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This page was generated on 2025-08-14 11:48 -0400 (Thu, 14 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
palomino7Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4566
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4604
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4545
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4579
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 2228/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
tRanslatome 1.46.0  (landing page)
Toma Tebaldi , Erik Dassi
Snapshot Date: 2025-08-11 13:40 -0400 (Mon, 11 Aug 2025)
git_url: https://git.bioconductor.org/packages/tRanslatome
git_branch: RELEASE_3_21
git_last_commit: 0750343
git_last_commit_date: 2025-04-15 10:24:21 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for tRanslatome on kunpeng2

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: tRanslatome
Version: 1.46.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:tRanslatome.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings tRanslatome_1.46.0.tar.gz
StartedAt: 2025-08-12 14:46:22 -0000 (Tue, 12 Aug 2025)
EndedAt: 2025-08-12 14:53:01 -0000 (Tue, 12 Aug 2025)
EllapsedTime: 398.4 seconds
RetCode: 0
Status:   OK  
CheckDir: tRanslatome.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:tRanslatome.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings tRanslatome_1.46.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/tRanslatome.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘tRanslatome/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘tRanslatome’ version ‘1.46.0’
* checking package namespace information ... OK
* checking package dependencies ... INFO
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 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
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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
GOComparison 19.613  0.806  20.455
GOEnrichment 15.983  0.244  16.270
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/tRanslatome.Rcheck/00check.log’
for details.


Installation output

tRanslatome.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL tRanslatome
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘tRanslatome’ ...
** this is package ‘tRanslatome’ version ‘1.46.0’
** 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
CVplot0.1000.0000.101
DEGs0.0010.0000.001
DEGs.table0.0730.0240.097
EnrichedSets0.0000.0010.001
FC.threshold0.0380.0030.041
GOComparison19.613 0.80620.455
GOEnrichment15.983 0.24416.270
GOsets000
GOsims000
Heatmap0.1170.0000.117
Histogram0.0450.0040.048
IdentityPlot0.0380.0040.042
MAplot0.0680.0000.069
Radar0.0910.0000.092
RegulatoryEnrichment1.8220.0161.843
SDplot0.0650.0040.068
Scatterplot0.1080.0000.108
SimilarityPlot0.0450.0000.045
TranslatomeDataset0.0010.0000.001
average.similarity.scores0.0410.0000.041
computeDEGs0.4550.0080.464
enriched.table0.0430.0040.047
getConditionA0.0400.0040.044
getConditionB0.0420.0000.042
getConditionC0.0420.0000.043
getConditionD0.0430.0000.042
getConditionLabels0.0390.0040.042
getDEGs0.0420.0000.042
getDEGsMethod0.0420.0000.043
getDataType0.0380.0040.043
getExprMatrix0.0530.0160.070
getLevelLabels0.0420.0000.042
identity.matrix0.0420.0000.043
label.condition0.0430.0000.043
label.level.DEGs0.0430.0000.042
label.level.enriched0.0420.0000.043
newTranslatomeDataset0.0440.0000.044
significance.threshold0.0380.0040.043
similarity.matrix0.0420.0000.043
tRanslatomeSampleData0.0420.0000.042