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CHECK report for diffuStats on malbec1

This page was generated on 2021-05-06 12:27:20 -0400 (Thu, 06 May 2021).

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 481/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
diffuStats 1.10.2  (landing page)
Sergio Picart-Armada
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/diffuStats
Branch: RELEASE_3_12
Last Commit: b578ed0
Last Changed Date: 2021-02-20 13:33:12 -0400 (Sat, 20 Feb 2021)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: diffuStats
Version: 1.10.2
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:diffuStats.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings diffuStats_1.10.2.tar.gz
StartedAt: 2021-05-06 00:58:06 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 00:59:29 -0400 (Thu, 06 May 2021)
EllapsedTime: 83.3 seconds
RetCode: 0
Status:   OK  
CheckDir: diffuStats.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:diffuStats.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings diffuStats_1.10.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/diffuStats.Rcheck’
* using R version 4.0.5 (2021-03-31)
* 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 ‘1.10.2’
* 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 use of PKG_*FLAGS in Makefiles ... 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-3.12-bioc/meat/diffuStats.Rcheck/00check.log’
for details.



Installation output

diffuStats.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL diffuStats
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘diffuStats’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.12-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 sparsify2(const mat&, int, const sp_mat&)’:
diffuse_parallel.cpp:54:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int i = 0; i < pos.size(); ++i) {
                   ~~^~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/lib -L/usr/local/lib -o diffuStats.so RcppExports.o diffuse_parallel.o init.o -L/home/biocbuild/bbs-3.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.12-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)

Tests output

diffuStats.Rcheck/tests/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 216 ]
> 
> proc.time()
   user  system elapsed 
 24.568   0.580  12.457 

Example timings

diffuStats.Rcheck/diffuStats-Ex.timings

nameusersystemelapsed
checks0.0920.0040.096
connect_undirected_graph0.0320.0040.035
diffuse1.3840.1321.323
diffuse_mc0.3800.0160.367
diffuse_raw0.0200.0040.021
generate_graph0.0200.0000.023
generate_input0.0320.0000.031
is_kernel0.0120.0000.014
kernels0.0360.0000.038
largest_cc0.0240.0000.021
metric_auc0.0920.0000.090
moments0.0120.0000.015
named.list000
perf0.2800.0000.279
perf_eval0.0640.0000.066
perf_wilcox0.0480.0000.046
scores2colours0.0000.0000.002
scores2shapes000
to_list0.0040.0000.001
to_x_from_list0.0000.0000.001
which_format0.0000.0040.001