Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-01-17 11:07:14 -0500 (Mon, 17 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4161
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4056
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 3998
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4115
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 riesling1


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? here 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 579/2074HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
EnrichedHeatmap 1.25.1  (landing page)
Zuguang Gu
Snapshot Date: 2022-01-16 13:55:18 -0500 (Sun, 16 Jan 2022)
git_url: https://git.bioconductor.org/packages/EnrichedHeatmap
git_branch: master
git_last_commit: ce99dbd
git_last_commit_date: 2021-11-17 09:02:10 -0500 (Wed, 17 Nov 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'ComplexHeatmap' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: EnrichedHeatmap
Version: 1.25.1
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:EnrichedHeatmap.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings EnrichedHeatmap_1.25.1.tar.gz
StartedAt: 2022-01-16 18:53:44 -0500 (Sun, 16 Jan 2022)
EndedAt: 2022-01-16 18:55:48 -0500 (Sun, 16 Jan 2022)
EllapsedTime: 124.7 seconds
RetCode: 0
Status:   OK  
CheckDir: EnrichedHeatmap.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:EnrichedHeatmap.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings EnrichedHeatmap_1.25.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/EnrichedHeatmap.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'EnrichedHeatmap/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'EnrichedHeatmap' version '1.25.1'
* 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 whether package 'EnrichedHeatmap' 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'D:/biocbuild/bbs-3.15-bioc/R/library/EnrichedHeatmap/libs/x64/EnrichedHeatmap.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
EnrichedHeatmap 9.16   0.39    9.55
* 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 NOTE
See
  'D:/biocbuild/bbs-3.15-bioc/meat/EnrichedHeatmap.Rcheck/00check.log'
for details.



Installation output

EnrichedHeatmap.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL EnrichedHeatmap
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'EnrichedHeatmap' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c dist_by_closeness.cpp -o dist_by_closeness.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o EnrichedHeatmap.dll tmp.def RcppExports.o dist_by_closeness.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-EnrichedHeatmap/00new/EnrichedHeatmap/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'EnrichedHeatmap'
    finding HTML links ... done
    EnrichedHeatmap                         html  
    finding level-2 HTML links ... done

    Extract.normalizedMatrix                html  
    anno_enriched                           html  
    as.normalizedMatrix                     html  
    copyAttr                                html  
    default_smooth_fun                      html  
    discretize                              html  
    dist_by_closeness                       html  
    enriched_score                          html  
    extract_anno_enriched                   html  
    failed_rows                             html  
    getSignalsFromList                      html  
    makeWindows                             html  
    normalizeToMatrix                       html  
    print.normalizedMatrix                  html  
    rbind.normalizedMatrix                  html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (EnrichedHeatmap)
Making 'packages.html' ... done

Tests output

EnrichedHeatmap.Rcheck/tests/test-all.Rout


R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 ]
> 
> proc.time()
   user  system elapsed 
   8.79    0.25    9.03 

Example timings

EnrichedHeatmap.Rcheck/EnrichedHeatmap-Ex.timings

nameusersystemelapsed
EnrichedHeatmap9.160.399.55
Extract.normalizedMatrix000
anno_enriched2.770.313.08
as.normalizedMatrix000
copyAttr0.30.00.3
default_smooth_fun000
discretize000
dist_by_closeness0.010.000.01
enriched_score000
extract_anno_enriched000
failed_rows000
getSignalsFromList000
makeWindows0.190.000.19
normalizeToMatrix2.910.002.91
print.normalizedMatrix000
rbind.normalizedMatrix000