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CHECK report for EnrichedHeatmap on malbec1

This page was generated on 2019-04-16 11:51:35 -0400 (Tue, 16 Apr 2019).

Package 471/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
EnrichedHeatmap 1.12.0
Zuguang Gu
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/EnrichedHeatmap
Branch: RELEASE_3_8
Last Commit: 4deed55
Last Changed Date: 2018-10-30 11:41:59 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: EnrichedHeatmap
Version: 1.12.0
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:EnrichedHeatmap.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings EnrichedHeatmap_1.12.0.tar.gz
StartedAt: 2019-04-15 23:44:32 -0400 (Mon, 15 Apr 2019)
EndedAt: 2019-04-15 23:46:26 -0400 (Mon, 15 Apr 2019)
EllapsedTime: 114.3 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: EnrichedHeatmap.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:EnrichedHeatmap.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings EnrichedHeatmap_1.12.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/EnrichedHeatmap.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.12.0’
* 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-3.8-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 ... NOTE
as.normalizedMatrix: no visible binding for global variable
  ‘target_is_single_point’
Undefined global functions or variables:
  target_is_single_point
* 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 10.308  0.096  10.456
* 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, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.8-bioc/meat/EnrichedHeatmap.Rcheck/00check.log’
for details.



Installation output

EnrichedHeatmap.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL EnrichedHeatmap
###
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘EnrichedHeatmap’ ...
** libs
g++  -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++  -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/lib -L/usr/local/lib -o EnrichedHeatmap.so RcppExports.o dist_by_closeness.o -L/home/biocbuild/bbs-3.8-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.8-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)

Tests output

EnrichedHeatmap.Rcheck/tests/test-all.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
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)
> suppressWarnings(suppressPackageStartupMessages(library(EnrichedHeatmap)))
> 
> test_check("EnrichedHeatmap")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 25 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 12.932   0.204  13.142 

Example timings

EnrichedHeatmap.Rcheck/EnrichedHeatmap-Ex.timings

nameusersystemelapsed
EnrichedHeatmap-class000
EnrichedHeatmap10.308 0.09610.456
EnrichedHeatmapList-class000
EnrichedHeatmapList000
Extract.normalizedMatrix000
add.AdditiveUnit000
anno_enriched3.6000.0203.624
as.normalizedMatrix000
copyAttr0.4080.0000.408
default_smooth_fun000
discretize000
dist_by_closeness0.0040.0000.003
draw-EnrichedHeatmap-method000
draw-EnrichedHeatmapList-method0.0000.0000.001
draw-dispatch000
enriched_score000
extract_anno_enriched000
getSignalsFromList000
makeWindows0.2880.0000.289
normalizeToMatrix3.2200.0003.221
print.normalizedMatrix000
rbind.normalizedMatrix000
show-EnrichedHeatmap-method0.0000.0000.001
show-EnrichedHeatmapList-method000
show-dispatch000