Back to Multiple platform build/check report for BioC 3.17
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This page was generated on 2023-01-27 11:05:42 -0500 (Fri, 27 Jan 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4465
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2023-01-10 r83596 ucrt) -- "Unsuffered Consequences" 4246
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4269
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for EnrichedHeatmap on nebbiolo1


To the developers/maintainers of the EnrichedHeatmap package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/EnrichedHeatmap.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 600/2162HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
EnrichedHeatmap 1.29.2  (landing page)
Zuguang Gu
Snapshot Date: 2023-01-26 14:00:20 -0500 (Thu, 26 Jan 2023)
git_url: https://git.bioconductor.org/packages/EnrichedHeatmap
git_branch: master
git_last_commit: 2d8fdf2
git_last_commit_date: 2022-11-10 07:27:51 -0500 (Thu, 10 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: EnrichedHeatmap
Version: 1.29.2
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:EnrichedHeatmap.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings EnrichedHeatmap_1.29.2.tar.gz
StartedAt: 2023-01-26 20:18:39 -0500 (Thu, 26 Jan 2023)
EndedAt: 2023-01-26 20:25:03 -0500 (Thu, 26 Jan 2023)
EllapsedTime: 384.6 seconds
RetCode: 0
Status:   OK  
CheckDir: EnrichedHeatmap.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:EnrichedHeatmap.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings EnrichedHeatmap_1.29.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/EnrichedHeatmap.Rcheck’
* using R Under development (unstable) (2023-01-10 r83596)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘EnrichedHeatmap/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘EnrichedHeatmap’ version ‘1.29.2’
* 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 ... OK
* used C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* 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 ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
EnrichedHeatmap 7.851  0.253   8.104
* 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 ...
  ‘EnrichedHeatmap.Rmd’ using ‘UTF-8’... OK
  ‘roadmap.Rmd’ using ‘UTF-8’... OK
  ‘row_odering.Rmd’ using ‘UTF-8’... OK
  ‘visualize_categorical_signals.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/EnrichedHeatmap.Rcheck/00check.log’
for details.



Installation output

EnrichedHeatmap.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL EnrichedHeatmap
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘EnrichedHeatmap’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c dist_by_closeness.cpp -o dist_by_closeness.o
g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o EnrichedHeatmap.so RcppExports.o dist_by_closeness.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-EnrichedHeatmap/00new/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 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 (EnrichedHeatmap)

Tests output

EnrichedHeatmap.Rcheck/tests/test-all.Rout


R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences"
Copyright (C) 2023 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")
[ FAIL 0 | WARN 6 | SKIP 0 | PASS 19 ]

[ FAIL 0 | WARN 6 | SKIP 0 | PASS 19 ]
> 
> proc.time()
   user  system elapsed 
 11.064   0.321  11.375 

Example timings

EnrichedHeatmap.Rcheck/EnrichedHeatmap-Ex.timings

nameusersystemelapsed
EnrichedHeatmap7.8510.2538.104
Extract.normalizedMatrix000
anno_enriched2.9950.3603.355
as.normalizedMatrix000
copyAttr0.4910.0000.491
default_smooth_fun000
discretize0.0010.0000.000
dist_by_closeness0.0020.0000.003
enriched_score000
extract_anno_enriched000
failed_rows0.0000.0000.001
getSignalsFromList000
makeWindows0.2460.0000.245
normalizeToMatrix3.7150.0083.722
print.normalizedMatrix000
rbind.normalizedMatrix0.0010.0000.000