Back to Build/check report for BioC 3.17 |
|
This page was generated on 2023-01-02 09:00:54 -0500 (Mon, 02 Jan 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
palomino5 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" | 4165 |
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 |
To the developers/maintainers of the transite package: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 2057/2158 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
transite 1.17.0 (landing page) Konstantin Krismer
| palomino5 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ||||||||
Package: transite |
Version: 1.17.0 |
Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:transite.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings transite_1.17.0.tar.gz |
StartedAt: 2022-12-29 04:17:23 -0500 (Thu, 29 Dec 2022) |
EndedAt: 2022-12-29 04:23:46 -0500 (Thu, 29 Dec 2022) |
EllapsedTime: 383.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: transite.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:transite.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings transite_1.17.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/transite.Rcheck' * using R Under development (unstable) (2022-12-25 r83502 ucrt) * using platform: x86_64-w64-mingw32 (64-bit) * R was compiled by gcc.exe (GCC) 10.4.0 GNU Fortran (GCC) 10.4.0 * running under: Windows Server x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'transite/DESCRIPTION' ... OK * this is package 'transite' version '1.17.0' * 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 whether package 'transite' can be installed ... OK * used C++ compiler: 'G__~1.EXE (GCC) 12.2.0' * 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 for x64 is not available File 'F:/biocbuild/bbs-3.17-bioc/R/library/transite/libs/x64/transite.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs nor [v]sprintf. The detected symbols are linked into the code but might come from libraries and not actually be called. See 'Writing portable packages' in the 'Writing R Extensions' manual. * checking files in 'vignettes' ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed run_kmer_tsma 35.25 0.38 36.69 run_kmer_spma 34.20 0.09 35.59 run_matrix_spma 2.83 0.11 5.53 * 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 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/transite.Rcheck/00check.log' for details.
transite.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL transite ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library' * installing *source* package 'transite' ... ** using staged installation ** libs using C++ compiler: 'G__~1.EXE (GCC) 12.2.0' using C++11 g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c scoring.cpp -o scoring.o g++ -shared -s -static-libgcc -o transite.dll tmp.def RcppExports.o scoring.o -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.17-bioc/R/library/00LOCK-transite/00new/transite/libs/x64 ** 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 ** 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 Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" Copyright (C) 2022 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (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 60.03 0.92 181.29
transite.Rcheck/transite-Ex.timings
name | user | system | elapsed | |
RBPMotif-class | 0 | 0 | 0 | |
SpectrumScore-class | 0 | 0 | 0 | |
calculate_kmer_enrichment | 3.45 | 0.05 | 3.50 | |
calculate_local_consistency | 0.39 | 0.01 | 0.40 | |
calculate_motif_enrichment | 2.17 | 0.00 | 2.18 | |
calculate_transcript_mc | 0 | 0 | 0 | |
check_kmers | 0 | 0 | 0 | |
classify_spectrum | 2.34 | 0.16 | 2.58 | |
compute_kmer_enrichment | 2.81 | 0.14 | 3.12 | |
create_kmer_motif | 0 | 0 | 0 | |
create_matrix_motif | 0.02 | 0.00 | 0.02 | |
draw_volcano_plot | 0.56 | 0.02 | 0.58 | |
estimate_significance_core | 0.02 | 0.00 | 0.01 | |
generate_iupac_by_kmers | 0 | 0 | 0 | |
generate_iupac_by_matrix | 0 | 0 | 0 | |
generate_kmers | 0.17 | 0.01 | 0.53 | |
generate_kmers_from_iupac | 0.00 | 0.00 | 0.04 | |
geometric_mean | 0 | 0 | 0 | |
get_motif_by_id | 0 | 0 | 0 | |
get_motif_by_rbp | 0.00 | 0.00 | 0.05 | |
get_motifs | 0 | 0 | 0 | |
get_motifs_meta_info | 0.02 | 0.02 | 0.03 | |
get_ppm | 0 | 0 | 0 | |
init_iupac_lookup_table | 0 | 0 | 0 | |
p_combine | 0.02 | 0.00 | 0.02 | |
run_kmer_spma | 34.20 | 0.09 | 35.59 | |
run_kmer_tsma | 35.25 | 0.38 | 36.69 | |
run_matrix_spma | 2.83 | 0.11 | 5.53 | |
run_matrix_tsma | 0.01 | 0.00 | 0.01 | |
score_sequences | 0.02 | 0.00 | 0.02 | |
score_spectrum | 1.86 | 0.00 | 1.86 | |
score_transcripts | 0.01 | 0.00 | 0.02 | |
set_motifs | 0 | 0 | 0 | |
subdivide_data | 0 | 0 | 0 | |