Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-24 11:47 -0500 (Tue, 24 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
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 2166/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
tRanslatome 1.45.0 (landing page) Toma Tebaldi
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | 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: 1.45.0 |
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_1.45.0.tar.gz |
StartedAt: 2024-12-24 12:13:00 -0000 (Tue, 24 Dec 2024) |
EndedAt: 2024-12-24 12:20:49 -0000 (Tue, 24 Dec 2024) |
EllapsedTime: 468.5 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_1.45.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/tRanslatome.Rcheck’ * using R Under development (unstable) (2024-11-24 r87369) * 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) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘tRanslatome/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘tRanslatome’ version ‘1.45.0’ * 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 20.166 0.579 25.774 GOEnrichment 15.040 0.144 16.856 * 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.
tRanslatome.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL tRanslatome ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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 | 0.141 | |
DEGs | 0.001 | 0.000 | 0.001 | |
DEGs.table | 0.076 | 0.024 | 0.200 | |
EnrichedSets | 0.001 | 0.000 | 0.000 | |
FC.threshold | 0.042 | 0.004 | 0.095 | |
GOComparison | 20.166 | 0.579 | 25.774 | |
GOEnrichment | 15.040 | 0.144 | 16.856 | |
GOsets | 0.000 | 0.000 | 0.001 | |
GOsims | 0.000 | 0.000 | 0.001 | |
Heatmap | 0.118 | 0.008 | 0.146 | |
Histogram | 0.050 | 0.004 | 0.085 | |
IdentityPlot | 0.041 | 0.004 | 0.046 | |
MAplot | 0.071 | 0.000 | 0.072 | |
Radar | 0.096 | 0.004 | 0.100 | |
RegulatoryEnrichment | 1.866 | 0.028 | 1.983 | |
SDplot | 0.064 | 0.008 | 0.072 | |
Scatterplot | 0.113 | 0.000 | 0.113 | |
SimilarityPlot | 0.048 | 0.000 | 0.049 | |
TranslatomeDataset | 0 | 0 | 0 | |
average.similarity.scores | 0.046 | 0.000 | 0.046 | |
computeDEGs | 0.337 | 0.000 | 0.337 | |
enriched.table | 0.048 | 0.000 | 0.048 | |
getConditionA | 0.041 | 0.004 | 0.045 | |
getConditionB | 0.041 | 0.004 | 0.045 | |
getConditionC | 0.045 | 0.000 | 0.046 | |
getConditionD | 0.045 | 0.000 | 0.045 | |
getConditionLabels | 0.045 | 0.000 | 0.045 | |
getDEGs | 0.045 | 0.000 | 0.045 | |
getDEGsMethod | 0.044 | 0.000 | 0.045 | |
getDataType | 0.041 | 0.004 | 0.045 | |
getExprMatrix | 0.058 | 0.012 | 0.070 | |
getLevelLabels | 0.037 | 0.008 | 0.045 | |
identity.matrix | 0.045 | 0.000 | 0.045 | |
label.condition | 0.041 | 0.004 | 0.058 | |
label.level.DEGs | 0.049 | 0.004 | 0.102 | |
label.level.enriched | 0.047 | 0.000 | 0.096 | |
newTranslatomeDataset | 0.047 | 0.000 | 0.059 | |
significance.threshold | 0.045 | 0.000 | 0.045 | |
similarity.matrix | 0.045 | 0.000 | 0.046 | |
tRanslatomeSampleData | 0.045 | 0.000 | 0.045 | |