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This page was generated on 2024-05-22 11:35:20 -0400 (Wed, 22 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4751
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4485
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 3444
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: 2024-05-21 14:00:15 -0400 (Tue, 21 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
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  ERROR    ERROR  skippedskipped
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for tRanslatome on nebbiolo1


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: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:tRanslatome.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings tRanslatome_1.42.0.tar.gz
StartedAt: 2024-05-22 03:52:32 -0400 (Wed, 22 May 2024)
EndedAt: 2024-05-22 03:58:26 -0400 (Wed, 22 May 2024)
EllapsedTime: 354.0 seconds
RetCode: 0
Status:   OK  
CheckDir: tRanslatome.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:tRanslatome.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings tRanslatome_1.42.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/tRanslatome.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* 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 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 12.917  0.635  13.553
GOEnrichment 12.002  0.140  12.143
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/tRanslatome.Rcheck/00check.log’
for details.


Installation output

tRanslatome.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL tRanslatome
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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
CVplot0.1090.0000.110
DEGs0.0010.0000.001
DEGs.table0.0710.1760.247
EnrichedSets0.0000.0010.001
FC.threshold0.0470.0030.049
GOComparison12.917 0.63513.553
GOEnrichment12.002 0.14012.143
GOsets0.0000.0000.001
GOsims000
Heatmap0.1080.0080.115
Histogram0.0500.0040.054
IdentityPlot0.0480.0000.049
MAplot0.0720.0120.083
Radar0.0960.0000.096
RegulatoryEnrichment1.2810.0351.318
SDplot0.0830.0000.082
Scatterplot0.1100.0040.114
SimilarityPlot0.0500.0000.051
TranslatomeDataset0.0010.0000.001
average.similarity.scores0.0490.0000.049
computeDEGs0.2120.0080.219
enriched.table0.0490.0040.052
getConditionA0.0460.0030.049
getConditionB0.0500.0010.050
getConditionC0.0490.0000.050
getConditionD0.0450.0040.049
getConditionLabels0.050.000.05
getDEGs0.0460.0030.050
getDEGsMethod0.0480.0000.049
getDataType0.0410.0070.049
getExprMatrix0.0700.0770.145
getLevelLabels0.0450.0030.049
identity.matrix0.0450.0050.048
label.condition0.0450.0040.049
label.level.DEGs0.0480.0000.049
label.level.enriched0.0530.0000.053
newTranslatomeDataset0.0430.0080.050
significance.threshold0.0490.0000.049
similarity.matrix0.050.000.05
tRanslatomeSampleData0.0450.0040.049