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This page was generated on 2021-11-29 15:06:13 -0500 (Mon, 29 Nov 2021).

CHECK results for spatialHeatmap on machv2

To the developers/maintainers of the spatialHeatmap package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/spatialHeatmap.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 1848/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
spatialHeatmap 2.0.0  (landing page)
Jianhai Zhang
Snapshot Date: 2021-11-28 04:15:06 -0500 (Sun, 28 Nov 2021)
git_url: https://git.bioconductor.org/packages/spatialHeatmap
git_branch: RELEASE_3_14
git_last_commit: 4bdc542
git_last_commit_date: 2021-10-26 13:03:26 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: spatialHeatmap
Version: 2.0.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:spatialHeatmap.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings spatialHeatmap_2.0.0.tar.gz
StartedAt: 2021-11-28 21:38:41 -0500 (Sun, 28 Nov 2021)
EndedAt: 2021-11-28 21:47:04 -0500 (Sun, 28 Nov 2021)
EllapsedTime: 503.2 seconds
RetCode: 0
Status:   OK  
CheckDir: spatialHeatmap.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:spatialHeatmap.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings spatialHeatmap_2.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/spatialHeatmap.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘spatialHeatmap/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘spatialHeatmap’ version ‘2.0.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘spatialHeatmap’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 13.1Mb
  sub-directories of 1Mb or more:
    extdata  11.4Mb
    script    1.2Mb
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
write_hdf5             20.475  0.957  21.447
spatial_hm             15.997  1.005  17.106
spatialHeatmap-package 15.584  1.022  16.741
spatial_enrich          6.868  0.257   7.186
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/spatialHeatmap.Rcheck/00check.log’
for details.



Installation output

spatialHeatmap.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL spatialHeatmap
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘spatialHeatmap’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (spatialHeatmap)

Tests output

spatialHeatmap.Rcheck/tests/runTests.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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.

> BiocGenerics:::testPackage("spatialHeatmap")

Loading required package: Biobase
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

Welcome to Bioconductor

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

Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'matrixStats'

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

    anyMissing, rowMedians


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

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

    rowMedians

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: limma

Attaching package: 'limma'

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

    plotMA

Loading required package: xml2
Normalising: ESF 
   type 
"ratio" 
Syntactically valid column names are made! 
Syntactically valid column names are made! 
All values before filtering:
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  0.000   0.000   0.287   2.442   4.268  19.991 
All coefficient of variances (CVs) before filtering:
     Min.   1st Qu.    Median      Mean   3rd Qu.      Max. 
0.0007742 0.0767696 0.4019655 0.6217813 0.9956157 2.0000000 
All values after filtering:
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  0.000   2.654   4.976   4.779   6.451  14.695 
All coefficient of variances (CVs) after filtering:
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
 0.3001  0.3648  0.4637  0.5651  0.7392  1.1548 
Warning: variables of sample/condition are less than 5! 
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
 ..done.
 ..done.
Normalising: ESF 
   type 
"ratio" 
Syntactically valid column names are made! 
Syntactically valid column names are made! 
All values before filtering:
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  0.000   0.000   0.287   2.442   4.268  19.991 
All coefficient of variances (CVs) before filtering:
     Min.   1st Qu.    Median      Mean   3rd Qu.      Max. 
0.0007742 0.0767696 0.4019655 0.6217813 0.9956157 2.0000000 
All values after filtering:
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  0.000   2.654   4.976   4.779   6.451  14.695 
All coefficient of variances (CVs) after filtering:
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
 0.3001  0.3648  0.4637  0.5651  0.7392  1.1548 


RUNIT TEST PROTOCOL -- Sun Nov 28 21:46:54 2021 
*********************************************** 
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
spatialHeatmap RUnit Tests - 2 test functions, 0 errors, 0 failures
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 40.327   1.477  41.806 

Example timings

spatialHeatmap.Rcheck/spatialHeatmap-Ex.timings

nameusersystemelapsed
aSVG.remote.repo0.0020.0010.004
adj_mod2.3530.0742.430
aggr_rep0.4930.0190.513
com_factor0.0170.0010.019
custom_shiny0.0150.0030.018
deg.table0.0260.0020.028
deg_ovl1.8400.0661.909
edit_tar0.0060.0010.007
filter_data0.9100.0410.952
lis.deg.up.down0.0010.0020.003
matrix_hm1.8920.0841.987
network2.0290.0662.096
norm_data0.7760.0440.833
profile_gene0.2340.0040.239
read_cache2.5450.0312.579
read_fr0.0080.0010.009
read_hdf50.0000.0000.001
return_feature1.8260.0271.864
save_cache2.1250.0142.141
shiny_shm000
spatialHeatmap-package15.584 1.02216.741
spatial_enrich6.8680.2577.186
spatial_hm15.997 1.00517.106
sub_data1.0500.0281.079
submatrix1.2500.0341.284
update_feature0.0000.0000.001
write_hdf520.475 0.95721.447