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This page was generated on 2023-10-16 11:36:41 -0400 (Mon, 16 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4626
palomino3Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4379
merida1macOS 12.6.4 Montereyx86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4395
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 1972/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
spatialDE 1.6.0  (landing page)
Gabriele Sales
Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/spatialDE
git_branch: RELEASE_3_17
git_last_commit: be7acd4
git_last_commit_date: 2023-04-25 11:32:03 -0400 (Tue, 25 Apr 2023)
nebbiolo1Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.6.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson2macOS 12.6.1 Monterey / arm64see weekly results here

CHECK results for spatialDE on palomino3


To the developers/maintainers of the spatialDE package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/spatialDE.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: spatialDE
Version: 1.6.0
Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:spatialDE.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings spatialDE_1.6.0.tar.gz
StartedAt: 2023-10-16 07:06:01 -0400 (Mon, 16 Oct 2023)
EndedAt: 2023-10-16 07:10:48 -0400 (Mon, 16 Oct 2023)
EllapsedTime: 286.6 seconds
RetCode: 0
Status:   OK  
CheckDir: spatialDE.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:spatialDE.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings spatialDE_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.17-bioc/meat/spatialDE.Rcheck'
* using R version 4.3.1 (2023-06-16 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.2.0
    GNU Fortran (GCC) 12.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'spatialDE/DESCRIPTION' ... OK
* this is package 'spatialDE' version '1.6.0'
* 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 'spatialDE' can be installed ... NOTE
Found the following notes/warnings:
  Non-staged installation was used
See 'F:/biocbuild/bbs-3.17-bioc/meat/spatialDE.Rcheck/00install.out' for details.
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in shell scripts ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
spatial_patterns 10.82   0.89    5.86
FSV_sig           4.14   2.16   30.06
* 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-3.17-bioc/meat/spatialDE.Rcheck/00check.log'
for details.



Installation output

spatialDE.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL spatialDE
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library'
* installing *source* package 'spatialDE' ...
** using non-staged installation via StagedInstall field
** R
** data
** 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
* DONE (spatialDE)

Tests output

spatialDE.Rcheck/tests/testthat.Rout


R version 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts"
Copyright (C) 2023 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(spatialDE)
> 
> test_check("spatialDE")
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, aperm, 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 object is masked from 'package:utils':

    findMatches

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


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C:\Users\BIOCBU~1\AppData\Local\R\cache\R\basilisk\112~1.1\SPATIA~1\1611D8~1.0\env\lib\site-packages\pandas\core\internals\blocks.py:351: RuntimeWarning: invalid value encountered in log
  result = func(self.values, **kwargs)

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Models:  70%|███████   | 7/10 [00:02<00:00,  3.18it/s]

  0%|          | 0/100 [00:00<?, ?it/s]

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Models:  80%|████████  | 8/10 [00:02<00:00,  3.09it/s]

  0%|          | 0/100 [00:00<?, ?it/s]

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Models:  90%|█████████ | 9/10 [00:02<00:00,  3.17it/s]

  0%|          | 0/100 [00:00<?, ?it/s]

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Models: 100%|██████████| 10/10 [00:03<00:00,  3.33it/s]
Models: 100%|██████████| 10/10 [00:03<00:00,  3.28it/s]

Models:   0%|          | 0/10 [00:00<?, ?it/s]

  0%|          | 0/100 [00:00<?, ?it/s]

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Models:  10%|█         | 1/10 [00:00<00:01,  4.92it/s]

  0%|          | 0/100 [00:00<?, ?it/s]

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Models:  20%|██        | 2/10 [00:00<00:02,  3.74it/s]

  0%|          | 0/100 [00:00<?, ?it/s]

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 71%|███████   | 71/100 [00:00<00:00, 323.77it/s]

                                                 
Models:  30%|███       | 3/10 [00:00<00:01,  3.56it/s]

  0%|          | 0/100 [00:00<?, ?it/s]

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 70%|███████   | 70/100 [00:00<00:00, 320.01it/s]

                                                 
Models:  40%|████      | 4/10 [00:01<00:01,  3.41it/s]

  0%|          | 0/100 [00:00<?, ?it/s]

 35%|███▌      | 35/100 [00:00<00:00, 319.99it/s]

 70%|███████   | 70/100 [00:00<00:00, 319.17it/s]

                                                 
Models:  50%|█████     | 5/10 [00:01<00:01,  3.33it/s]

  0%|          | 0/100 [00:00<?, ?it/s]

 35%|███▌      | 35/100 [00:00<00:00, 319.97it/s]

 68%|██████▊   | 68/100 [00:00<00:00, 309.24it/s]

                                                 
Models:  60%|██████    | 6/10 [00:01<00:01,  3.26it/s]

  0%|          | 0/100 [00:00<?, ?it/s]

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 68%|██████▊   | 68/100 [00:00<00:00, 338.97it/s]

                                                 
Models:  70%|███████   | 7/10 [00:02<00:00,  3.28it/s]

  0%|          | 0/100 [00:00<?, ?it/s]

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 99%|█████████▉| 99/100 [00:00<00:00, 328.90it/s]

                                                 
Models:  80%|████████  | 8/10 [00:02<00:00,  3.28it/s]

  0%|          | 0/100 [00:00<?, ?it/s]

 39%|███▉      | 39/100 [00:00<00:00, 354.91it/s]

 75%|███████▌  | 75/100 [00:00<00:00, 338.84it/s]

                                                 
Models:  90%|█████████ | 9/10 [00:02<00:00,  3.36it/s]

  0%|          | 0/100 [00:00<?, ?it/s]

 36%|███▌      | 36/100 [00:00<00:00, 327.73it/s]

 76%|███████▌  | 76/100 [00:00<00:00, 349.15it/s]

                                                 
Models: 100%|██████████| 10/10 [00:02<00:00,  3.41it/s]
Models: 100%|██████████| 10/10 [00:02<00:00,  3.41it/s][ FAIL 0 | WARN 0 | SKIP 0 | PASS 29 ]

> 
> proc.time()
   user  system elapsed 
  46.29    2.40   58.78 

Example timings

spatialDE.Rcheck/spatialDE-Ex.timings

nameusersystemelapsed
FSV_sig 4.14 2.1630.06
mockSVG0.310.020.28
modelSearch2.520.321.53
model_search1.960.221.09
multiGenePlots2.460.221.69
regress_out0.170.020.14
run1.020.140.58
spatialDE1.320.110.77
spatialPatterns1.210.120.70
spatial_patterns10.82 0.89 5.86
stabilize0.930.030.78