| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-10-16 11:37:34 -0400 (Mon, 16 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4626 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4379 |
| merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (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 1976/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| spatialHeatmap 2.6.2 (landing page) Jianhai Zhang
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the spatialHeatmap package: - 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 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. |
| Package: spatialHeatmap |
| Version: 2.6.2 |
| 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_2.6.2.tar.gz |
| StartedAt: 2023-10-16 07:25:45 -0400 (Mon, 16 Oct 2023) |
| EndedAt: 2023-10-16 07:41:40 -0400 (Mon, 16 Oct 2023) |
| EllapsedTime: 954.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: spatialHeatmap.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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_2.6.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/spatialHeatmap.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.3 (clang-1403.0.22.14.1)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘spatialHeatmap/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘spatialHeatmap’ version ‘2.6.2’
* 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 30.6Mb
sub-directories of 1Mb or more:
R 1.2Mb
extdata 29.0Mb
* 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
covis 25.315 1.296 32.817
SPHM 22.399 1.502 29.475
cell_group 15.386 0.375 19.413
process_cell_meta 10.853 0.155 13.606
spatial_hm 9.844 0.479 12.860
reduce_dim 9.927 0.123 12.394
SpatialEnrichment 8.557 0.583 10.819
shm 7.013 0.449 9.122
write_svg 6.097 0.570 8.107
plot_meta 5.462 0.858 7.521
adj_mod 4.976 0.238 6.340
norm_srsc 4.149 0.233 5.352
submatrix 4.198 0.084 5.435
matrix_hm 4.077 0.097 5.191
* 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-3.17-bioc/meat/spatialHeatmap.Rcheck/00check.log’
for details.
spatialHeatmap.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL spatialHeatmap ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’ * installing *source* package ‘spatialHeatmap’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘svg’ in package ‘spatialHeatmap’ Creating a new generic function for ‘match’ in package ‘spatialHeatmap’ ** 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)
spatialHeatmap.Rcheck/tests/runTests.Rout
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (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")
Attaching package: 'spatialHeatmap'
The following object is masked from 'package:grDevices':
svg
The following object is masked from 'package:base':
match
Loading required package: Biobase
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following object is masked from 'package:spatialHeatmap':
match
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
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 object is masked from 'package:utils':
findMatches
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
Loading required package: RCurl
Loading required package: jsonlite
Loading required package: BiocStyle
Attaching package: 'BiocStyle'
The following object is masked from 'package:spatialHeatmap':
output
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.
..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 -- Mon Oct 16 07:41:11 2023
***********************************************
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
51.888 2.282 66.809
spatialHeatmap.Rcheck/spatialHeatmap-Ex.timings
| name | user | system | elapsed | |
| Database | 0.788 | 0.043 | 1.036 | |
| SPHM | 22.399 | 1.502 | 29.475 | |
| SPHMMethods | 3.487 | 0.562 | 4.800 | |
| SVG | 1.332 | 0.432 | 1.978 | |
| SVGMethods | 0.860 | 0.246 | 1.210 | |
| SpatialEnrichment | 8.557 | 0.583 | 10.819 | |
| aSVG.remote.repo | 0.004 | 0.003 | 0.008 | |
| adj_mod | 4.976 | 0.238 | 6.340 | |
| aggr_rep | 1.918 | 0.049 | 2.408 | |
| cell_group | 15.386 | 0.375 | 19.413 | |
| cluster_cell | 2.487 | 0.036 | 3.100 | |
| coclus_opt | 0.481 | 0.020 | 0.607 | |
| cocluster | 0.403 | 0.039 | 0.546 | |
| com_factor | 0.333 | 0.020 | 0.436 | |
| covis | 25.315 | 1.296 | 32.817 | |
| custom_shiny | 0.035 | 0.011 | 0.055 | |
| cut_dendro | 1.677 | 0.026 | 2.053 | |
| cvt_id | 0.908 | 0.031 | 1.143 | |
| edit_tar | 0.008 | 0.001 | 0.015 | |
| filter_data | 2.004 | 0.062 | 2.626 | |
| matrix_hm | 4.077 | 0.097 | 5.191 | |
| network | 3.848 | 0.105 | 4.841 | |
| norm_cell | 3.790 | 0.067 | 4.724 | |
| norm_data | 1.937 | 0.046 | 2.413 | |
| norm_srsc | 4.149 | 0.233 | 5.352 | |
| opt_bar | 0.258 | 0.003 | 0.320 | |
| opt_setting | 0.018 | 0.008 | 0.032 | |
| opt_violin | 0.488 | 0.011 | 0.618 | |
| optimal_k | 0.298 | 0.003 | 0.369 | |
| plot_dim | 3.136 | 0.044 | 3.872 | |
| plot_kmeans | 1.185 | 0.038 | 1.544 | |
| plot_meta | 5.462 | 0.858 | 7.521 | |
| process_cell_meta | 10.853 | 0.155 | 13.606 | |
| qc_cell | 2.292 | 0.034 | 2.856 | |
| read_cache | 2.482 | 0.050 | 3.119 | |
| read_fr | 0.009 | 0.002 | 0.012 | |
| read_svg | 0.905 | 0.447 | 1.496 | |
| reduce_dim | 9.927 | 0.123 | 12.394 | |
| reduce_rep | 0.002 | 0.002 | 0.010 | |
| return_feature | 1.605 | 0.035 | 1.968 | |
| save_cache | 2.422 | 0.034 | 3.105 | |
| shiny_shm | 0.000 | 0.001 | 0.001 | |
| shm | 7.013 | 0.449 | 9.122 | |
| spatialHeatmap-package | 0.001 | 0.001 | 0.003 | |
| spatial_hm | 9.844 | 0.479 | 12.860 | |
| submatrix | 4.198 | 0.084 | 5.435 | |
| true_bulk | 0.643 | 0.026 | 0.945 | |
| update_feature | 0.002 | 0.003 | 0.005 | |
| write_svg | 6.097 | 0.570 | 8.107 | |