Back to Build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-03-01 07:38:44 -0000 (Wed, 01 Mar 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4266 |
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 martini package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/martini.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1083/2171 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
martini 1.19.0 (landing page) Hector Climente-Gonzalez
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
Package: martini |
Version: 1.19.0 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:martini.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings martini_1.19.0.tar.gz |
StartedAt: 2023-02-28 07:12:16 -0000 (Tue, 28 Feb 2023) |
EndedAt: 2023-02-28 07:16:56 -0000 (Tue, 28 Feb 2023) |
EllapsedTime: 279.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: martini.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:martini.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings martini_1.19.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/martini.Rcheck’ * using R Under development (unstable) (2023-01-14 r83615) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.1 LTS * using session charset: UTF-8 * checking for file ‘martini/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘martini’ version ‘1.19.0’ * 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 ‘martini’ can be installed ... OK * used C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’ * 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 ... NOTE get_GI_network: no visible binding for global variable ‘gene1’ get_GI_network: no visible binding for global variable ‘gene2’ get_GM_network: no visible binding for global variable ‘gene’ group_snps: no visible binding for global variable ‘.’ Undefined global functions or variables: . gene gene1 gene2 * 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 line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files is not available File ‘/home/biocbuild/bbs-3.17-bioc/R/library/martini/libs/martini.so’: Found ‘exit’, possibly from ‘exit’ (C) 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 * 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 ... ‘scones_usage.Rmd’ using ‘UTF-8’... OK ‘simulate_phenotype.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/home/biocbuild/bbs-3.17-bioc/meat/martini.Rcheck/00check.log’ for details.
martini.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL martini ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘martini’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’ g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include' -I/usr/local/include -std=c++11 -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -I./lib `/home/biocbuild/bbs-3.17-bioc/R/bin/Rscript -e "Rcpp:::CxxFlags()"` -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -fopenmp -fPIC -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include' -I/usr/local/include -std=c++11 -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -I./lib `/home/biocbuild/bbs-3.17-bioc/R/bin/Rscript -e "Rcpp:::CxxFlags()"` -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -fopenmp -fPIC -g -O2 -Wall -c mincut.cpp -o mincut.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include' -I/usr/local/include -std=c++11 -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -I./lib `/home/biocbuild/bbs-3.17-bioc/R/bin/Rscript -e "Rcpp:::CxxFlags()"` -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -fopenmp -fPIC -g -O2 -Wall -c lib/maxflow/maxflow.cpp -o lib/maxflow/maxflow.o ar -crus libmaxflow.a lib/maxflow/maxflow.o ar: `u' modifier ignored since `D' is the default (see `U') cp -r lib/maxflow "/home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-martini/00new/martini/include" mkdir -p "/home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-martini/00new/martini/usrlib" cp libmaxflow.a "/home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-martini/00new/martini/usrlib" g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o martini.so RcppExports.o mincut.o -pthread -fopenmp /home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-martini/00new/martini/usrlib/libmaxflow.a -fopenmp -pthread -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-martini/00new/martini/libs ** 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 ** 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 (martini)
martini.Rcheck/tests/testthat.Rout
R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu (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(martini) > library(igraph) Attaching package: 'igraph' The following object is masked from 'package:testthat': compare The following objects are masked from 'package:stats': decompose, spectrum The following object is masked from 'package:base': union > > test_check("martini") trying URL 'https://stringdb-static.org/download/protein.links.v11.5/9606.protein.links.v11.5.txt.gz' Content type 'application/octet-stream' length 72718210 bytes (69.3 MB) ================================================== downloaded 69.3 MB [ FAIL 0 | WARN 1 | SKIP 4 | PASS 232 ] ══ Skipped tests ═══════════════════════════════════════════════════════════════ • On Bioconductor (3) • empty test (1) [ FAIL 0 | WARN 1 | SKIP 4 | PASS 232 ] > > proc.time() user system elapsed 89.223 3.183 188.461
martini.Rcheck/martini-Ex.timings
name | user | system | elapsed | |
check_installed | 0 | 0 | 0 | |
get_GI_network | 0.058 | 0.000 | 0.059 | |
get_GM_network | 0.032 | 0.000 | 0.032 | |
get_GS_network | 0.009 | 0.000 | 0.008 | |
get_grid | 0.003 | 0.000 | 0.003 | |
get_gxg_biogrid | 0.001 | 0.000 | 0.000 | |
get_gxg_string | 0 | 0 | 0 | |
get_snp_modules | 0 | 0 | 0 | |
is_coherent | 0.004 | 0.000 | 0.003 | |
ldweight_edges | 0.070 | 0.000 | 0.069 | |
mget_gxg_biogrid | 0 | 0 | 0 | |
mget_gxg_string | 0 | 0 | 0 | |
minigwas | 0.024 | 0.000 | 0.024 | |
minippi | 0.003 | 0.000 | 0.002 | |
minisnpMapping | 0.002 | 0.000 | 0.002 | |
scones | 0.061 | 0.027 | 0.090 | |
scones.cv | 0.201 | 0.008 | 0.210 | |
scones.cv_ | 0.114 | 0.004 | 0.117 | |
scones_ | 0.142 | 0.000 | 0.141 | |
search_cones | 0 | 0 | 0 | |
sigmod | 0.044 | 0.000 | 0.044 | |
sigmod.cv | 0.180 | 0.000 | 0.181 | |
sigmod.cv_ | 0.123 | 0.000 | 0.123 | |
sigmod_ | 0.047 | 0.000 | 0.048 | |
simulate_causal_snps | 0.045 | 0.000 | 0.045 | |
simulate_phenotype | 0.043 | 0.004 | 0.047 | |
subnet | 0.046 | 0.004 | 0.049 | |
subvert | 0.032 | 0.004 | 0.037 | |