Sergio Picart-Armada
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/diffuStats |
| Branch: master |
| Last Commit: 11cb135 |
| Last Changed Date: 2019-03-28 11:51:37 -0400 (Thu, 28 Mar 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 11:48:24 -0400 (Tue, 09 Apr 2019).
| Package 431/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| diffuStats 1.3.1 Sergio Picart-Armada
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
| Package: diffuStats |
| Version: 1.3.1 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:diffuStats.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings diffuStats_1.3.1.tar.gz |
| StartedAt: 2019-04-09 00:05:48 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 00:07:32 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 104.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: diffuStats.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:diffuStats.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings diffuStats_1.3.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/diffuStats.Rcheck’ * using R Under development (unstable) (2019-03-18 r76245) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘diffuStats/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘diffuStats’ version ‘1.3.1’ * 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 ‘diffuStats’ 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 ... OK * 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 ... NOTE GNU make is a SystemRequirements. * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking compiled code ... NOTE Note: information on .o files is not available * 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: 2 NOTEs See ‘/home/biocbuild/bbs-3.9-bioc/meat/diffuStats.Rcheck/00check.log’ for details.
diffuStats.Rcheck/00install.out
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### Running command:
###
### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL diffuStats
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘diffuStats’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include" -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include" -I/usr/local/include -fpic -g -O2 -Wall -c diffuse_parallel.cpp -o diffuse_parallel.o
diffuse_parallel.cpp: In function ‘arma::sp_mat convertSparse(Rcpp::S4)’:
diffuse_parallel.cpp:28:84: warning: ‘static eT* arma::memory::acquire_chunked(arma::uword) [with eT = double; arma::uword = unsigned int]’ is deprecated [-Wdeprecated-declarations]
arma::access::rw(res.values) = arma::memory::acquire_chunked<double>(x.size() + 1);
^
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include/armadillo:355:0,
from /home/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include/RcppArmadilloForward.h:46,
from /home/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:31,
from diffuse_parallel.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include/armadillo_bits/memory.hpp:117:1: note: declared here
memory::acquire_chunked(const uword n_elem)
^˜˜˜˜˜
diffuse_parallel.cpp:32:94: warning: ‘static eT* arma::memory::acquire_chunked(arma::uword) [with eT = unsigned int; arma::uword = unsigned int]’ is deprecated [-Wdeprecated-declarations]
arma::access::rw(res.row_indices) = arma::memory::acquire_chunked<arma::uword>(i.size() + 1);
^
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include/armadillo:355:0,
from /home/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include/RcppArmadilloForward.h:46,
from /home/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:31,
from diffuse_parallel.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include/armadillo_bits/memory.hpp:117:1: note: declared here
memory::acquire_chunked(const uword n_elem)
^˜˜˜˜˜
diffuse_parallel.cpp: In function ‘arma::sp_mat sparsify2(const mat&, int, const sp_mat&)’:
diffuse_parallel.cpp:69:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < pos.size(); ++i) {
˜˜^˜˜˜˜˜˜˜˜˜˜˜
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include" -I/usr/local/include -fpic -g -O2 -Wall -c init.c -o init.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o diffuStats.so RcppExports.o diffuse_parallel.o init.o -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-diffuStats/00new/diffuStats/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 (diffuStats)
diffuStats.Rcheck/tests/testthat.Rout
R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
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(diffuStats)
>
> test_check("diffuStats")
══ testthat results ═══════════════════════════════════════════════════════════
OK: 208 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
23.897 0.590 12.338
diffuStats.Rcheck/diffuStats-Ex.timings
| name | user | system | elapsed | |
| checks | 0.083 | 0.004 | 0.119 | |
| connect_undirected_graph | 0.027 | 0.000 | 0.026 | |
| diffuse | 1.650 | 0.077 | 1.612 | |
| diffuse_mc | 0.377 | 0.024 | 0.342 | |
| diffuse_raw | 0.015 | 0.004 | 0.018 | |
| generate_graph | 0.011 | 0.000 | 0.011 | |
| generate_input | 0.03 | 0.00 | 0.03 | |
| is_kernel | 0.013 | 0.000 | 0.014 | |
| kernels | 0.039 | 0.000 | 0.038 | |
| largest_cc | 0.021 | 0.000 | 0.022 | |
| metric_auc | 0.083 | 0.000 | 0.084 | |
| named.list | 0.001 | 0.000 | 0.000 | |
| perf | 0.3 | 0.0 | 0.3 | |
| perf_eval | 0.179 | 0.000 | 0.179 | |
| perf_wilcox | 0.072 | 0.000 | 0.072 | |
| scores2colours | 0.004 | 0.000 | 0.003 | |
| scores2shapes | 0.001 | 0.000 | 0.000 | |
| to_list | 0.002 | 0.000 | 0.002 | |
| to_x_from_list | 0.000 | 0.002 | 0.002 | |
| which_format | 0.001 | 0.001 | 0.002 | |