Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2021-10-23 14:06:19 -0400 (Sat, 23 Oct 2021).

CHECK results for BayesSpace on riesling1

To the developers/maintainers of the BayesSpace package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BayesSpace.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 125/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BayesSpace 1.3.1  (landing page)
Matt Stone
Snapshot Date: 2021-10-22 14:50:11 -0400 (Fri, 22 Oct 2021)
git_url: https://git.bioconductor.org/packages/BayesSpace
git_branch: master
git_last_commit: f7aeef9
git_last_commit_date: 2021-10-06 10:38:23 -0400 (Wed, 06 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / 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: BayesSpace
Version: 1.3.1
Command: D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BayesSpace.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings BayesSpace_1.3.1.tar.gz
StartedAt: 2021-10-23 05:02:20 -0400 (Sat, 23 Oct 2021)
EndedAt: 2021-10-23 05:09:08 -0400 (Sat, 23 Oct 2021)
EllapsedTime: 408.7 seconds
RetCode: 0
Status:   OK  
CheckDir: BayesSpace.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BayesSpace.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings BayesSpace_1.3.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.14-bioc/meat/BayesSpace.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'BayesSpace/DESCRIPTION' ... OK
* this is package 'BayesSpace' version '1.3.1'
* package encoding: UTF-8
* 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 'BayesSpace' 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 line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... 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 'D:/biocbuild/bbs-3.14-bioc/R/library/BayesSpace/libs/i386/BayesSpace.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'D:/biocbuild/bbs-3.14-bioc/R/library/BayesSpace/libs/x64/BayesSpace.dll':
  Found '_exit', possibly from '_exit' (C)
  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
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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
  'D:/biocbuild/bbs-3.14-bioc/meat/BayesSpace.Rcheck/00check.log'
for details.



Installation output

BayesSpace.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/BayesSpace_1.3.1.tar.gz && rm -rf BayesSpace.buildbin-libdir && mkdir BayesSpace.buildbin-libdir && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BayesSpace.buildbin-libdir BayesSpace_1.3.1.tar.gz && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL BayesSpace_1.3.1.zip && rm BayesSpace_1.3.1.tar.gz BayesSpace_1.3.1.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
 56  717k   56  408k    0     0  1559k      0 --:--:-- --:--:-- --:--:-- 1553k
100  717k  100  717k    0     0  2359k      0 --:--:-- --:--:-- --:--:-- 2351k

install for i386

* installing *source* package 'BayesSpace' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/RcppDist/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/RcppProgress/include'   -I"C:/extsoft/include"  -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/RcppDist/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/RcppProgress/include'   -I"C:/extsoft/include"  -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cluster.cpp -o cluster.o
C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o BayesSpace.dll tmp.def RcppExports.o cluster.o -fopenmp -LD:/biocbuild/bbs-3.14-bioc/R/bin/i386 -lRlapack -LD:/biocbuild/bbs-3.14-bioc/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.14-bioc/R/bin/i386 -lR
installing to D:/biocbuild/bbs-3.14-bioc/meat/BayesSpace.buildbin-libdir/00LOCK-BayesSpace/00new/BayesSpace/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'BayesSpace'
    finding HTML links ... done
    BayesSpace                              html  
    Mode                                    html  
    cluster                                 html  
    clusterPlot                             html  
    deconvolve                              html  
    dot-adjust_hex_centers                  html  
    dot-bsData                              html  
    dot-clean_chain                         html  
    dot-compute_interspot_distances         html  
    dot-find_neighbors                      html  
    dot-flatten_matrix_list                 html  
    dot-infer_param_dims                    html  
    dot-init_cluster                        html  
    dot-make_hex_spots                      html  
    dot-make_index_names                    html  
    dot-make_spot_vertices                  html  
    dot-make_square_spots                   html  
    dot-make_subspot_coldata                html  
    dot-make_subspot_offsets                html  
    dot-make_triangle_subspots              html  
    dot-make_vertices                       html  
    dot-prepare_inputs                      html  
    dot-read_chain                          html  
    dot-select_spot_positions               html  
    dot-select_subspot_positions            html  
    enhanceFeatures                         html  
    exampleSCE                              html  
    featurePlot                             html  
    find_neighbors                          html  
    getRDS                                  html  
    mcmcChain                               html  
    qTune                                   html  
    readVisium                              html  
    spatialCluster                          html  
    spatialEnhance                          html  
    spatialPlot                             html  
    spatialPreprocess                       html  
    finding level-2 HTML links ... done

** 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 'BayesSpace' ...
** libs
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/RcppDist/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/RcppProgress/include'   -I"C:/extsoft/include"  -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/RcppDist/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/RcppProgress/include'   -I"C:/extsoft/include"  -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cluster.cpp -o cluster.o
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o BayesSpace.dll tmp.def RcppExports.o cluster.o -fopenmp -LD:/biocbuild/bbs-3.14-bioc/R/bin/x64 -lRlapack -LD:/biocbuild/bbs-3.14-bioc/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.14-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.14-bioc/meat/BayesSpace.buildbin-libdir/BayesSpace/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BayesSpace' as BayesSpace_1.3.1.zip
* DONE (BayesSpace)
* installing to library 'D:/biocbuild/bbs-3.14-bioc/R/library'
package 'BayesSpace' successfully unpacked and MD5 sums checked

Tests output

BayesSpace.Rcheck/tests_i386/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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(BayesSpace)
Loading required package: SingleCellExperiment
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

> 
> test_check("BayesSpace")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 43 ]
> 
> proc.time()
   user  system elapsed 
  24.81    2.29   27.68 

BayesSpace.Rcheck/tests_x64/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
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)
> library(BayesSpace)
Loading required package: SingleCellExperiment
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

> 
> test_check("BayesSpace")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 43 ]
> 
> proc.time()
   user  system elapsed 
  23.43    2.50   27.34 

Example timings

BayesSpace.Rcheck/examples_i386/BayesSpace-Ex.timings

nameusersystemelapsed
clusterPlot0.620.010.64
enhanceFeatures2.910.143.07
exampleSCE0.330.000.32
featurePlot0.400.000.41
getRDS0.440.162.97
mcmcChain0.530.030.61
qTune0.810.000.81
readVisium000
spatialCluster0.520.000.52
spatialEnhance1.720.031.75
spatialPreprocess0.580.000.57

BayesSpace.Rcheck/examples_x64/BayesSpace-Ex.timings

nameusersystemelapsed
clusterPlot0.650.080.73
enhanceFeatures2.860.123.05
exampleSCE0.370.000.38
featurePlot0.440.000.44
getRDS0.380.222.73
mcmcChain0.670.000.67
qTune0.830.000.83
readVisium000
spatialCluster0.530.020.55
spatialEnhance1.620.011.64
spatialPreprocess0.640.020.65