| Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-05-09 11:41:03 -0400 (Thu, 09 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4748 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4484 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4514 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4480 |
| 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 | ||||
| Package 1162/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| martini 1.24.0 (landing page) Hector Climente-Gonzalez
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | ||||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the martini package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: martini |
| Version: 1.24.0 |
| Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:martini.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings martini_1.24.0.tar.gz |
| StartedAt: 2024-05-09 09:00:07 -0000 (Thu, 09 May 2024) |
| EndedAt: 2024-05-09 09:04:13 -0000 (Thu, 09 May 2024) |
| EllapsedTime: 245.5 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: martini.Rcheck |
| Warnings: NA |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:martini.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings martini_1.24.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/martini.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘martini/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘martini’ version ‘1.24.0’
* 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++ (GCC) 10.3.1’
* 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 code 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 loading without being on the library search path ... 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 ... NOTE
Documented arguments not in \usage in Rd file 'organism_id2name.Rd':
‘organism’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/martini/libs/martini.so’:
Found ‘exit’, possibly from ‘exit’ (C)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
[1] 25 - 12 == 13
── Failure ('test_scones.cv.R:33:3'): we recover causal SNPs ───────────────────
sort(names(V(cones))) not equal to sort(grep("[AC]", test_map$snp, value = TRUE)).
Lengths differ: 25 is not 12
── Failure ('test_sigmod.cv.R:32:3'): we recover causal SNPs ───────────────────
gorder(cones) not equal to sum(grepl("[AC]", test_map$snp)).
1/1 mismatches
[1] 25 - 12 == 13
── Failure ('test_sigmod.cv.R:33:3'): we recover causal SNPs ───────────────────
sort(names(V(cones))) not equal to sort(grep("[AC]", test_map$snp, value = TRUE)).
Lengths differ: 25 is not 12
[ FAIL 4 | WARN 3 | SKIP 4 | PASS 228 ]
Error: Test failures
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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, 3 NOTEs
See
‘/home/biocbuild/bbs-3.19-bioc/meat/martini.Rcheck/00check.log’
for details.
martini.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL martini ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library’ * installing *source* package ‘martini’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (GCC) 10.3.1’ g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/bin/Rscript -e "Rcpp:::CxxFlags()"` -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -fopenmp -fPIC -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/bin/Rscript -e "Rcpp:::CxxFlags()"` -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -fopenmp -fPIC -g -O2 -Wall -c mincut.cpp -o mincut.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/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 cp -r lib/maxflow "/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/00LOCK-martini/00new/martini/include" mkdir -p "/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/00LOCK-martini/00new/martini/usrlib" cp libmaxflow.a "/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/00LOCK-martini/00new/martini/usrlib" g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-beta-2024-04-15_r86425/lib -L/usr/local/lib -o martini.so RcppExports.o mincut.o -pthread -fopenmp /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/00LOCK-martini/00new/martini/usrlib/libmaxflow.a -fopenmp -pthread -L/home/biocbuild/R/R-beta-2024-04-15_r86425/lib -lR installing to /home/biocbuild/R/R-beta-2024-04-15_r86425/site-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 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
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-downloads.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 4 | WARN 3 | SKIP 4 | PASS 228 ]
══ Skipped tests (4) ═══════════════════════════════════════════════════════════
• On Bioconductor (3): 'test_connect_biomart.R:1:1', 'test_get_gxg.R:1:1',
'test_snp2ensembl.R:1:1'
• empty test (1): 'test_plot_ideogram.R:3:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_scones.cv.R:32:3'): we recover causal SNPs ───────────────────
gorder(cones) not equal to sum(grepl("[AC]", test_map$snp)).
1/1 mismatches
[1] 25 - 12 == 13
── Failure ('test_scones.cv.R:33:3'): we recover causal SNPs ───────────────────
sort(names(V(cones))) not equal to sort(grep("[AC]", test_map$snp, value = TRUE)).
Lengths differ: 25 is not 12
── Failure ('test_sigmod.cv.R:32:3'): we recover causal SNPs ───────────────────
gorder(cones) not equal to sum(grepl("[AC]", test_map$snp)).
1/1 mismatches
[1] 25 - 12 == 13
── Failure ('test_sigmod.cv.R:33:3'): we recover causal SNPs ───────────────────
sort(names(V(cones))) not equal to sort(grep("[AC]", test_map$snp, value = TRUE)).
Lengths differ: 25 is not 12
[ FAIL 4 | WARN 3 | SKIP 4 | PASS 228 ]
Error: Test failures
Execution halted
martini.Rcheck/martini-Ex.timings
| name | user | system | elapsed | |
| check_installed | 0 | 0 | 0 | |
| get_GI_network | 0.059 | 0.000 | 0.059 | |
| get_GM_network | 0.022 | 0.000 | 0.022 | |
| get_GS_network | 0.008 | 0.000 | 0.009 | |
| get_grid | 0.003 | 0.000 | 0.004 | |
| get_gxg_biogrid | 0 | 0 | 0 | |
| get_gxg_string | 0 | 0 | 0 | |
| get_snp_modules | 0 | 0 | 0 | |
| is_coherent | 0.003 | 0.000 | 0.003 | |
| ldweight_edges | 0.142 | 0.000 | 0.142 | |
| mget_gxg_biogrid | 0.000 | 0.000 | 0.001 | |
| mget_gxg_string | 0 | 0 | 0 | |
| minigwas | 0.019 | 0.003 | 0.022 | |
| minippi | 0.002 | 0.000 | 0.002 | |
| minisnpMapping | 0.002 | 0.000 | 0.002 | |
| scones | 0.07 | 0.00 | 0.07 | |
| scones.cv | 0.182 | 0.016 | 0.198 | |
| scones.cv_ | 0.124 | 0.012 | 0.136 | |
| scones_ | 0.047 | 0.000 | 0.047 | |
| search_cones | 0 | 0 | 0 | |
| sigmod | 0.045 | 0.000 | 0.045 | |
| sigmod.cv | 0.166 | 0.004 | 0.170 | |
| sigmod.cv_ | 0.105 | 0.004 | 0.109 | |
| sigmod_ | 0.055 | 0.000 | 0.056 | |
| simulate_causal_snps | 0.044 | 0.000 | 0.044 | |
| simulate_phenotype | 0.046 | 0.000 | 0.046 | |
| subnet | 0.04 | 0.00 | 0.04 | |
| subvert | 0.046 | 0.000 | 0.047 | |