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) |
| Back to Multiple platform build/check report for BioC 3.13 experimental data |
|
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 347/391 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | ||||||||
| spatialLIBD 1.3.5 Leonardo Collado-Torres
| rex3 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | | |||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | ERROR | |||||||||
| 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 |
##############################################################################
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###
### 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
###
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* 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.
spatialLIBD.Rcheck/00install.out
##############################################################################
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###
### 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
###
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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
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
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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
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spatialLIBD.Rcheck/examples_i386/spatialLIBD-Ex.timings
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spatialLIBD.Rcheck/examples_x64/spatialLIBD-Ex.timings
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