Konstantin Krismer
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/transite |
| Branch: RELEASE_3_11 |
| Last Commit: 487aea9 |
| Last Changed Date: 2020-08-25 11:18:31 -0400 (Tue, 25 Aug 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:59:48 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE transite PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1824/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| transite 1.6.2 Konstantin Krismer
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | NA | |||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | [ OK ] | OK | |
| Package: transite |
| Version: 1.6.2 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:transite.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings transite_1.6.2.tar.gz |
| StartedAt: 2020-10-17 06:00:55 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 06:13:07 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 731.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: transite.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:transite.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings transite_1.6.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/transite.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘transite/DESCRIPTION’ ... OK
* this is package ‘transite’ version ‘1.6.2’
* 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
* 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 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 76.932 0.156 91.761
run_kmer_spma 65.951 0.594 66.595
calculate_kmer_enrichment 9.740 0.024 9.773
run_matrix_spma 5.013 0.055 10.622
score_spectrum 3.527 0.035 5.478
* 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: 1 NOTE
See
‘/Users/biocbuild/bbs-3.11-bioc/meat/transite.Rcheck/00check.log’
for details.
transite.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL transite ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’ * installing *source* package ‘transite’ ... ** using staged installation ** libs clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I/usr/local/include -fPIC -Wall -g -O2 -c scoring.cpp -o scoring.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/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/4.0/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 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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")
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 95 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
151.797 2.637 380.526
transite.Rcheck/transite-Ex.timings
| name | user | system | elapsed | |
| RBPMotif-class | 0.008 | 0.001 | 0.008 | |
| SpectrumScore-class | 0.003 | 0.001 | 0.004 | |
| calculate_kmer_enrichment | 9.740 | 0.024 | 9.773 | |
| calculate_local_consistency | 0.554 | 0.018 | 0.573 | |
| calculate_motif_enrichment | 2.021 | 0.035 | 2.060 | |
| calculate_transcript_mc | 0.009 | 0.000 | 0.010 | |
| check_kmers | 0.001 | 0.000 | 0.001 | |
| classify_spectrum | 3.448 | 0.132 | 3.583 | |
| compute_kmer_enrichment | 4.762 | 0.045 | 4.810 | |
| create_kmer_motif | 0.006 | 0.000 | 0.006 | |
| create_matrix_motif | 0.005 | 0.000 | 0.006 | |
| draw_volcano_plot | 0.308 | 0.008 | 0.315 | |
| estimate_significance_core | 0.004 | 0.001 | 0.005 | |
| generate_iupac_by_kmers | 0.002 | 0.001 | 0.001 | |
| generate_iupac_by_matrix | 0.005 | 0.000 | 0.005 | |
| generate_kmers | 0.222 | 0.002 | 0.223 | |
| generate_kmers_from_iupac | 0.005 | 0.001 | 0.005 | |
| geometric_mean | 0 | 0 | 0 | |
| get_motif_by_id | 0.008 | 0.001 | 0.009 | |
| get_motif_by_rbp | 0.005 | 0.002 | 0.007 | |
| get_motifs | 0 | 0 | 0 | |
| get_motifs_meta_info | 0.037 | 0.017 | 0.054 | |
| get_ppm | 0.006 | 0.001 | 0.007 | |
| init_iupac_lookup_table | 0.005 | 0.000 | 0.006 | |
| p_combine | 0.002 | 0.001 | 0.002 | |
| run_kmer_spma | 65.951 | 0.594 | 66.595 | |
| run_kmer_tsma | 76.932 | 0.156 | 91.761 | |
| run_matrix_spma | 5.013 | 0.055 | 10.622 | |
| run_matrix_tsma | 0.039 | 0.002 | 0.077 | |
| score_sequences | 0.010 | 0.001 | 0.019 | |
| score_spectrum | 3.527 | 0.035 | 5.478 | |
| score_transcripts | 0.010 | 0.000 | 0.011 | |
| set_motifs | 0.004 | 0.000 | 0.005 | |
| subdivide_data | 0.009 | 0.000 | 0.010 | |