| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-10-19 13:23:12 -0400 (Wed, 19 Oct 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4386 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" | 4138 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4205 |
| 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 1075/2140 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| martini 1.16.0 (landing page) Hector Climente-Gonzalez
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | ERROR | OK | |||||||||
| Package: martini |
| Version: 1.16.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:martini.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings martini_1.16.0.tar.gz |
| StartedAt: 2022-10-19 04:11:16 -0400 (Wed, 19 Oct 2022) |
| EndedAt: 2022-10-19 04:16:05 -0400 (Wed, 19 Oct 2022) |
| EllapsedTime: 288.6 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: martini.Rcheck |
| Warnings: NA |
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### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:martini.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings martini_1.16.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/martini.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘martini/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘martini’ version ‘1.16.0’
* 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
* 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 ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/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. 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:
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_mincut_c.R:9'): output is as expected ──────────────────────────
Error in `mincut_c(c, 1, 2, W)`: Need S4 class dgCMatrix for a sparse matrix
Backtrace:
▆
1. └─martini:::mincut_c(c, 1, 2, W) at test_mincut_c.R:9:2
── Error ('test_mincut_c.R:29'): we recover causal SNPs ────────────────────────
Error in `mincut_c(c, 1, 2, W)`: Need S4 class dgCMatrix for a sparse matrix
Backtrace:
▆
1. └─martini:::mincut_c(c, 1, 2, W) at test_mincut_c.R:29:2
[ FAIL 2 | WARN 1 | SKIP 4 | PASS 228 ]
Error: Test failures
Execution halted
* 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 ERROR, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.15-bioc/meat/martini.Rcheck/00check.log’
for details.
martini.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL martini ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’ * installing *source* package ‘martini’ ... ** using staged installation ** libs clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include' -I/usr/local/include -std=c++11 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -I./lib `/Library/Frameworks/R.framework/Resources/bin/Rscript -e "Rcpp:::CxxFlags()"` -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include' -I/usr/local/include -std=c++11 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -I./lib `/Library/Frameworks/R.framework/Resources/bin/Rscript -e "Rcpp:::CxxFlags()"` -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -fPIC -Wall -g -O2 -c mincut.cpp -o mincut.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include' -I/usr/local/include -std=c++11 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -I./lib `/Library/Frameworks/R.framework/Resources/bin/Rscript -e "Rcpp:::CxxFlags()"` -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -fPIC -Wall -g -O2 -c lib/maxflow/maxflow.cpp -o lib/maxflow/maxflow.o ar -crus libmaxflow.a lib/maxflow/maxflow.o cp -r lib/maxflow "/Library/Frameworks/R.framework/Versions/4.2/Resources/library/00LOCK-martini/00new/martini/include" mkdir -p "/Library/Frameworks/R.framework/Versions/4.2/Resources/library/00LOCK-martini/00new/martini/usrlib" cp libmaxflow.a "/Library/Frameworks/R.framework/Versions/4.2/Resources/library/00LOCK-martini/00new/martini/usrlib" clang++ -mmacosx-version-min=10.13 -std=gnu++14 -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 martini.so RcppExports.o mincut.o -pthread /Library/Frameworks/R.framework/Versions/4.2/Resources/library/00LOCK-martini/00new/martini/usrlib/libmaxflow.a -pthread -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.2/Resources/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 version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 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(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.v11.0/9606.protein.links.v11.0.txt.gz'
Content type 'application/octet-stream' length 71241372 bytes (67.9 MB)
==================================================
downloaded 67.9 MB
[ FAIL 2 | WARN 1 | SKIP 4 | PASS 228 ]
══ Skipped tests ═══════════════════════════════════════════════════════════════
• On Bioconductor (3)
• empty test (1)
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_mincut_c.R:9'): output is as expected ──────────────────────────
Error in `mincut_c(c, 1, 2, W)`: Need S4 class dgCMatrix for a sparse matrix
Backtrace:
▆
1. └─martini:::mincut_c(c, 1, 2, W) at test_mincut_c.R:9:2
── Error ('test_mincut_c.R:29'): we recover causal SNPs ────────────────────────
Error in `mincut_c(c, 1, 2, W)`: Need S4 class dgCMatrix for a sparse matrix
Backtrace:
▆
1. └─martini:::mincut_c(c, 1, 2, W) at test_mincut_c.R:29:2
[ FAIL 2 | WARN 1 | SKIP 4 | PASS 228 ]
Error: Test failures
Execution halted
martini.Rcheck/martini-Ex.timings
| name | user | system | elapsed | |
| check_installed | 0.000 | 0.000 | 0.001 | |
| get_GI_network | 0.080 | 0.005 | 0.084 | |
| get_GM_network | 0.027 | 0.002 | 0.028 | |
| get_GS_network | 0.012 | 0.001 | 0.012 | |
| get_grid | 0.003 | 0.000 | 0.003 | |
| get_gxg_biogrid | 0 | 0 | 0 | |
| get_gxg_string | 0.000 | 0.000 | 0.001 | |
| get_snp_modules | 0 | 0 | 0 | |
| is_coherent | 0.019 | 0.000 | 0.019 | |
| ldweight_edges | 0.090 | 0.003 | 0.094 | |
| mget_gxg_biogrid | 0.000 | 0.000 | 0.001 | |
| mget_gxg_string | 0 | 0 | 0 | |
| minigwas | 0.031 | 0.007 | 0.037 | |
| minippi | 0.004 | 0.002 | 0.005 | |
| minisnpMapping | 0.004 | 0.002 | 0.005 | |
| scones | 0.089 | 0.004 | 0.094 | |
| scones.cv | 0.294 | 0.007 | 0.302 | |
| scones.cv_ | 0.171 | 0.004 | 0.175 | |
| scones_ | 0.064 | 0.003 | 0.066 | |
| search_cones | 0 | 0 | 0 | |
| sigmod | 0.058 | 0.002 | 0.061 | |
| sigmod.cv | 0.274 | 0.005 | 0.279 | |
| sigmod.cv_ | 0.167 | 0.003 | 0.171 | |
| sigmod_ | 0.067 | 0.002 | 0.069 | |
| simulate_causal_snps | 0.065 | 0.002 | 0.067 | |
| simulate_phenotype | 0.063 | 0.005 | 0.067 | |
| subnet | 0.054 | 0.002 | 0.056 | |
| subvert | 0.049 | 0.002 | 0.051 | |