Hector Climente-Gonzalez
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/martini |
| Branch: RELEASE_3_8 |
| Last Commit: 803ac70 |
| Last Changed Date: 2018-10-30 11:42:08 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:53:19 -0400 (Tue, 16 Apr 2019).
| Package 878/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| martini 1.2.0 Hector Climente-Gonzalez
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: martini |
| Version: 1.2.0 |
| Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:martini.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings martini_1.2.0.tar.gz |
| StartedAt: 2019-04-16 01:07:28 -0400 (Tue, 16 Apr 2019) |
| EndedAt: 2019-04-16 01:09:14 -0400 (Tue, 16 Apr 2019) |
| EllapsedTime: 106.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: martini.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:martini.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings martini_1.2.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/martini.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (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 ‘1.2.0’
* 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 ... NOTE
installed size is 37.3Mb
sub-directories of 1Mb or more:
libs 37.1Mb
* 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’
test_cones_modules : <anonymous> : <anonymous>: no visible binding for
global variable ‘snp’
Undefined global functions or variables:
gene gene1 gene2 snp
* 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 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 compiled code ... NOTE
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.8-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. 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
‘/home/biocbuild/bbs-3.8-bioc/meat/martini.Rcheck/00check.log’
for details.
martini.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL martini
###
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘martini’ ...
** libs
g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -DAS_GINLIB -DAS_RGINLIB -fopenmp -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rgin/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/Rcpp/r/headers.h:61:0,
from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/RcppCommon.h:29,
from /home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include/RcppEigenForward.h:26,
from /home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include/RcppEigen.h:25,
from ../inst/include/martini_RcppExports.h:7,
from ../inst/include/martini.h:7,
from RcppExports.cpp:4:
RcppExports.cpp: In function ‘SEXPREC* _martini_run_scones_try(SEXP, SEXP, SEXP, SEXP)’:
/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/Rcpp/macros/macros.h:32:9: warning: unused variable ‘nprot’ [-Wunused-variable]
int nprot = 0; \
^
RcppExports.cpp:29:1: note: in expansion of macro ‘BEGIN_RCPP’
BEGIN_RCPP
^
/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/Rcpp/macros/macros.h:36:17: warning: unused variable ‘stop_sym’ [-Wunused-variable]
static SEXP stop_sym = Rf_install("stop"); \
^
RcppExports.cpp:29:1: note: in expansion of macro ‘BEGIN_RCPP’
BEGIN_RCPP
^
g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -DAS_GINLIB -DAS_RGINLIB -fopenmp -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rgin/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c evo.cpp -o evo.o
g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -DAS_GINLIB -DAS_RGINLIB -fopenmp -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rgin/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c run_scones.cpp -o run_scones.o
g++ -shared -L/home/biocbuild/bbs-3.8-bioc/R/lib -L/usr/local/lib -o martini.so RcppExports.o evo.o run_scones.o /home/biocbuild/bbs-3.8-bioc/R/library/Rgin/usrlib//libgin.a /home/biocbuild/bbs-3.8-bioc/R/library/Rgin/usrlib//libmaxflow.a /home/biocbuild/bbs-3.8-bioc/R/library/Rgin/usrlib//libcephes.a -lz -pthread -fopenmp -L/home/biocbuild/bbs-3.8-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.8-bioc/R/library/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
* DONE (martini)
martini.Rcheck/tests/testthat.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-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")
[0;32mComputing univariate association.[0m
[0;34mSelecting the best hyperparameters...[0m
[0;32mRunning models.[0m
[0;32mFinding best model.[0m
[0;33mFinished in 0.001472 sec
[0m
[0;34mSearching ConES with eta = 1 and lambda = 2.5
[0m
[0;33mFinished in 3.6e-05 sec
[0m
[0;32mComputing univariate association.[0m
[0;34mSelecting the best hyperparameters...[0m
[0;32mRunning models.[0m
[0;32mFinding best model.[0m
[0;33mFinished in 0.000696 sec
[0m
[0;34mSearching ConES with eta = 1 and lambda = 2
[0m
[0;33mFinished in 3.2e-05 sec
[0m
[0;32mComputing univariate association.[0m
[0;34mSelecting the best hyperparameters...[0m
[0;32mRunning models.[0m
[0;32mFinding best model.[0m
[0;33mFinished in 0.012367 sec
[0m
[0;34mSearching ConES with eta = 1e-06 and lambda = 1e-07
[0m
[0;33mFinished in 4.1e-05 sec
[0m
[0;32mComputing univariate association.[0m
[0;34mSelecting the best hyperparameters...[0m
[0;32mRunning models.[0m
[0;32mFinding best model.[0m
[0;33mFinished in 0.022129 sec
[0m
[0;34mSearching ConES with eta = 1e-06 and lambda = 1e-07
[0m
[0;33mFinished in 6.1e-05 sec
[0m
eta = 1e-06
lambda = 1e-07
[0;32mComputing univariate association.[0m
[0;34mSelecting the best hyperparameters...[0m
[0;32mRunning models.[0m
[0;32mFinding best model.[0m
[0;33mFinished in 0.013585 sec
[0m
[0;34mSearching ConES with eta = 1e-06 and lambda = 1e-07
[0m
[0;33mFinished in 4.1e-05 sec
[0m
eta = 1e-06
lambda = 1e-07
[0;32mComputing univariate association.[0m
[0;34mSelecting the best hyperparameters...[0m
[0;32mRunning models.[0m
[0;32mFinding best model.[0m
[0;33mFinished in 0.000788 sec
[0m
[0;34mSearching ConES with eta = 1 and lambda = 2
[0m
[0;33mFinished in 3.8e-05 sec
[0m
eta = 1
lambda = 2
[0;32mComputing univariate association.[0m
[0;34mSelecting the best hyperparameters...[0m
[0;32mRunning models.[0m
[0;32mFinding best model.[0m
[0;33mFinished in 0.013073 sec
[0m
[0;34mSearching ConES with eta = 1e-06 and lambda = 1e-07
[0m
[0;33mFinished in 4.1e-05 sec
[0m
eta = 1e-06
lambda = 1e-07
[0;32mComputing univariate association.[0m
[0;34mSelecting the best hyperparameters...[0m
[0;32mRunning models.[0m
[0;32mFinding best model.[0m
[0;33mFinished in 0.013546 sec
[0m
[0;34mSearching ConES with eta = 1e-06 and lambda = 1e-07
[0m
[0;33mFinished in 4e-05 sec
[0m
eta = 1e-06
lambda = 1e-07
[0;32mComputing univariate association.[0m
[0;34mSelecting the best hyperparameters...[0m
[0;32mRunning models.[0m
[0;32mFinding best model.[0m
[0;33mFinished in 0.01458 sec
[0m
[0;34mSearching ConES with eta = 1e-06 and lambda = 1e-07
[0m
[0;33mFinished in 4.3e-05 sec
[0m
eta = 1e-06
lambda = 1e-07
══ testthat results ═══════════════════════════════════════════════════════════
OK: 200 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
15.980 0.500 51.821
martini.Rcheck/martini-Ex.timings
| name | user | system | elapsed | |
| check_installed | 0 | 0 | 0 | |
| encode_gwas | 0.008 | 0.000 | 0.009 | |
| get_GI_network | 0.080 | 0.000 | 0.079 | |
| get_GM_network | 0.016 | 0.004 | 0.019 | |
| get_GS_network | 0.008 | 0.000 | 0.008 | |
| get_evo_settings | 0.000 | 0.000 | 0.001 | |
| get_ppi | 0.620 | 0.012 | 0.813 | |
| get_snp_modules | 0.128 | 0.004 | 0.161 | |
| is_coherent | 0.004 | 0.000 | 0.005 | |
| ldweight_edges | 0.08 | 0.00 | 0.08 | |
| minigwas | 0.04 | 0.00 | 0.04 | |
| minippi | 0.000 | 0.000 | 0.002 | |
| minisnpMapping | 0.004 | 0.000 | 0.002 | |
| search_cones | 0.156 | 0.008 | 0.164 | |
| simulate_causal_snps | 0.064 | 0.000 | 0.062 | |
| simulate_phenotype | 0.072 | 0.000 | 0.073 | |
| subnet | 0.048 | 0.000 | 0.051 | |
| subvert | 0.052 | 0.000 | 0.049 | |
| test_cones_modules | 0.184 | 0.000 | 0.187 | |