Back to Multiple platform build/check report for BioC 3.13
ABCDEFGHIJKL[M]NOPQRSTUVWXYZ

This page was generated on 2021-09-17 15:06:42 -0400 (Fri, 17 Sep 2021).

CHECK results for martini on machv2

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? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1034/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
martini 1.12.0  (landing page)
Hector Climente-Gonzalez
Snapshot Date: 2021-09-16 04:50:11 -0400 (Thu, 16 Sep 2021)
git_url: https://git.bioconductor.org/packages/martini
git_branch: RELEASE_3_13
git_last_commit: 21f22dd
git_last_commit_date: 2021-06-29 09:35:34 -0400 (Tue, 29 Jun 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: martini
Version: 1.12.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:martini.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings martini_1.12.0.tar.gz
StartedAt: 2021-09-16 20:45:40 -0400 (Thu, 16 Sep 2021)
EndedAt: 2021-09-16 20:49:15 -0400 (Thu, 16 Sep 2021)
EllapsedTime: 214.7 seconds
RetCode: 0
Status:   OK  
CheckDir: martini.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:martini.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings martini_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/martini.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.12.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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/4.1/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’
 OK
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/martini.Rcheck/00check.log’
for details.



Installation output

martini.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL martini
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/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/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/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/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/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/4.1/Resources/library/00LOCK-martini/00new/martini/include"
mkdir -p "/Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-martini/00new/martini/usrlib"
cp libmaxflow.a "/Library/Frameworks/R.framework/Versions/4.1/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/4.1/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/4.1/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)

Tests output

martini.Rcheck/tests/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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

══ Skipped tests ═══════════════════════════════════════════════════════════════
• On Bioconductor (3)

[ FAIL 0 | WARN 0 | SKIP 3 | PASS 232 ]
> 
> proc.time()
   user  system elapsed 
107.719   2.838 128.160 

Example timings

martini.Rcheck/martini-Ex.timings

nameusersystemelapsed
check_installed0.0000.0000.001
get_GI_network0.0620.0040.067
get_GM_network0.0280.0020.030
get_GS_network0.0130.0010.013
get_grid0.0050.0000.005
get_gxg_biogrid0.0010.0000.000
get_gxg_string000
get_snp_modules0.0000.0010.001
is_coherent0.0040.0010.004
ldweight_edges0.0830.0030.087
mget_gxg_biogrid000
mget_gxg_string0.0000.0000.001
minigwas0.0280.0120.040
minippi0.0030.0020.004
minisnpMapping0.0030.0020.005
scones0.0640.0030.069
scones.cv0.2350.0060.242
scones.cv_0.1590.0050.165
scones_0.0500.0020.052
search_cones0.0010.0010.001
sigmod0.0530.0030.056
sigmod.cv0.2450.0050.249
sigmod.cv_0.1250.0040.127
sigmod_0.0460.0030.049
simulate_causal_snps0.0530.0030.056
simulate_phenotype0.0510.0070.058
subnet0.0410.0010.043
subvert0.0340.0020.035