Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-02 12:09 -0400 (Sat, 02 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4796 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4535 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4578 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4519 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4517 |
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 2199/2313 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
transcriptogramer 1.31.0 (landing page) Diego Morais
| nebbiolo2 | Linux (Ubuntu 24.04.2 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 | ![]() | ||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the transcriptogramer package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/transcriptogramer.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. |
Package: transcriptogramer |
Version: 1.31.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:transcriptogramer.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings transcriptogramer_1.31.0.tar.gz |
StartedAt: 2025-08-02 00:30:56 -0400 (Sat, 02 Aug 2025) |
EndedAt: 2025-08-02 00:35:33 -0400 (Sat, 02 Aug 2025) |
EllapsedTime: 277.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: transcriptogramer.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:transcriptogramer.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings transcriptogramer_1.31.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/transcriptogramer.Rcheck’ * using R version 4.5.1 (2025-06-13) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘transcriptogramer/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘transcriptogramer’ version ‘1.31.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * 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 ‘transcriptogramer’ can be installed ... OK * checking installed package size ... INFO installed size is 5.2Mb sub-directories of 1Mb or more: data 4.6Mb * 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 ... OK * 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 LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.R’ OK * 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: OK
transcriptogramer.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL transcriptogramer ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘transcriptogramer’ ... ** this is package ‘transcriptogramer’ version ‘1.31.0’ ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (transcriptogramer)
transcriptogramer.Rcheck/tests/runTests.Rout
R version 4.5.1 (2025-06-13) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > BiocGenerics:::testPackage("transcriptogramer") preprocessing input data... step 1 of 1 calculating node properties... step 1 of 2 ** this may take some time... applying sliding window and mounting resulting data... step 2 of 2 ** this may take some time... done! mapping identifiers to ENSEMBL Peptide ID... step 1 of 2 averaging over all identifiers related to the same protein... step 2 of 2 done! applying sliding window and mounting resulting data... step 1 of 1 done! RUNIT TEST PROTOCOL -- Sat Aug 2 00:35:20 2025 *********************************************** Number of test functions: 3 Number of errors: 0 Number of failures: 0 1 Test Suite : transcriptogramer RUnit Tests - 3 test functions, 0 errors, 0 failures Number of test functions: 3 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 10.667 1.545 112.587
transcriptogramer.Rcheck/transcriptogramer-Ex.timings
name | user | system | elapsed | |
DE-method | 1.172 | 0.044 | 1.222 | |
DEsymbols | 0.158 | 0.172 | 0.334 | |
GPL570 | 0.627 | 0.460 | 1.098 | |
GSE9988 | 0.531 | 0.559 | 1.097 | |
Hs700 | 0.115 | 0.127 | 0.244 | |
Hs800 | 0.086 | 0.096 | 0.182 | |
Hs900 | 0.061 | 0.083 | 0.145 | |
HsBPTerms | 0.758 | 0.629 | 1.394 | |
Mm700 | 0.110 | 0.140 | 0.251 | |
Mm800 | 0.092 | 0.116 | 0.208 | |
Mm900 | 0.073 | 0.093 | 0.167 | |
Rn700 | 0.113 | 0.140 | 0.256 | |
Rn800 | 0.089 | 0.114 | 0.204 | |
Rn900 | 0.075 | 0.100 | 0.176 | |
Sc700 | 0.026 | 0.040 | 0.066 | |
Sc800 | 0.02 | 0.03 | 0.05 | |
Sc900 | 0.021 | 0.029 | 0.050 | |
Terms-method | 0.078 | 0.007 | 0.086 | |
association | 0.843 | 0.612 | 1.462 | |
clusterEnrichment-method | 0.034 | 0.005 | 0.038 | |
clusterVisualization-method | 0.061 | 0.008 | 0.068 | |
connectivityProperties-method | 0.037 | 0.001 | 0.037 | |
differentiallyExpressed-method | 0.061 | 0.007 | 0.069 | |
enrichmentPlot-method | 0.039 | 0.000 | 0.039 | |
orderingProperties-method | 0.056 | 0.004 | 0.060 | |
radius-method | 0.035 | 0.003 | 0.037 | |
transcriptogramPreprocess | 0.506 | 0.009 | 0.518 | |
transcriptogramStep1-method | 0.037 | 0.001 | 0.039 | |
transcriptogramStep2-method | 0.033 | 0.001 | 0.034 | |