Back to Mac ARM64 build report for BioC 3.20 |
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This page was generated on 2024-05-20 11:32:22 -0400 (Mon, 20 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4381 |
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 2124/2233 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
transcriptogramer 1.27.0 (landing page) Diego Morais
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | ||||||||
To the developers/maintainers of the transcriptogramer package: - 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: 1.27.0 |
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_1.27.0.tar.gz |
StartedAt: 2024-05-20 05:27:19 -0400 (Mon, 20 May 2024) |
EndedAt: 2024-05-20 05:31:10 -0400 (Mon, 20 May 2024) |
EllapsedTime: 231.2 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_1.27.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/transcriptogramer.Rcheck’ * using R version 4.4.0 Patched (2024-04-24 r86482) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.6.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘transcriptogramer/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘transcriptogramer’ version ‘1.27.0’ * 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 ... NOTE installed size is 5.6Mb sub-directories of 1Mb or more: data 5.0Mb * 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: 1 NOTE See ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/transcriptogramer.Rcheck/00check.log’ for details.
transcriptogramer.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL transcriptogramer ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘transcriptogramer’ ... ** 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 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-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 -- Mon May 20 05:30:57 2024 *********************************************** 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 10.097 0.793 61.276
transcriptogramer.Rcheck/transcriptogramer-Ex.timings
name | user | system | elapsed | |
DE-method | 1.524 | 0.032 | 1.561 | |
DEsymbols | 0.187 | 0.143 | 0.332 | |
GPL570 | 0.777 | 0.427 | 1.213 | |
GSE9988 | 0.653 | 0.514 | 1.173 | |
Hs700 | 0.134 | 0.111 | 0.249 | |
Hs800 | 0.111 | 0.095 | 0.215 | |
Hs900 | 0.076 | 0.078 | 0.158 | |
HsBPTerms | 0.913 | 0.585 | 1.529 | |
Mm700 | 0.137 | 0.129 | 0.270 | |
Mm800 | 0.108 | 0.107 | 0.222 | |
Mm900 | 0.089 | 0.086 | 0.183 | |
Rn700 | 0.139 | 0.131 | 0.271 | |
Rn800 | 0.109 | 0.106 | 0.216 | |
Rn900 | 0.086 | 0.082 | 0.168 | |
Sc700 | 0.032 | 0.035 | 0.069 | |
Sc800 | 0.027 | 0.034 | 0.061 | |
Sc900 | 0.024 | 0.030 | 0.057 | |
Terms-method | 0.079 | 0.004 | 0.084 | |
association | 1.079 | 0.581 | 1.681 | |
clusterEnrichment-method | 0.040 | 0.004 | 0.044 | |
clusterVisualization-method | 0.065 | 0.007 | 0.072 | |
connectivityProperties-method | 0.043 | 0.003 | 0.048 | |
differentiallyExpressed-method | 0.066 | 0.005 | 0.071 | |
enrichmentPlot-method | 0.041 | 0.003 | 0.044 | |
orderingProperties-method | 0.063 | 0.003 | 0.066 | |
radius-method | 0.042 | 0.001 | 0.043 | |
transcriptogramPreprocess | 0.579 | 0.009 | 0.589 | |
transcriptogramStep1-method | 0.040 | 0.002 | 0.043 | |
transcriptogramStep2-method | 0.040 | 0.001 | 0.041 | |