Sergio Picart-Armada
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/diffuStats |
| Branch: RELEASE_3_11 |
| Last Commit: a8f7c98 |
| Last Changed Date: 2020-04-27 15:08:52 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:58:23 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE diffuStats PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 476/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| diffuStats 1.8.0 Sergio Picart-Armada
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | [ WARNINGS ] | OK | |
| Package: diffuStats |
| Version: 1.8.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:diffuStats.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings diffuStats_1.8.0.tar.gz |
| StartedAt: 2020-10-17 00:32:25 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 00:34:11 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 105.5 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: diffuStats.Rcheck |
| Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:diffuStats.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings diffuStats_1.8.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/diffuStats.Rcheck’ * using R version 4.0.3 (2020-10-10) * using platform: x86_64-apple-darwin17.0 (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 ‘1.8.0’ * 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 ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘diffuStats’ can be installed ... WARNING Found the following significant warnings: diffuse_parallel.cpp:28:48: warning: 'acquire_chunked<double>' is deprecated [-Wdeprecated-declarations] diffuse_parallel.cpp:32:53: warning: 'acquire_chunked<unsigned int>' is deprecated [-Wdeprecated-declarations] See ‘/Users/biocbuild/bbs-3.11-bioc/meat/diffuStats.Rcheck/00install.out’ for details. * 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 use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking sizes of PDF files under ‘inst/doc’ ... OK * 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: 1 WARNING, 2 NOTEs See ‘/Users/biocbuild/bbs-3.11-bioc/meat/diffuStats.Rcheck/00check.log’ for details.
diffuStats.Rcheck/00install.out
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL diffuStats
###
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##############################################################################
* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘diffuStats’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include -fPIC -Wall -g -O2 -c diffuse_parallel.cpp -o diffuse_parallel.o
diffuse_parallel.cpp:28:48: warning: 'acquire_chunked<double>' is deprecated [-Wdeprecated-declarations]
arma::access::rw(res.values) = arma::memory::acquire_chunked<double>(x.size() + 1);
^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include/armadillo_bits/memory.hpp:115:1: note: 'acquire_chunked<double>' has been explicitly marked deprecated here
arma_deprecated
^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include/armadillo_bits/compiler_setup.hpp:286:44: note: expanded from macro 'arma_deprecated'
#define arma_deprecated __attribute__((__deprecated__))
^
diffuse_parallel.cpp:32:53: warning: 'acquire_chunked<unsigned int>' is deprecated [-Wdeprecated-declarations]
arma::access::rw(res.row_indices) = arma::memory::acquire_chunked<arma::uword>(i.size() + 1);
^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include/armadillo_bits/memory.hpp:115:1: note: 'acquire_chunked<unsigned int>' has been explicitly marked deprecated here
arma_deprecated
^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include/armadillo_bits/compiler_setup.hpp:286:44: note: expanded from macro 'arma_deprecated'
#define arma_deprecated __attribute__((__deprecated__))
^
2 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include -fPIC -Wall -g -O2 -c init.c -o init.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -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 diffuStats.so RcppExports.o diffuse_parallel.o init.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/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 version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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(diffuStats)
>
> test_check("diffuStats")
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 208 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
22.139 1.012 14.897
diffuStats.Rcheck/diffuStats-Ex.timings
| name | user | system | elapsed | |
| checks | 0.116 | 0.011 | 0.130 | |
| connect_undirected_graph | 0.027 | 0.002 | 0.030 | |
| diffuse | 1.844 | 0.148 | 1.743 | |
| diffuse_mc | 0.377 | 0.035 | 0.321 | |
| diffuse_raw | 0.022 | 0.002 | 0.024 | |
| generate_graph | 0.011 | 0.001 | 0.012 | |
| generate_input | 0.028 | 0.002 | 0.030 | |
| is_kernel | 0.013 | 0.002 | 0.014 | |
| kernels | 0.040 | 0.002 | 0.043 | |
| largest_cc | 0.016 | 0.002 | 0.016 | |
| metric_auc | 0.102 | 0.002 | 0.104 | |
| named.list | 0.001 | 0.000 | 0.000 | |
| perf | 0.298 | 0.003 | 0.300 | |
| perf_eval | 0.179 | 0.005 | 0.184 | |
| perf_wilcox | 0.072 | 0.002 | 0.073 | |
| scores2colours | 0.002 | 0.001 | 0.003 | |
| scores2shapes | 0.001 | 0.001 | 0.001 | |
| to_list | 0.002 | 0.001 | 0.004 | |
| to_x_from_list | 0.002 | 0.001 | 0.004 | |
| which_format | 0.002 | 0.002 | 0.004 | |