tue, 24 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4373
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 1308/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
motifbreakR 2.21.0  (landing page)
Simon Gert Coetzee
Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024)
git_url: https://git.bioconductor.org/packages/motifbreakR
git_branch: devel
git_last_commit: 81a16d2
git_last_commit_date: 2024-10-29 10:03:45 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino7Windows 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  NO, package depends on 'rtracklayer' which is only available as a source package that needs compilation
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    WARNINGS    OK  NO, package depends on 'rtracklayer' which is only available as a source package that needs compilation
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  


CHECK results for motifbreakR on nebbiolo1

To the developers/maintainers of the motifbreakR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/motifbreakR.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: motifbreakR
Version: 2.21.0
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:motifbreakR.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings motifbreakR_2.21.0.tar.gz
StartedAt: 2024-12-24 00:01:53 -0500 (Tue, 24 Dec 2024)
EndedAt: 2024-12-24 00:18:24 -0500 (Tue, 24 Dec 2024)
EllapsedTime: 991.3 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: motifbreakR.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:motifbreakR.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings motifbreakR_2.21.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/motifbreakR.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘motifbreakR/DESCRIPTION’ ... OK
* this is package ‘motifbreakR’ version ‘2.21.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 24 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 ‘motifbreakR’ 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 ... NOTE
Package in Depends field not imported from: 'MotifDb'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
biomartToGranges: no visible binding for global variable 'chr_name'
biomartToGranges: no visible binding for global variable 'chrom_start'
biomartToGranges: no visible binding for global variable 'chrom_end'
biomartToGranges: no visible binding for global variable 'SNP_id'
biomartToGranges: no visible binding for global variable 'REF'
biomartToGranges: no visible binding for global variable 'ALT'
calculatePvalue: no visible binding for global variable 'Refpvalue'
calculatePvalue: no visible binding for global variable 'Altpvalue'
convertPeakFile: no visible binding for global variable 'chr'
convertPeakFile: no visible binding for global variable 'name'
Undefined global functions or variables:
  ALT Altpvalue REF Refpvalue SNP_id chr chr_name chrom_end chrom_start
  name
* checking Rd files ... NOTE
checkRd: (-1) calculatePvalue.Rd:7: Lost braces
     7 | H{\'e}l{\`e}ne Touzet and Jean-St{\'e}phane Varr{\'e} (2007) Efficient and accurate P-value computation for Position Weight Matrices.
       |  ^
checkRd: (-1) calculatePvalue.Rd:7: Lost braces
     7 | H{\'e}l{\`e}ne Touzet and Jean-St{\'e}phane Varr{\'e} (2007) Efficient and accurate P-value computation for Position Weight Matrices.
       |        ^
checkRd: (-1) calculatePvalue.Rd:7: Lost braces
     7 | H{\'e}l{\`e}ne Touzet and Jean-St{\'e}phane Varr{\'e} (2007) Efficient and accurate P-value computation for Position Weight Matrices.
       |                                  ^
checkRd: (-1) calculatePvalue.Rd:7: Lost braces
     7 | H{\'e}l{\`e}ne Touzet and Jean-St{\'e}phane Varr{\'e} (2007) Efficient and accurate P-value computation for Position Weight Matrices.
       |                                                 ^
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  calculatePvalue.Rd: TFMsc2pv
  findSupportingRemapPeaks.Rd: MotifDb, associateTranscriptionFactors
  motifbreakR.Rd: TFMPvalue-package, TFMsc2pv
  shiny_motifbreakR.Rd: shinyAppDir
  snps.from.file.Rd: useEnsembl
  snps.from.rsid.Rd: useEnsembl
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... WARNING
Undocumented data sets:
  'example.pvalue'
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... INFO
  Note: found 12 marked UTF-8 strings
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
snps.from.rsid  104.167 22.478 129.911
calculatePvalue  46.556  0.525  47.087
motifbreakR       9.927  0.681  10.608
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: ‘SNPlocs.Hsapiens.dbSNP142.GRCh37’
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/motifbreakR.Rcheck/00check.log’
for details.


Installation output

motifbreakR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL motifbreakR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘motifbreakR’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
See system.file("LICENSE", package="MotifDb") for use restrictions.
No methods found in package 'Biostrings' for request: 'pattern' when loading 'TFBSTools'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
See system.file("LICENSE", package="MotifDb") for use restrictions.
No methods found in package 'Biostrings' for request: 'pattern' when loading 'TFBSTools'
** testing if installed package can be loaded from final location
See system.file("LICENSE", package="MotifDb") for use restrictions.
No methods found in package 'Biostrings' for request: 'pattern' when loading 'TFBSTools'
** testing if installed package keeps a record of temporary installation path
* DONE (motifbreakR)

Tests output


Example timings

motifbreakR.Rcheck/motifbreakR-Ex.timings

nameusersystemelapsed
calculatePvalue46.556 0.52547.087
encodemotif0.0630.0050.068
example.results0.0800.0040.085
exportMBbed0.0500.0020.052
exportMBtable0.0470.0030.051
factorbook0.0110.0000.011
findSupportingRemapPeaks0.0160.0010.017
hocomoco0.0220.0010.024
homer0.0130.0010.015
motifbreakR 9.927 0.68110.608
motifbreakR_motif0.0840.0040.088
plotMB0.0560.0030.059
shiny_motifbreakR0.1480.0240.172
snps.from.file1.6480.1371.787
snps.from.rsid104.167 22.478129.911