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This page was generated on 2024-05-25 11:36:01 -0400 (Sat, 25 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4751
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4516
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 2195/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
tRanslatome 1.42.0  (landing page)
Toma Tebaldi , Erik Dassi
Snapshot Date: 2024-05-24 14:00:07 -0400 (Fri, 24 May 2024)
git_url: https://git.bioconductor.org/packages/tRanslatome
git_branch: RELEASE_3_19
git_last_commit: 7fa9e77
git_last_commit_date: 2024-04-30 10:32:02 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for tRanslatome on lconway


To the developers/maintainers of the tRanslatome package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/tRanslatome.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: tRanslatome
Version: 1.42.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:tRanslatome.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings tRanslatome_1.42.0.tar.gz
StartedAt: 2024-05-25 00:32:35 -0400 (Sat, 25 May 2024)
EndedAt: 2024-05-25 00:38:38 -0400 (Sat, 25 May 2024)
EllapsedTime: 363.1 seconds
RetCode: 0
Status:   OK  
CheckDir: tRanslatome.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:tRanslatome.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings tRanslatome_1.42.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/tRanslatome.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘tRanslatome/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘tRanslatome’ version ‘1.42.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'limma', 'anota', 'DESeq2', 'edgeR', 'RankProd', 'topGO',
  'org.Hs.eg.db', 'GOSemSim', 'Heatplus', 'gplots', 'plotrix',
  'Biobase'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘tRanslatome’ 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 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
methodLimma: no visible global function definition for ‘lmFit’
methodTTest: no visible global function definition for ‘calcTStatFast’
GOEnrichment,DEGs: no visible global function definition for ‘toTable’
Undefined global functions or variables:
  calcTStatFast lmFit toTable
* 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
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
GOComparison 20.323  1.355  21.860
GOEnrichment 15.829  0.259  16.226
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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-3.19-bioc/meat/tRanslatome.Rcheck/00check.log’
for details.


Installation output

tRanslatome.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL tRanslatome
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘tRanslatome’ ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
** testing if installed package can be loaded from final location

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
** testing if installed package keeps a record of temporary installation path
* DONE (tRanslatome)

Tests output


Example timings

tRanslatome.Rcheck/tRanslatome-Ex.timings

nameusersystemelapsed
CVplot0.0890.0080.098
DEGs0.0010.0000.002
DEGs.table0.0930.1280.222
EnrichedSets0.0010.0000.001
FC.threshold0.0490.0040.053
GOComparison20.323 1.35521.860
GOEnrichment15.829 0.25916.226
GOsets0.0000.0000.001
GOsims0.0000.0010.001
Heatmap0.1200.0070.130
Histogram0.0560.0050.062
IdentityPlot0.0500.0050.055
MAplot0.0670.0080.075
Radar0.1020.0070.110
RegulatoryEnrichment2.1380.0542.213
SDplot0.0610.0070.068
Scatterplot0.1090.0060.117
SimilarityPlot0.0500.0030.053
TranslatomeDataset0.0010.0010.002
average.similarity.scores0.0510.0040.054
computeDEGs0.2500.0090.259
enriched.table0.0540.0070.060
getConditionA0.0490.0040.053
getConditionB0.0460.0040.051
getConditionC0.0480.0040.053
getConditionD0.0490.0040.053
getConditionLabels0.0500.0040.054
getDEGs0.0470.0040.051
getDEGsMethod0.0490.0040.053
getDataType0.0430.0030.046
getExprMatrix0.0740.0760.151
getLevelLabels0.0500.0040.054
identity.matrix0.0520.0050.059
label.condition0.0500.0040.055
label.level.DEGs0.0480.0030.052
label.level.enriched0.0490.0050.054
newTranslatomeDataset0.0510.0050.057
significance.threshold0.0470.0030.051
similarity.matrix0.0500.0040.054
tRanslatomeSampleData0.0500.0050.055