Multiple platform build/check report for BioC 3.19 - CHECK results for martini on kunpeng2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 22.04.3 LTS)	x86_64	R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences"	4708
palomino3	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences"	4446
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences"	4471
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences"	4426
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*

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### Running command:
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###   /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:martini.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings martini_1.23.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/martini.Rcheck’
* using R Under development (unstable) (2024-03-19 r86153)
* 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 ‘1.23.0’
* 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-4.4-devel-2024.03.20/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 5 | WARN 4 | SKIP 4 | PASS 218 ]
  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.

Installation output

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### Running command:
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###   /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD INSTALL martini
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* installing to library ‘/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/site-library/00LOCK-martini/00new/martini/include"
mkdir -p "/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/00LOCK-martini/00new/martini/usrlib"
cp libmaxflow.a "/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/00LOCK-martini/00new/martini/usrlib"
g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.4-devel-2024.03.20/lib -L/usr/local/lib -o martini.so RcppExports.o mincut.o -pthread -fopenmp /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/00LOCK-martini/00new/martini/usrlib/libmaxflow.a -fopenmp -pthread -L/home/biocbuild/R/R-4.4-devel-2024.03.20/lib -lR
installing to /home/biocbuild/R/R-4.4-devel-2024.03.20/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)

Tests output


R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences"
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 5 | WARN 4 | SKIP 4 | PASS 218 ]

══ 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 ════════════════════════════════════════════════════════════════
── Error ('test_get_gxg_string.R:3:1'): (code run outside of `test_that()`) ────
Error in `value[[3L]](cond)`: unable to find an appropriate database for hsapiens.
Backtrace:
     ▆
  1. └─martini:::get_gxg_string(9606) at test_get_gxg_string.R:3:1
  2.   └─martini:::connect_biomart(organism)
  3.     └─base::tryCatch(...)
  4.       └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  5.         └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
  6.           └─value[[3L]](cond)
  7.             └─base::tryCatch(...)
  8.               └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  9.                 └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 10.                   └─value[[3L]](cond)
── 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 5 | WARN 4 | SKIP 4 | PASS 218 ]
Error: Test failures
Execution halted

name	user	system	elapsed
check_installed	0	0	0
get_GI_network	0.056	0.004	0.060
get_GM_network	0.022	0.000	0.021
get_GS_network	0.009	0.000	0.009
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	0.003	0.000	0.004
ldweight_edges	0.144	0.000	0.145
mget_gxg_biogrid	0	0	0
mget_gxg_string	0	0	0
minigwas	0.019	0.004	0.024
minippi	0.002	0.000	0.002
minisnpMapping	0.002	0.000	0.002
scones	0.080	0.024	0.104
scones.cv	0.189	0.012	0.202
scones.cv_	0.123	0.012	0.135
scones_	0.046	0.000	0.046
search_cones	0	0	0
sigmod	0.044	0.000	0.044
sigmod.cv	0.179	0.000	0.178
sigmod.cv_	0.113	0.000	0.113
sigmod_	0.06	0.00	0.06
simulate_causal_snps	0.041	0.008	0.049
simulate_phenotype	0.048	0.000	0.048
subnet	0.042	0.000	0.041
subvert	0.044	0.004	0.047

CHECK results for martini on kunpeng2

Summary

Command output

Installation output

Tests output

Example timings