| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2024-04-17 11:38:21 -0400 (Wed, 17 Apr 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4676 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4414 |
| merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4437 |
| 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 2164/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| transite 1.20.1 (landing page) Konstantin Krismer
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the transite package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/transite.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: transite |
| Version: 1.20.1 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:transite.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings transite_1.20.1.tar.gz |
| StartedAt: 2024-04-16 10:04:54 -0400 (Tue, 16 Apr 2024) |
| EndedAt: 2024-04-16 10:19:13 -0400 (Tue, 16 Apr 2024) |
| EllapsedTime: 858.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: transite.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:transite.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings transite_1.20.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/transite.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘transite/DESCRIPTION’ ... OK
* this is package ‘transite’ version ‘1.20.1’
* 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 ‘transite’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
* 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 R 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 startup messages can be suppressed ... 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 data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
run_kmer_tsma 85.606 0.347 89.758
run_kmer_spma 77.363 0.791 112.582
calculate_kmer_enrichment 10.054 0.048 10.405
run_matrix_spma 7.844 0.129 11.629
score_spectrum 5.366 0.043 5.598
compute_kmer_enrichment 5.207 0.040 10.602
classify_spectrum 4.840 0.203 7.129
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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
‘/Users/biocbuild/bbs-3.18-bioc/meat/transite.Rcheck/00check.log’
for details.
transite.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL transite ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’ * installing *source* package ‘transite’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using C++11 using SDK: ‘MacOSX11.3.sdk’ clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c scoring.cpp -o scoring.o clang++ -arch x86_64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o transite.so RcppExports.o scoring.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/00LOCK-transite/00new/transite/libs ** R ** data ** 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 ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (transite)
transite.Rcheck/tests/testthat.Rout
R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (64-bit)
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.
> library(testthat)
> library(transite)
>
> test_check("transite")
[ FAIL 0 | WARN 6 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 6 | SKIP 0 | PASS 95 ]
>
> proc.time()
user system elapsed
174.257 4.562 377.205
transite.Rcheck/transite-Ex.timings
| name | user | system | elapsed | |
| RBPMotif-class | 0.010 | 0.002 | 0.037 | |
| SpectrumScore-class | 0.003 | 0.002 | 0.004 | |
| calculate_kmer_enrichment | 10.054 | 0.048 | 10.405 | |
| calculate_local_consistency | 0.952 | 0.022 | 1.009 | |
| calculate_motif_enrichment | 2.272 | 0.059 | 2.555 | |
| calculate_transcript_mc | 0.010 | 0.001 | 0.012 | |
| check_kmers | 0.000 | 0.001 | 0.002 | |
| classify_spectrum | 4.840 | 0.203 | 7.129 | |
| compute_kmer_enrichment | 5.207 | 0.040 | 10.602 | |
| create_kmer_motif | 0.005 | 0.000 | 0.006 | |
| create_matrix_motif | 0.006 | 0.001 | 0.018 | |
| draw_volcano_plot | 0.755 | 0.018 | 1.585 | |
| estimate_significance_core | 0.005 | 0.001 | 0.015 | |
| generate_iupac_by_kmers | 0.001 | 0.000 | 0.002 | |
| generate_iupac_by_matrix | 0.005 | 0.000 | 0.017 | |
| generate_kmers | 0.262 | 0.002 | 0.530 | |
| generate_kmers_from_iupac | 0.005 | 0.001 | 0.015 | |
| geometric_mean | 0 | 0 | 0 | |
| get_motif_by_id | 0.010 | 0.001 | 0.031 | |
| get_motif_by_rbp | 0.012 | 0.004 | 0.027 | |
| get_motifs | 0.000 | 0.001 | 0.000 | |
| get_motifs_meta_info | 0.030 | 0.018 | 0.096 | |
| get_ppm | 0.010 | 0.001 | 0.021 | |
| init_iupac_lookup_table | 0.006 | 0.000 | 0.006 | |
| p_combine | 0.001 | 0.001 | 0.001 | |
| run_kmer_spma | 77.363 | 0.791 | 112.582 | |
| run_kmer_tsma | 85.606 | 0.347 | 89.758 | |
| run_matrix_spma | 7.844 | 0.129 | 11.629 | |
| run_matrix_tsma | 0.046 | 0.003 | 0.052 | |
| score_sequences | 0.010 | 0.002 | 0.013 | |
| score_spectrum | 5.366 | 0.043 | 5.598 | |
| score_transcripts | 0.016 | 0.002 | 0.027 | |
| set_motifs | 0.005 | 0.000 | 0.039 | |
| subdivide_data | 0.009 | 0.002 | 0.011 | |