Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:06:02 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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

CHECK results for TargetScore on nebbiolo2


To the developers/maintainers of the TargetScore package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/TargetScore.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1932/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TargetScore 1.32.0  (landing page)
Yue Li
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/TargetScore
git_branch: RELEASE_3_14
git_last_commit: 1b24f38
git_last_commit_date: 2021-10-26 12:08:57 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: TargetScore
Version: 1.32.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:TargetScore.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings TargetScore_1.32.0.tar.gz
StartedAt: 2022-04-12 09:37:55 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 09:38:27 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 32.3 seconds
RetCode: 0
Status:   OK  
CheckDir: TargetScore.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:TargetScore.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings TargetScore_1.32.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/TargetScore.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TargetScore/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TargetScore’ version ‘1.32.0’
* 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 ‘TargetScore’ 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 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
dot.ext: no visible global function definition for ‘size’
getTargetScores: no visible global function definition for
  ‘get_TargetScanHuman_contextScore’
getTargetScores: no visible global function definition for
  ‘get_TargetScanHuman_PCT’
getTargetScores: no visible global function definition for
  ‘get_validated_targets’
getTargetScores: no visible global function definition for
  ‘get_miRNA_family_info’
getTargetScores: no visible binding for global variable ‘logFC.imputed’
getTargetScores : <anonymous>: no visible global function definition
  for ‘cor’
getTargetScores: no visible global function definition for ‘aggregate’
logmvgamma: no visible global function definition for ‘size’
targetScore: no visible global function definition for ‘as.roman’
targetScore : <anonymous>: no visible global function definition for
  ‘as.roman’
targetScore: no visible global function definition for ‘sigmoid’
Undefined global functions or variables:
  aggregate as.roman cor get_TargetScanHuman_PCT
  get_TargetScanHuman_contextScore get_miRNA_family_info
  get_validated_targets logFC.imputed sigmoid size
Consider adding
  importFrom("stats", "aggregate", "cor")
  importFrom("utils", "as.roman")
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 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.14-bioc/meat/TargetScore.Rcheck/00check.log’
for details.



Installation output

TargetScore.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL TargetScore
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘TargetScore’ ...
** using staged installation
** R
** 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 (TargetScore)

Tests output


Example timings

TargetScore.Rcheck/TargetScore-Ex.timings

nameusersystemelapsed
TargetScore-package0.0000.0000.001
bsxfun.se0.0010.0000.000
dot.ext000
getTargetScores0.0010.0000.001
initialization0.0070.0040.010
logmvgamma0.0010.0000.001
logsumexp0.0010.0000.001
sort_components0.0800.0150.096
targetScore0.3620.0040.367
vbgmm0.0630.0000.064
vbound0.0690.0000.070
vexp0.0650.0000.066
vmax0.0690.0000.069