| Back to Build/check report for BioC 3.17 |
|
This page was generated on 2023-02-08 01:15:12 -0000 (Wed, 08 Feb 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4164 |
| 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 1081/2164 | 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 | ERROR | |||||||||
| 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: 2023-02-07 06:47:00 -0000 (Tue, 07 Feb 2023) |
| EndedAt: 2023-02-07 06:50:28 -0000 (Tue, 07 Feb 2023) |
| EllapsedTime: 208.3 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: martini.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### 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’
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
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
Killed
* 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: 1 ERROR, 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.fail
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
Killed
martini.Rcheck/martini-Ex.timings
| name | user | system | elapsed | |
| check_installed | 0.001 | 0.000 | 0.000 | |
| get_GI_network | 0.054 | 0.001 | 0.061 | |
| get_GM_network | 0.03 | 0.00 | 0.03 | |
| get_GS_network | 0.008 | 0.000 | 0.008 | |
| get_grid | 0.003 | 0.000 | 0.003 | |
| get_gxg_biogrid | 0 | 0 | 0 | |
| get_gxg_string | 0 | 0 | 0 | |
| get_snp_modules | 0 | 0 | 0 | |
| is_coherent | 0.004 | 0.000 | 0.003 | |
| ldweight_edges | 0.063 | 0.000 | 0.064 | |
| mget_gxg_biogrid | 0 | 0 | 0 | |
| mget_gxg_string | 0.001 | 0.000 | 0.000 | |
| minigwas | 0.023 | 0.000 | 0.023 | |
| minippi | 0.002 | 0.000 | 0.002 | |
| minisnpMapping | 0.002 | 0.000 | 0.002 | |
| scones | 0.055 | 0.000 | 0.056 | |
| scones.cv | 0.184 | 0.004 | 0.189 | |
| scones.cv_ | 0.113 | 0.004 | 0.118 | |
| scones_ | 0.039 | 0.000 | 0.040 | |
| search_cones | 0 | 0 | 0 | |
| sigmod | 0.125 | 0.008 | 0.132 | |
| sigmod.cv | 0.164 | 0.004 | 0.167 | |
| sigmod.cv_ | 0.105 | 0.000 | 0.106 | |
| sigmod_ | 0.04 | 0.00 | 0.04 | |
| simulate_causal_snps | 0.046 | 0.000 | 0.045 | |
| simulate_phenotype | 0.04 | 0.00 | 0.04 | |
| subnet | 0.030 | 0.004 | 0.033 | |
| subvert | 0.026 | 0.004 | 0.030 | |