Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-11-20 12:08 -0500 (Wed, 20 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
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 2182/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
tRanslatome 1.44.0 (landing page) Toma Tebaldi
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
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. |
Package: tRanslatome |
Version: 1.44.0 |
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_1.44.0.tar.gz |
StartedAt: 2024-11-20 13:24:45 -0000 (Wed, 20 Nov 2024) |
EndedAt: 2024-11-20 13:31:18 -0000 (Wed, 20 Nov 2024) |
EllapsedTime: 392.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: tRanslatome.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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_1.44.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/tRanslatome.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14) GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (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 ‘1.44.0’ * 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 20.118 0.491 20.649 GOEnrichment 16.669 0.184 16.885 * 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 ‘/home/biocbuild/bbs-3.20-bioc/meat/tRanslatome.Rcheck/00check.log’ for details.
tRanslatome.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL tRanslatome ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/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)
tRanslatome.Rcheck/tRanslatome-Ex.timings
name | user | system | elapsed | |
CVplot | 0.102 | 0.000 | 0.103 | |
DEGs | 0.000 | 0.000 | 0.001 | |
DEGs.table | 0.077 | 0.020 | 0.097 | |
EnrichedSets | 0.001 | 0.000 | 0.000 | |
FC.threshold | 0.044 | 0.000 | 0.044 | |
GOComparison | 20.118 | 0.491 | 20.649 | |
GOEnrichment | 16.669 | 0.184 | 16.885 | |
GOsets | 0.000 | 0.000 | 0.001 | |
GOsims | 0.000 | 0.000 | 0.001 | |
Heatmap | 0.121 | 0.000 | 0.121 | |
Histogram | 0.052 | 0.000 | 0.052 | |
IdentityPlot | 0.043 | 0.004 | 0.047 | |
MAplot | 0.067 | 0.008 | 0.075 | |
Radar | 0.095 | 0.004 | 0.099 | |
RegulatoryEnrichment | 1.763 | 0.000 | 1.767 | |
SDplot | 0.065 | 0.008 | 0.074 | |
Scatterplot | 0.108 | 0.004 | 0.112 | |
SimilarityPlot | 0.048 | 0.000 | 0.048 | |
TranslatomeDataset | 0 | 0 | 0 | |
average.similarity.scores | 0.038 | 0.008 | 0.046 | |
computeDEGs | 0.396 | 0.000 | 0.397 | |
enriched.table | 0.046 | 0.004 | 0.051 | |
getConditionA | 0.043 | 0.004 | 0.047 | |
getConditionB | 0.047 | 0.000 | 0.047 | |
getConditionC | 0.047 | 0.000 | 0.047 | |
getConditionD | 0.048 | 0.000 | 0.048 | |
getConditionLabels | 0.043 | 0.004 | 0.047 | |
getDEGs | 0.045 | 0.004 | 0.049 | |
getDEGsMethod | 0.046 | 0.000 | 0.047 | |
getDataType | 0.039 | 0.008 | 0.047 | |
getExprMatrix | 0.058 | 0.016 | 0.074 | |
getLevelLabels | 0.042 | 0.004 | 0.047 | |
identity.matrix | 0.047 | 0.000 | 0.048 | |
label.condition | 0.047 | 0.000 | 0.047 | |
label.level.DEGs | 0.047 | 0.000 | 0.047 | |
label.level.enriched | 0.046 | 0.000 | 0.046 | |
newTranslatomeDataset | 0.049 | 0.000 | 0.049 | |
significance.threshold | 0.047 | 0.000 | 0.048 | |
similarity.matrix | 0.039 | 0.008 | 0.047 | |
tRanslatomeSampleData | 0.047 | 0.000 | 0.046 | |