Konstantin Krismer
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/transite |
| Branch: RELEASE_3_12 |
| Last Commit: 9f50c01 |
| Last Changed Date: 2020-10-29 13:19:46 -0400 (Thu, 29 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:37:14 -0400 (Thu, 06 May 2021).
|
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 1888/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| transite 1.8.0 (landing page) Konstantin Krismer
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: transite |
| Version: 1.8.0 |
| 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_1.8.0.tar.gz |
| StartedAt: 2021-05-06 07:00:10 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 07:10:39 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 629.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: transite.Rcheck |
| Warnings: 0 |
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### Running command:
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### /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_1.8.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/transite.Rcheck’
* using R version 4.0.5 (2021-03-31)
* 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 ‘1.8.0’
* 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 ‘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_spma 63.847 0.515 77.117
run_kmer_tsma 62.501 0.168 66.717
calculate_kmer_enrichment 8.346 0.024 8.383
run_matrix_spma 4.067 0.072 8.515
* 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-3.12-bioc/meat/transite.Rcheck/00check.log’
for details.
transite.Rcheck/00install.out
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL transite
###
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* 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/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
SEXP data = Parent::get__();
^
1 warning generated.
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/usr/local/include -fPIC -Wall -g -O2 -c scoring.cpp -o scoring.o
In file included from scoring.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
SEXP data = Parent::get__();
^
1 warning generated.
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 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 95 ]
>
> proc.time()
user system elapsed
124.610 2.406 319.044
transite.Rcheck/transite-Ex.timings
| name | user | system | elapsed | |
| RBPMotif-class | 0.005 | 0.000 | 0.006 | |
| SpectrumScore-class | 0.002 | 0.001 | 0.003 | |
| calculate_kmer_enrichment | 8.346 | 0.024 | 8.383 | |
| calculate_local_consistency | 0.368 | 0.014 | 0.382 | |
| calculate_motif_enrichment | 1.768 | 0.029 | 1.799 | |
| calculate_transcript_mc | 0.01 | 0.00 | 0.01 | |
| check_kmers | 0.001 | 0.000 | 0.001 | |
| classify_spectrum | 3.070 | 0.110 | 3.185 | |
| compute_kmer_enrichment | 4.077 | 0.046 | 4.128 | |
| create_kmer_motif | 0.004 | 0.000 | 0.003 | |
| create_matrix_motif | 0.004 | 0.000 | 0.004 | |
| draw_volcano_plot | 0.287 | 0.008 | 0.295 | |
| estimate_significance_core | 0.003 | 0.000 | 0.003 | |
| generate_iupac_by_kmers | 0.001 | 0.001 | 0.001 | |
| generate_iupac_by_matrix | 0.003 | 0.000 | 0.003 | |
| generate_kmers | 0.162 | 0.001 | 0.165 | |
| generate_kmers_from_iupac | 0.003 | 0.000 | 0.003 | |
| geometric_mean | 0.001 | 0.000 | 0.000 | |
| get_motif_by_id | 0.006 | 0.000 | 0.007 | |
| get_motif_by_rbp | 0.006 | 0.001 | 0.008 | |
| get_motifs | 0 | 0 | 0 | |
| get_motifs_meta_info | 0.028 | 0.009 | 0.036 | |
| get_ppm | 0.006 | 0.000 | 0.007 | |
| init_iupac_lookup_table | 0.005 | 0.000 | 0.005 | |
| p_combine | 0.001 | 0.000 | 0.002 | |
| run_kmer_spma | 63.847 | 0.515 | 77.117 | |
| run_kmer_tsma | 62.501 | 0.168 | 66.717 | |
| run_matrix_spma | 4.067 | 0.072 | 8.515 | |
| run_matrix_tsma | 0.022 | 0.001 | 0.023 | |
| score_sequences | 0.005 | 0.001 | 0.006 | |
| score_spectrum | 3.260 | 0.016 | 3.280 | |
| score_transcripts | 0.008 | 0.000 | 0.008 | |
| set_motifs | 0.003 | 0.000 | 0.003 | |
| subdivide_data | 0.006 | 0.001 | 0.007 | |