Back to Multiple platform build/check report for BioC 3.16
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This page was generated on 2022-07-01 11:05:50 -0400 (Fri, 01 Jul 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics" 4343
palomino4Windows Server 2022 Datacenterx644.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics" 4147
lconwaymacOS 12.2.1 Montereyx86_644.2.0 Patched (2022-05-29 r82424) -- "Vigorous Calisthenics" 4159
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 bluster on palomino4


To the developers/maintainers of the bluster package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/bluster.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 209/2124HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
bluster 1.7.0  (landing page)
Aaron Lun
Snapshot Date: 2022-06-30 14:00:04 -0400 (Thu, 30 Jun 2022)
git_url: https://git.bioconductor.org/packages/bluster
git_branch: master
git_last_commit: bd460bc
git_last_commit_date: 2022-04-26 12:06:42 -0400 (Tue, 26 Apr 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.2.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: bluster
Version: 1.7.0
Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:bluster.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings bluster_1.7.0.tar.gz
StartedAt: 2022-06-30 23:48:03 -0400 (Thu, 30 Jun 2022)
EndedAt: 2022-06-30 23:50:31 -0400 (Thu, 30 Jun 2022)
EllapsedTime: 148.2 seconds
RetCode: 0
Status:   OK  
CheckDir: bluster.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:bluster.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings bluster_1.7.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/bluster.Rcheck'
* using R version 4.2.0 Patched (2022-06-02 r82447 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'bluster/DESCRIPTION' ... OK
* this is package 'bluster' version '1.7.0'
* 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 'bluster' 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 'F:/biocbuild/bbs-3.16-bioc/R/library/bluster/libs/x64/bluster.dll':
  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. 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
MbkmeansParam-class 4.77   0.29    5.27
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.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
  'F:/biocbuild/bbs-3.16-bioc/meat/bluster.Rcheck/00check.log'
for details.



Installation output

bluster.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.16/bioc/src/contrib/bluster_1.7.0.tar.gz && rm -rf bluster.buildbin-libdir && mkdir bluster.buildbin-libdir && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=bluster.buildbin-libdir bluster_1.7.0.tar.gz && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL bluster_1.7.0.zip && rm bluster_1.7.0.tar.gz bluster_1.7.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 81064  100 81064    0     0  1373k      0 --:--:-- --:--:-- --:--:-- 1388k
only one architecture so ignoring '--merge-multiarch'
* installing *source* package 'bluster' ...
** using staged installation
** libs
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c build_snn.cpp -o build_snn.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c sum_neighbor_weights.cpp -o sum_neighbor_weights.o
g++ -shared -s -static-libgcc -o bluster.dll tmp.def RcppExports.o build_snn.o sum_neighbor_weights.o -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.16-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.16-bioc/meat/bluster.buildbin-libdir/00LOCK-bluster/00new/bluster/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
* MD5 sums
packaged installation of 'bluster' as bluster_1.7.0.zip
* DONE (bluster)
* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library'
package 'bluster' successfully unpacked and MD5 sums checked

Tests output

bluster.Rcheck/tests/testthat.Rout


R version 4.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics"
Copyright (C) 2022 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)
> library(bluster)
> test_check("bluster")
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 2228 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 2228 ]
> 
> proc.time()
   user  system elapsed 
  36.84    2.07   39.04 

Example timings

bluster.Rcheck/bluster-Ex.timings

nameusersystemelapsed
AffinityParam-class0.540.050.61
AgnesParam-class0.020.000.02
ClaraParam-class0.020.000.02
DbscanParam-class0.230.000.23
DianaParam-class0.040.000.04
HclustParam-class000
KmeansParam-class000
MbkmeansParam-class4.770.295.27
NNGraphParam-class0.10.00.1
PamParam-class0.000.020.01
SomParam-class0.040.030.11
TwoStepParam-class0.280.000.28
approxSilhouette0.080.000.08
bootstrapStability0.800.020.81
clusterRMSD000
clusterRows0.470.020.48
clusterSweep0.650.000.66
compareClusterings0.210.000.22
defaultArguments000
linkClusters0.060.000.06
makeSNNGraph1.020.001.02
mergeCommunities0.030.000.03
neighborPurity0.140.000.14
nestedClusters0.060.000.06
pairwiseModularity0.880.000.88
pairwiseRand0.010.000.01