Multiple platform build/check report for BioC 3.14 - CHECK results for bluster on tokay2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 20.04.4 LTS)	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4324
tokay2	Windows Server 2012 R2 Standard	x64	4.1.3 (2022-03-10) -- "One Push-Up"	4077
machv2	macOS 10.14.6 Mojave	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4137
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: bluster

Version: 1.4.0

Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:bluster.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings bluster_1.4.0.tar.gz

StartedAt: 2022-04-12 16:33:09 -0400 (Tue, 12 Apr 2022)

EndedAt: 2022-04-12 16:36:52 -0400 (Tue, 12 Apr 2022)

EllapsedTime: 222.9 seconds

RetCode: 1

Status: ERROR

CheckDir: bluster.Rcheck

Warnings: NA

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:bluster.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings bluster_1.4.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/bluster.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'bluster/DESCRIPTION' ... OK
* this is package 'bluster' version '1.4.0'
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/bluster/libs/i386/bluster.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/bluster/libs/x64/bluster.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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
MbkmeansParam-class 4.59   0.32    5.39
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
MbkmeansParam-class 4.81   0.14    5.01
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  out$clusters[, choice] not identical to clusterRows(x, param).
  109 string mismatches
  -- Failure (test-sweep.R:11:9): clusterSweep works correctly in simple cases ---
  out$clusters[, choice] not identical to clusterRows(x, param).
  133 string mismatches
  -- Failure (test-sweep.R:21:9): clusterSweep works correctly in simple cases ---
  out$clusters[, choice] not identical to clusterRows(x, param).
  92 string mismatches
  -- Failure (test-sweep.R:31:5): clusterSweep reports full objects correctly ----
  out[1:2] not identical to `ref`.
  Attributes: < Component "listData": Component "clusters": Attributes: < Component "listData": Component "cluster.fun.louvain": 136 string mismatches > >
  
  [ FAIL 6 | WARN 1 | SKIP 0 | PASS 2222 ]
  Error: Test failures
  Execution halted
** running tests for arch 'x64' ...
  Running 'testthat.R'
 ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  out$clusters[, choice] not identical to clusterRows(x, param).
  109 string mismatches
  -- Failure (test-sweep.R:11:9): clusterSweep works correctly in simple cases ---
  out$clusters[, choice] not identical to clusterRows(x, param).
  133 string mismatches
  -- Failure (test-sweep.R:21:9): clusterSweep works correctly in simple cases ---
  out$clusters[, choice] not identical to clusterRows(x, param).
  92 string mismatches
  -- Failure (test-sweep.R:31:5): clusterSweep reports full objects correctly ----
  out[1:2] not identical to `ref`.
  Attributes: < Component "listData": Component "clusters": Attributes: < Component "listData": Component "cluster.fun.louvain": 136 string mismatches > >
  
  [ FAIL 6 | WARN 1 | SKIP 0 | PASS 2222 ]
  Error: Test failures
  Execution halted
* 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: 2 ERRORs, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/bluster.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/bluster_1.4.0.tar.gz && rm -rf bluster.buildbin-libdir && mkdir bluster.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=bluster.buildbin-libdir bluster_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL bluster_1.4.0.zip && rm bluster_1.4.0.tar.gz bluster_1.4.0.zip
###
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  % 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 80908  100 80908    0     0   417k      0 --:--:-- --:--:-- --:--:--  420k

install for i386

* installing *source* package 'bluster' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c build_snn.cpp -o build_snn.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c sum_neighbor_weights.cpp -o sum_neighbor_weights.o
C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o bluster.dll tmp.def RcppExports.o build_snn.o sum_neighbor_weights.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/bluster.buildbin-libdir/00LOCK-bluster/00new/bluster/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'bluster'
    finding HTML links ... done
    AffinityParam-class                     html  
    AgnesParam-class                        html  
    BlusterParam-class                      html  
    ClaraParam-class                        html  
    DbscanParam-class                       html  
    finding level-2 HTML links ... done

    DianaParam-class                        html  
    FixedNumberParam-class                  html  
    HclustParam-class                       html  
    HierarchicalParam-class                 html  
    KmeansParam-class                       html  
    MbkmeansParam-class                     html  
    NNGraphParam-class                      html  
    PamParam-class                          html  
    SomParam-class                          html  
    TwoStepParam-class                      html  
    approxSilhouette                        html  
    bluster-package                         html  
    bootstrapStability                      html  
    clusterRMSD                             html  
    clusterRows                             html  
    clusterSweep                            html  
    compareClusterings                      html  
    defaultArguments                        html  
    linkClusters                            html  
    makeSNNGraph                            html  
    mergeCommunities                        html  
    neighborPurity                          html  
    nestedClusters                          html  
    pairwiseModularity                      html  
    pairwiseRand                            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

install for x64

* installing *source* package 'bluster' ...
** libs
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c build_snn.cpp -o build_snn.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c sum_neighbor_weights.cpp -o sum_neighbor_weights.o
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o bluster.dll tmp.def RcppExports.o build_snn.o sum_neighbor_weights.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/bluster.buildbin-libdir/bluster/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'bluster' as bluster_1.4.0.zip
* DONE (bluster)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'bluster' successfully unpacked and MD5 sums checked


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 6 | WARN 1 | SKIP 0 | PASS 2222 ]

== Failed tests ================================================================
-- Failure (test-nngraph-param.R:45:5): clusterRows works correctly ------------
`out3` not identical to `out4`.
2 string mismatches
-- Failure (test-sweep.R:11:9): clusterSweep works correctly in simple cases ---
out$clusters[, choice] not identical to clusterRows(x, param).
Attributes: < Component "levels": Lengths (8, 7) differ (string compare on first 7) >
118 string mismatches
-- Failure (test-sweep.R:11:9): clusterSweep works correctly in simple cases ---
out$clusters[, choice] not identical to clusterRows(x, param).
109 string mismatches
-- Failure (test-sweep.R:11:9): clusterSweep works correctly in simple cases ---
out$clusters[, choice] not identical to clusterRows(x, param).
133 string mismatches
-- Failure (test-sweep.R:21:9): clusterSweep works correctly in simple cases ---
out$clusters[, choice] not identical to clusterRows(x, param).
92 string mismatches
-- Failure (test-sweep.R:31:5): clusterSweep reports full objects correctly ----
out[1:2] not identical to `ref`.
Attributes: < Component "listData": Component "clusters": Attributes: < Component "listData": Component "cluster.fun.louvain": 136 string mismatches > >

[ FAIL 6 | WARN 1 | SKIP 0 | PASS 2222 ]
Error: Test failures
Execution halted


R version 4.1.3 (2022-03-10) -- "One Push-Up"
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 6 | WARN 1 | SKIP 0 | PASS 2222 ]

== Failed tests ================================================================
-- Failure (test-nngraph-param.R:45:5): clusterRows works correctly ------------
`out3` not identical to `out4`.
2 string mismatches
-- Failure (test-sweep.R:11:9): clusterSweep works correctly in simple cases ---
out$clusters[, choice] not identical to clusterRows(x, param).
Attributes: < Component "levels": Lengths (8, 7) differ (string compare on first 7) >
118 string mismatches
-- Failure (test-sweep.R:11:9): clusterSweep works correctly in simple cases ---
out$clusters[, choice] not identical to clusterRows(x, param).
109 string mismatches
-- Failure (test-sweep.R:11:9): clusterSweep works correctly in simple cases ---
out$clusters[, choice] not identical to clusterRows(x, param).
133 string mismatches
-- Failure (test-sweep.R:21:9): clusterSweep works correctly in simple cases ---
out$clusters[, choice] not identical to clusterRows(x, param).
92 string mismatches
-- Failure (test-sweep.R:31:5): clusterSweep reports full objects correctly ----
out[1:2] not identical to `ref`.
Attributes: < Component "listData": Component "clusters": Attributes: < Component "listData": Component "cluster.fun.louvain": 136 string mismatches > >

[ FAIL 6 | WARN 1 | SKIP 0 | PASS 2222 ]
Error: Test failures
Execution halted

name	user	system	elapsed
AffinityParam-class	0.83	0.05	1.08
AgnesParam-class	0.03	0.00	0.03
ClaraParam-class	0.01	0.00	0.02
DbscanParam-class	0.14	0.00	0.14
DianaParam-class	0.02	0.00	0.02
HclustParam-class	0.01	0.00	0.01
KmeansParam-class	0.02	0.00	0.02
MbkmeansParam-class	4.59	0.32	5.39
NNGraphParam-class	0.11	0.00	0.11
PamParam-class	0.02	0.02	0.03
SomParam-class	0.05	0.08	0.45
TwoStepParam-class	0.53	0.01	0.55
approxSilhouette	0.04	0.05	0.09
bootstrapStability	0.18	0.03	0.21
clusterRMSD	0	0	0
clusterRows	0.78	0.00	0.78
clusterSweep	0.47	0.00	0.47
compareClusterings	0.18	0.00	0.18
defaultArguments	0	0	0
linkClusters	0.07	0.00	0.07
makeSNNGraph	0.93	0.05	0.98
mergeCommunities	0.03	0.00	0.03
neighborPurity	0.60	0.01	0.61
nestedClusters	0.03	0.00	0.03
pairwiseModularity	0.67	0.00	0.67
pairwiseRand	0.02	0.00	0.02

name	user	system	elapsed
AffinityParam-class	0.56	0.08	0.64
AgnesParam-class	0.01	0.00	0.02
ClaraParam-class	0.02	0.00	0.02
DbscanParam-class	0.12	0.00	0.12
DianaParam-class	0.03	0.00	0.03
HclustParam-class	0	0	0
KmeansParam-class	0.00	0.02	0.02
MbkmeansParam-class	4.81	0.14	5.01
NNGraphParam-class	0.05	0.00	0.05
PamParam-class	0.03	0.00	0.03
SomParam-class	0.05	0.00	0.05
TwoStepParam-class	0.31	0.00	0.31
approxSilhouette	0.06	0.00	0.06
bootstrapStability	0.22	0.00	0.22
clusterRMSD	0.02	0.00	0.02
clusterRows	1.00	0.01	1.01
clusterSweep	0.42	0.00	0.43
compareClusterings	0.16	0.00	0.15
defaultArguments	0	0	0
linkClusters	0.06	0.00	0.06
makeSNNGraph	0.84	0.02	0.86
mergeCommunities	0.05	0.00	0.05
neighborPurity	0.13	0.00	0.13
nestedClusters	0.04	0.00	0.04
pairwiseModularity	0.67	0.00	0.67
pairwiseRand	0.02	0.00	0.02

CHECK results for bluster on tokay2

Summary

Command output

Installation output

Tests output

Example timings