Hector Climente-Gonzalez
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/martini |
| Branch: RELEASE_3_7 |
| Last Commit: 5f5a74c |
| Last Changed Date: 2018-04-30 10:35:49 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:31:18 -0400 (Wed, 17 Oct 2018).
| Package 830/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| martini 1.0.0 Hector Climente-Gonzalez
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: martini |
| Version: 1.0.0 |
| Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:martini.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings martini_1.0.0.tar.gz |
| StartedAt: 2018-10-16 01:40:14 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-16 01:42:06 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 112.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: martini.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:martini.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings martini_1.0.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/martini.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.0.0’
* 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 35.6Mb
sub-directories of 1Mb or more:
libs 35.4Mb
* 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-3.7-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
Examples with CPU or elapsed time > 5s
user system elapsed
get_ppi 0.38 0.016 11.054
* 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-3.7-bioc/meat/martini.Rcheck/00check.log’
for details.
martini.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL martini ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’ * installing *source* package ‘martini’ ... ** libs g++ -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -DAS_GINLIB -DAS_RGINLIB -fopenmp -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rgin/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -DAS_GINLIB -DAS_RGINLIB -fopenmp -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rgin/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c evo.cpp -o evo.o g++ -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -DAS_GINLIB -DAS_RGINLIB -fopenmp -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rgin/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-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-3.7-bioc/R/lib -L/usr/local/lib -o martini.so RcppExports.o evo.o run_scones.o /home/biocbuild/bbs-3.7-bioc/R/library/Rgin/usrlib//libgin.a /home/biocbuild/bbs-3.7-bioc/R/library/Rgin/usrlib//libmaxflow.a /home/biocbuild/bbs-3.7-bioc/R/library/Rgin/usrlib//libcephes.a -lz -pthread -fopenmp -L/home/biocbuild/bbs-3.7-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.7-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 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 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 0.001692 sec
[0m
[0;34mSearching ConES with eta = 1 and lambda = 2.5
[0m
[0;33mFinished in 4e-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 0.000665 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 0.011796 sec
[0m
[0;34mSearching ConES with eta = 1e-06 and lambda = 1e-07
[0m
[0;33mFinished in 4e-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 0.013249 sec
[0m
[0;34mSearching ConES with eta = 1e-06 and lambda = 1e-07
[0m
[0;33mFinished in 3.6e-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 0.014438 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 0.000724 sec
[0m
[0;34mSearching ConES with eta = 1 and lambda = 2
[0m
[0;33mFinished in 3.6e-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 0.014587 sec
[0m
[0;34mSearching ConES with eta = 1e-06 and lambda = 1e-07
[0m
[0;33mFinished in 3.8e-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 0.012868 sec
[0m
[0;34mSearching ConES with eta = 1e-06 and lambda = 1e-07
[0m
[0;33mFinished in 3.8e-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 0.013942 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
══ testthat results ═══════════════════════════════════════════════════════════
OK: 200 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
16.960 0.408 53.504
martini.Rcheck/martini-Ex.timings
| name | user | system | elapsed | |
| check_installed | 0.000 | 0.000 | 0.001 | |
| encode_gwas | 0.008 | 0.008 | 0.016 | |
| get_GI_network | 0.052 | 0.000 | 0.053 | |
| get_GM_network | 0.016 | 0.000 | 0.018 | |
| get_GS_network | 0.008 | 0.000 | 0.008 | |
| get_evo_settings | 0 | 0 | 0 | |
| get_ppi | 0.380 | 0.016 | 11.054 | |
| get_snp_modules | 0.116 | 0.004 | 0.140 | |
| is_coherent | 0.004 | 0.000 | 0.004 | |
| ldweight_edges | 0.088 | 0.000 | 0.090 | |
| minigwas | 0.020 | 0.008 | 0.026 | |
| minippi | 0.004 | 0.000 | 0.004 | |
| minisnpMapping | 0.004 | 0.000 | 0.003 | |
| search_cones | 0.160 | 0.004 | 0.164 | |
| simulate_causal_snps | 0.036 | 0.000 | 0.040 | |
| simulate_phenotype | 0.036 | 0.000 | 0.038 | |
| subnet | 0.036 | 0.000 | 0.035 | |
| subvert | 0.028 | 0.000 | 0.027 | |
| test_cones_modules | 0.108 | 0.000 | 0.110 | |