Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-03-27 11:37:52 -0400 (Wed, 27 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4698
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" 4436
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4461
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" 4376
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

Package 643/2264HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
EnrichedHeatmap 1.33.0  (landing page)
Zuguang Gu
Snapshot Date: 2024-03-26 14:00:18 -0400 (Tue, 26 Mar 2024)
git_url: https://git.bioconductor.org/packages/EnrichedHeatmap
git_branch: devel
git_last_commit: 7deb036
git_last_commit_date: 2023-10-24 10:45:26 -0400 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 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
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for EnrichedHeatmap on palomino3


To the developers/maintainers of the EnrichedHeatmap package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: EnrichedHeatmap
Version: 1.33.0
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:EnrichedHeatmap.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings EnrichedHeatmap_1.33.0.tar.gz
StartedAt: 2024-03-27 01:35:33 -0400 (Wed, 27 Mar 2024)
EndedAt: 2024-03-27 01:38:16 -0400 (Wed, 27 Mar 2024)
EllapsedTime: 162.8 seconds
RetCode: 0
Status:   OK  
CheckDir: EnrichedHeatmap.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:EnrichedHeatmap.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings EnrichedHeatmap_1.33.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/EnrichedHeatmap.Rcheck'
* using R Under development (unstable) (2024-03-16 r86144 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'EnrichedHeatmap/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'EnrichedHeatmap' version '1.33.0'
* 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 whether package 'EnrichedHeatmap' can be installed ... OK
* used C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
* 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 code 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 whether startup messages can be suppressed ... 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 'F:/biocbuild/bbs-3.19-bioc/R/library/EnrichedHeatmap/libs/x64/EnrichedHeatmap.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

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 nor [v]sprintf. 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 10.36   1.28   11.44
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'test-all.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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
  'F:/biocbuild/bbs-3.19-bioc/meat/EnrichedHeatmap.Rcheck/00check.log'
for details.


Installation output

EnrichedHeatmap.Rcheck/00install.out

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##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL EnrichedHeatmap
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-bioc/R/library'
* installing *source* package 'EnrichedHeatmap' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c dist_by_closeness.cpp -o dist_by_closeness.o
g++ -std=gnu++17 -shared -s -static-libgcc -o EnrichedHeatmap.dll tmp.def RcppExports.o dist_by_closeness.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.19-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.19-bioc/R/library/00LOCK-EnrichedHeatmap/00new/EnrichedHeatmap/libs/x64
** 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
** 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) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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 
  12.71    0.51   13.28 

Example timings

EnrichedHeatmap.Rcheck/EnrichedHeatmap-Ex.timings

nameusersystemelapsed
EnrichedHeatmap10.36 1.2811.44
Extract.normalizedMatrix000
anno_enriched3.220.183.39
as.normalizedMatrix000
copyAttr0.420.000.43
default_smooth_fun000
discretize000
dist_by_closeness000
enriched_score000
extract_anno_enriched000
failed_rows000
getSignalsFromList000
makeWindows0.330.020.35
normalizeToMatrix3.920.033.95
print.normalizedMatrix000
rbind.normalizedMatrix000