Package: EnrichedHeatmap

Version: 1.10.0

Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:EnrichedHeatmap.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings EnrichedHeatmap_1.10.0.tar.gz

StartedAt: 2018-10-16 00:08:59 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 00:10:28 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 89.5 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: EnrichedHeatmap.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:EnrichedHeatmap.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings EnrichedHeatmap_1.10.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/EnrichedHeatmap.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 ‘EnrichedHeatmap/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘EnrichedHeatmap’ version ‘1.10.0’
* 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 ‘EnrichedHeatmap’ can be installed ... WARNING
Found the following significant warnings:
  dist_by_closeness.cpp:12:27: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
See ‘/home/biocbuild/bbs-3.7-bioc/meat/EnrichedHeatmap.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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
EnrichedHeatmap 7.804  0.072   7.886
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.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
See
  ‘/home/biocbuild/bbs-3.7-bioc/meat/EnrichedHeatmap.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL EnrichedHeatmap
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘EnrichedHeatmap’ ...
** libs
g++  -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/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  -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c dist_by_closeness.cpp -o dist_by_closeness.o
dist_by_closeness.cpp: In function ‘float closeness(Rcpp::NumericVector, Rcpp::NumericVector)’:
dist_by_closeness.cpp:12:27: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
    if(std::abs(x1[i] - 0) < 1e-6 | std::abs(x2[j] - 0) < 1e-6) {
                           ^
g++ -shared -L/home/biocbuild/bbs-3.7-bioc/R/lib -L/usr/local/lib -o EnrichedHeatmap.so RcppExports.o dist_by_closeness.o -L/home/biocbuild/bbs-3.7-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.7-bioc/R/library/EnrichedHeatmap/libs
** R
** 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 (EnrichedHeatmap)

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)
> suppressWarnings(suppressPackageStartupMessages(library(EnrichedHeatmap)))
> 
> test_check("EnrichedHeatmap")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 25 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  8.804   0.120   8.926 

name	user	system	elapsed
EnrichedHeatmap-class	0.000	0.000	0.001
EnrichedHeatmap	7.804	0.072	7.886
EnrichedHeatmapList-class	0.000	0.000	0.001
EnrichedHeatmapList	0.000	0.000	0.001
Extract.normalizedMatrix	0	0	0
add.AdditiveUnit	0	0	0
anno_enriched	3.276	0.032	3.309
copyAttr	0.340	0.000	0.343
default_smooth_fun	0	0	0
discretize	0	0	0
dist_by_closeness	0.004	0.000	0.002
draw-EnrichedHeatmap-method	0.000	0.000	0.001
draw-EnrichedHeatmapList-method	0.000	0.000	0.001
draw-dispatch	0	0	0
enriched_score	0	0	0
extract_anno_enriched	0.004	0.000	0.000
getSignalsFromList	0	0	0
makeWindows	0.184	0.000	0.184
normalizeToMatrix	2.740	0.004	2.744
print.normalizedMatrix	0.000	0.000	0.001
rbind.normalizedMatrix	0.000	0.000	0.001
show-EnrichedHeatmap-method	0.004	0.000	0.000
show-EnrichedHeatmapList-method	0	0	0
show-dispatch	0.000	0.000	0.001