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CHECK report for spatialLIBD on riesling1

This page was generated on 2021-03-01 15:56:11 -0500 (Mon, 01 Mar 2021).

To the developers/maintainers of the spatialLIBD package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 347/391HostnameOS / ArchINSTALLBUILDCHECK
spatialLIBD 1.3.5
Leonardo Collado-Torres
Snapshot Date: 2021-03-01 09:00:05 -0500 (Mon, 01 Mar 2021)
URL: https://git.bioconductor.org/packages/spatialLIBD
Branch: master
Last Commit: 3fbc875
Last Changed Date: 2021-02-16 14:50:48 -0500 (Tue, 16 Feb 2021)
rex3Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
riesling1Windows Server 2019 Standard / x64  OK    OK    ERROR  

Summary

Package: spatialLIBD
Version: 1.3.5
Command: D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:spatialLIBD.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings spatialLIBD_1.3.5.tar.gz
StartedAt: 2021-03-01 11:58:47 -0500 (Mon, 01 Mar 2021)
EndedAt: 2021-03-01 12:06:45 -0500 (Mon, 01 Mar 2021)
EllapsedTime: 477.3 seconds
RetCode: 1
Status:   ERROR   
CheckDir: spatialLIBD.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:spatialLIBD.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings spatialLIBD_1.3.5.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.13-data-experiment/meat/spatialLIBD.Rcheck'
* using R Under development (unstable) (2021-02-08 r79971)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'spatialLIBD/DESCRIPTION' ... OK
* this is package 'spatialLIBD' version '1.3.5'
* 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 'spatialLIBD' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  8.6Mb
  sub-directories of 1Mb or more:
    app    5.6Mb
    help   2.4Mb
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... ERROR
Running examples in 'spatialLIBD-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: sce_to_spe
> ### Title: Convert a SCE object to a SPE one
> ### Aliases: sce_to_spe
> 
> ### ** Examples
> 
> 
> if (enough_ram()) {
+     ## Download the sce data
+     sce <- fetch_data("sce")
+     ## Transform it to a SpatialExperiment object
+     spe <- sce_to_spe(sce)
+ }
snapshotDate(): 2021-02-19
2021-03-01 12:03:20 loading file C:\Users\BIOCBU~1\AppData\Local/BiocFileCache/BiocFileCache/Cache/6cb43dabeef_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
Error: cannot allocate vector of size 630.6 Mb
Execution halted
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
vis_grid_clus    12.92   1.25   14.97
vis_grid_gene    12.26   1.47   14.62
check_image_path 13.02   0.56   14.50
vis_gene         11.88   1.12   13.91
vis_clus_p       11.39   0.96   13.09
vis_gene_p       11.30   1.02   13.00
vis_clus         11.28   0.89   12.89
check_sce        10.81   0.83   12.22
geom_spatial     10.97   0.50   12.31
sce_to_spe       10.56   0.53   11.75
layer_boxplot     4.08   0.58    5.03
* 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 ERROR, 1 NOTE
See
  'D:/biocbuild/bbs-3.13-data-experiment/meat/spatialLIBD.Rcheck/00check.log'
for details.


Installation output

spatialLIBD.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.173.35/BBS/3.13/data-experiment/src/contrib/spatialLIBD_1.3.5.tar.gz && rm -rf spatialLIBD.buildbin-libdir && mkdir spatialLIBD.buildbin-libdir && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=spatialLIBD.buildbin-libdir spatialLIBD_1.3.5.tar.gz && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL spatialLIBD_1.3.5.zip && rm spatialLIBD_1.3.5.tar.gz spatialLIBD_1.3.5.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
  0 8494k    0  1105    0     0  21666      0  0:06:41 --:--:--  0:06:41 21250
 17 8494k   17 1497k    0     0  1427k      0  0:00:05  0:00:01  0:00:04 1427k
100 8494k  100 8494k    0     0  4516k      0  0:00:01  0:00:01 --:--:-- 4513k

install for i386

* installing *source* package 'spatialLIBD' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'spatialLIBD'
    finding HTML links ... done
    check_image_path                        html  
REDIRECT:topic	 check_image_path -> check_image_path.html [ SUCCESS ]
    finding level-2 HTML links ... done

    check_modeling_results                  html  
REDIRECT:topic	 check_modeling_results -> check_modeling_results.html [ SUCCESS ]
    check_sce                               html  
REDIRECT:topic	 check_sce -> check_sce.html [ SUCCESS ]
    check_sce_layer                         html  
REDIRECT:topic	 check_sce_layer -> check_sce_layer.html [ SUCCESS ]
    enough_ram                              html  
REDIRECT:topic	 enough_ram -> enough_ram.html [ SUCCESS ]
    fetch_data                              html  
REDIRECT:topic	 fetch_data -> fetch_data.html [ SUCCESS ]
    gene_set_enrichment                     html  
REDIRECT:topic	 gene_set_enrichment -> gene_set_enrichment.html [ SUCCESS ]
    gene_set_enrichment_plot                html  
REDIRECT:topic	 gene_set_enrichment_plot -> gene_set_enrichment_plot.html [ SUCCESS ]
    geom_spatial                            html  
REDIRECT:topic	 geom_spatial -> geom_spatial.html [ SUCCESS ]
    get_colors                              html  
REDIRECT:topic	 get_colors -> get_colors.html [ SUCCESS ]
    layer_boxplot                           html  
REDIRECT:topic	 layer_boxplot -> layer_boxplot.html [ SUCCESS ]
    layer_matrix_plot                       html  
REDIRECT:topic	 layer_matrix_plot -> layer_matrix_plot.html [ SUCCESS ]
    layer_stat_cor                          html  
REDIRECT:topic	 layer_stat_cor -> layer_stat_cor.html [ SUCCESS ]
    layer_stat_cor_plot                     html  
REDIRECT:topic	 layer_stat_cor_plot -> layer_stat_cor_plot.html [ SUCCESS ]
    libd_layer_colors                       html  
REDIRECT:topic	 libd_layer_colors -> libd_layer_colors.html [ SUCCESS ]
    run_app                                 html  
REDIRECT:topic	 run_app -> run_app.html [ SUCCESS ]
    sce_to_spe                              html  
REDIRECT:topic	 sce_to_spe -> sce_to_spe.html [ SUCCESS ]
    sig_genes_extract                       html  
REDIRECT:topic	 sig_genes_extract -> sig_genes_extract.html [ SUCCESS ]
    sig_genes_extract_all                   html  
REDIRECT:topic	 sig_genes_extract_all -> sig_genes_extract_all.html [ SUCCESS ]
    sort_clusters                           html  
REDIRECT:topic	 sort_clusters -> sort_clusters.html [ SUCCESS ]
    spatialLIBD-package                     html  
REDIRECT:topic	 spatialLIBD -> spatialLIBD-package.html [ SUCCESS ]
REDIRECT:topic	 spatialLIBD-package -> spatialLIBD-package.html [ SUCCESS ]
    tstats_Human_DLPFC_snRNAseq_Nguyen_topLayer
                                            html  
REDIRECT:topic	 tstats_Human_DLPFC_snRNAseq_Nguyen_topLayer -> tstats_Human_DLPFC_snRNAseq_Nguyen_topLayer.html [ SUCCESS ]
    vis_clus                                html  
REDIRECT:topic	 vis_clus -> vis_clus.html [ SUCCESS ]
    vis_clus_p                              html  
REDIRECT:topic	 vis_clus_p -> vis_clus_p.html [ SUCCESS ]
    vis_gene                                html  
REDIRECT:topic	 vis_gene -> vis_gene.html [ SUCCESS ]
    vis_gene_p                              html  
REDIRECT:topic	 vis_gene_p -> vis_gene_p.html [ SUCCESS ]
    vis_grid_clus                           html  
REDIRECT:topic	 vis_grid_clus -> vis_grid_clus.html [ SUCCESS ]
    vis_grid_gene                           html  
REDIRECT:topic	 vis_grid_gene -> vis_grid_gene.html [ SUCCESS ]
*** copying figures
** 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 'spatialLIBD' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'spatialLIBD' as spatialLIBD_1.3.5.zip
* DONE (spatialLIBD)
* installing to library 'D:/biocbuild/bbs-3.13-bioc/R/library'
package 'spatialLIBD' successfully unpacked and MD5 sums checked

Tests output

spatialLIBD.Rcheck/tests_i386/testthat.Rout


R Under development (unstable) (2021-02-08 r79971) -- "Unsuffered Consequences"
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(spatialLIBD)
Loading required package: SpatialExperiment
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
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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("spatialLIBD")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
> 
> proc.time()
   user  system elapsed 
   7.34    0.48    7.76 

spatialLIBD.Rcheck/tests_x64/testthat.Rout


R Under development (unstable) (2021-02-08 r79971) -- "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)
> library(spatialLIBD)
Loading required package: SpatialExperiment
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
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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("spatialLIBD")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
> 
> proc.time()
   user  system elapsed 
   7.92    0.68    8.60 

Example timings

spatialLIBD.Rcheck/examples_i386/spatialLIBD-Ex.timings

nameusersystemelapsed
check_image_path12.95 1.0822.26
check_modeling_results1.550.071.83
check_sce10.85 0.8512.33
check_sce_layer1.610.081.89
enough_ram0.000.020.46
fetch_data1.570.452.17
gene_set_enrichment1.670.111.92
gene_set_enrichment_plot1.810.021.98
geom_spatial10.78 0.5412.02
get_colors1.520.502.28
layer_boxplot3.540.134.03
layer_matrix_plot0.020.000.02
layer_stat_cor1.520.011.69
layer_stat_cor_plot1.450.111.71
run_app000

spatialLIBD.Rcheck/examples_x64/spatialLIBD-Ex.timings

nameusersystemelapsed
check_image_path13.02 0.5614.50
check_modeling_results1.520.111.85
check_sce10.81 0.8312.22
check_sce_layer1.580.081.89
enough_ram0.000.000.33
fetch_data2.170.422.71
gene_set_enrichment1.660.131.92
gene_set_enrichment_plot1.680.111.97
geom_spatial10.97 0.5012.31
get_colors1.660.041.93
layer_boxplot4.080.585.03
layer_matrix_plot0.000.000.01
layer_stat_cor1.550.101.85
layer_stat_cor_plot1.610.031.80
run_app000
sce_to_spe10.56 0.5311.75
sig_genes_extract3.800.644.82
sig_genes_extract_all3.230.223.75
sort_clusters000
vis_clus11.28 0.8912.89
vis_clus_p11.39 0.9613.09
vis_gene11.88 1.1213.91
vis_gene_p11.30 1.0213.00
vis_grid_clus12.92 1.2514.97
vis_grid_gene12.26 1.4714.62