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 08:45:21 -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: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:martini.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings martini_1.0.0.tar.gz |
| StartedAt: 2018-10-17 03:04:23 -0400 (Wed, 17 Oct 2018) |
| EndedAt: 2018-10-17 03:07:27 -0400 (Wed, 17 Oct 2018) |
| EllapsedTime: 184.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: martini.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:martini.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings martini_1.0.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/martini.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.7-bioc/R/library/martini/libs/i386/martini.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
get_ppi 0.32 0.12 9.33
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
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: 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.7-bioc/meat/martini.Rcheck/00check.log'
for details.
martini.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/martini_1.0.0.tar.gz && rm -rf martini.buildbin-libdir && mkdir martini.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=martini.buildbin-libdir martini_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL martini_1.0.0.zip && rm martini_1.0.0.tar.gz martini_1.0.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 2497k 100 2497k 0 0 23.6M 0 --:--:-- --:--:-- --:--:-- 25.1M
install for i386
* installing *source* package 'martini' ...
** libs
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DAS_GINLIB -DAS_RGINLIB -fopenmp -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rgin/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RcppEigen/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DAS_GINLIB -DAS_RGINLIB -fopenmp -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rgin/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RcppEigen/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c evo.cpp -o evo.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DAS_GINLIB -DAS_RGINLIB -fopenmp -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rgin/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RcppEigen/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c run_scones.cpp -o run_scones.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o martini.dll tmp.def RcppExports.o evo.o run_scones.o C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rgin/usrlib/i386/libgin.a C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rgin/usrlib/i386/libmaxflow.a C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rgin/usrlib/i386/libcephes.a -lz -pthread -fopenmp -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/martini.buildbin-libdir/martini/libs/i386
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'martini'
finding HTML links ... done
calculateE html
calculateG html
check_installed html
encode_gwas html
evo html
get_GI_network html
get_GM_network html
get_GS_network html
get_evo_settings html
get_ppi html
get_snp_modules html
is_coherent html
ldweight_edges html
minigwas html
minippi html
minisnpMapping html
run_scones html
search_cones html
simulate_causal_snps html
simulate_phenotype html
snp2gene html
subnet html
subvert html
test_cones_modules html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'martini' ...
** libs
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DAS_GINLIB -DAS_RGINLIB -fopenmp -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rgin/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RcppEigen/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DAS_GINLIB -DAS_RGINLIB -fopenmp -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rgin/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RcppEigen/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c evo.cpp -o evo.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DAS_GINLIB -DAS_RGINLIB -fopenmp -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rgin/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RcppEigen/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c run_scones.cpp -o run_scones.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o martini.dll tmp.def RcppExports.o evo.o run_scones.o C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rgin/usrlib/x64/libgin.a C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rgin/usrlib/x64/libmaxflow.a C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rgin/usrlib/x64/libcephes.a -lz -pthread -fopenmp -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/martini.buildbin-libdir/martini/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'martini' as martini_1.0.0.zip
* DONE (martini)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'martini' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
martini.Rcheck/tests_i386/testthat.Rout
R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 sec
[0m
[0;34mSearching ConES with eta = 1 and lambda = 2.5
[0m
[0;33mFinished in 0 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 sec
[0m
[0;34mSearching ConES with eta = 1 and lambda = 2
[0m
[0;33mFinished in 0 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 0.016 sec
[0m
[0;34mSearching ConES with eta = 1.36018e-032 and lambda = 1.36018e-033
[0m
[0;33mFinished in 0 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 0.031 sec
[0m
[0;34mSearching ConES with eta = 1.36018e-032 and lambda = 1.36018e-033
[0m
[0;33mFinished in 0 sec
[0m
eta = 1.360181e-32
lambda = 1.360181e-33
[0;32mComputing univariate association.[0m
[0;34mSelecting the best hyperparameters...[0m
[0;32mRunning models.[0m
[0;32mFinding best model.[0m
[0;33mFinished in 0.015 sec
[0m
[0;34mSearching ConES with eta = 1.36018e-032 and lambda = 1.36018e-033
[0m
[0;33mFinished in 0 sec
[0m
eta = 1.360181e-32
lambda = 1.360181e-33
[0;32mComputing univariate association.[0m
[0;34mSelecting the best hyperparameters...[0m
[0;32mRunning models.[0m
[0;32mFinding best model.[0m
[0;33mFinished in 0 sec
[0m
[0;34mSearching ConES with eta = 1 and lambda = 2
[0m
[0;33mFinished in 0 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 0.016 sec
[0m
[0;34mSearching ConES with eta = 1.36018e-032 and lambda = 1.36018e-033
[0m
[0;33mFinished in 0 sec
[0m
eta = 1.360181e-32
lambda = 1.360181e-33
[0;32mComputing univariate association.[0m
[0;34mSelecting the best hyperparameters...[0m
[0;32mRunning models.[0m
[0;32mFinding best model.[0m
[0;33mFinished in 0.016 sec
[0m
[0;34mSearching ConES with eta = 1.36018e-032 and lambda = 1.36018e-033
[0m
[0;33mFinished in 0 sec
[0m
eta = 1.360181e-32
lambda = 1.360181e-33
[0;32mComputing univariate association.[0m
[0;34mSelecting the best hyperparameters...[0m
[0;32mRunning models.[0m
[0;32mFinding best model.[0m
[0;33mFinished in 0.015 sec
[0m
[0;34mSearching ConES with eta = 1.36018e-032 and lambda = 1.36018e-033
[0m
[0;33mFinished in 0 sec
[0m
eta = 1.360181e-32
lambda = 1.360181e-33
== testthat results ===========================================================
OK: 196 SKIPPED: 2 FAILED: 0
>
> proc.time()
user system elapsed
16.57 1.18 33.01
|
martini.Rcheck/tests_x64/testthat.Rout
R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 sec
[0m
[0;34mSearching ConES with eta = 1 and lambda = 2.5
[0m
[0;33mFinished in 0 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 sec
[0m
[0;34mSearching ConES with eta = 1 and lambda = 2
[0m
[0;33mFinished in 0 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 0.015 sec
[0m
[0;34mSearching ConES with eta = 1e-006 and lambda = 1e-007
[0m
[0;33mFinished in 0 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 0.031 sec
[0m
[0;34mSearching ConES with eta = 1e-006 and lambda = 1e-007
[0m
[0;33mFinished in 0 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 0.016 sec
[0m
[0;34mSearching ConES with eta = 1e-006 and lambda = 1e-007
[0m
[0;33mFinished in 0 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 sec
[0m
[0;34mSearching ConES with eta = 1 and lambda = 2
[0m
[0;33mFinished in 0 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 0.015 sec
[0m
[0;34mSearching ConES with eta = 1e-006 and lambda = 1e-007
[0m
[0;33mFinished in 0 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 0.016 sec
[0m
[0;34mSearching ConES with eta = 1e-006 and lambda = 1e-007
[0m
[0;33mFinished in 0 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 0.016 sec
[0m
[0;34mSearching ConES with eta = 1e-006 and lambda = 1e-007
[0m
[0;33mFinished in 0 sec
[0m
eta = 1e-06
lambda = 1e-07
== testthat results ===========================================================
OK: 196 SKIPPED: 2 FAILED: 0
>
> proc.time()
user system elapsed
16.00 0.81 35.09
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martini.Rcheck/examples_i386/martini-Ex.timings
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martini.Rcheck/examples_x64/martini-Ex.timings
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