Jianhai Zhang
| Snapshot Date: 2024-05-18 09:00:01 -0400 (Sat, 18 May 2024) |
| git_url: https://git.bioconductor.org/packages/spatialHeatmap |
| git_branch: devel |
| git_last_commit: 5909972 |
| git_last_commit_date: 2024-04-30 11:27:48 -0400 (Tue, 30 Apr 2024) |
| Back to Mac ARM64 build report for BioC 3.20 |
|
This page was generated on 2024-05-20 11:32:21 -0400 (Mon, 20 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4381 |
| 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 1974/2233 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| spatialHeatmap 2.11.0 (landing page) Jianhai Zhang
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | |||||||
|
To the developers/maintainers of the spatialHeatmap package: - 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: 2.11.0 |
| 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_2.11.0.tar.gz |
| StartedAt: 2024-05-20 03:40:30 -0400 (Mon, 20 May 2024) |
| EndedAt: 2024-05-20 03:48:39 -0400 (Mon, 20 May 2024) |
| EllapsedTime: 488.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: spatialHeatmap.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### 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_2.11.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/spatialHeatmap.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘spatialHeatmap/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘spatialHeatmap’ version ‘2.11.0’
* 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 31.8Mb
sub-directories of 1Mb or more:
R 1.2Mb
extdata 30.2Mb
* 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 code 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 19.750 0.736 20.636
SPHM 19.419 0.657 20.267
cell_group 14.289 0.300 14.672
process_cell_meta 9.851 0.106 10.017
reduce_dim 9.424 0.105 9.592
spatial_hm 4.901 0.236 5.190
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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-3.20-bioc-mac-arm64/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/4.4-arm64/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 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
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, 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 May 20 03:48:21 2024
***********************************************
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
30.421 1.201 31.875
spatialHeatmap.Rcheck/spatialHeatmap-Ex.timings
| name | user | system | elapsed | |
| Database | 0.523 | 0.025 | 0.554 | |
| SPHM | 19.419 | 0.657 | 20.267 | |
| SPHMMethods | 1.804 | 0.215 | 2.041 | |
| SVG | 0.789 | 0.262 | 1.123 | |
| SVGMethods | 0.479 | 0.149 | 0.659 | |
| SpatialEnrichment | 4.315 | 0.252 | 4.614 | |
| aSVG.remote.repo | 0.003 | 0.002 | 0.005 | |
| adj_mod | 3.058 | 0.118 | 3.200 | |
| aggr_rep | 0.966 | 0.031 | 1.003 | |
| cell_group | 14.289 | 0.300 | 14.672 | |
| cluster_cell | 1.593 | 0.029 | 1.626 | |
| coclus_opt | 0.279 | 0.012 | 0.295 | |
| cocluster | 0.262 | 0.018 | 0.283 | |
| com_factor | 0.259 | 0.017 | 0.285 | |
| covis | 19.750 | 0.736 | 20.636 | |
| custom_shiny | 0.023 | 0.006 | 0.029 | |
| cut_dendro | 0.598 | 0.012 | 0.617 | |
| cvt_id | 0.704 | 0.026 | 0.743 | |
| data_ref | 0.947 | 0.019 | 0.975 | |
| edit_tar | 0.005 | 0.001 | 0.007 | |
| filter_data | 1.138 | 0.049 | 1.200 | |
| matrix_hm | 2.771 | 0.063 | 2.844 | |
| network | 2.548 | 0.049 | 2.610 | |
| norm_cell | 2.383 | 0.045 | 2.436 | |
| norm_data | 0.972 | 0.038 | 1.018 | |
| norm_srsc | 3.172 | 0.188 | 3.385 | |
| opt_bar | 0.109 | 0.002 | 0.111 | |
| opt_setting | 0.007 | 0.003 | 0.010 | |
| opt_violin | 0.183 | 0.003 | 0.193 | |
| optimal_k | 0.128 | 0.003 | 0.131 | |
| plot_dim | 1.985 | 0.037 | 2.037 | |
| plot_kmeans | 0.648 | 0.030 | 0.682 | |
| plot_meta | 2.874 | 0.303 | 3.207 | |
| process_cell_meta | 9.851 | 0.106 | 10.017 | |
| qc_cell | 1.231 | 0.025 | 1.260 | |
| read_cache | 2.974 | 0.033 | 3.021 | |
| read_fr | 0.006 | 0.001 | 0.008 | |
| read_svg | 0.625 | 0.258 | 0.974 | |
| reduce_dim | 9.424 | 0.105 | 9.592 | |
| reduce_rep | 0.002 | 0.001 | 0.002 | |
| return_feature | 0.782 | 0.019 | 0.810 | |
| save_cache | 2.827 | 0.028 | 2.870 | |
| shiny_shm | 0.000 | 0.001 | 0.000 | |
| shm | 3.674 | 0.225 | 3.996 | |
| spatialHeatmap-package | 0.001 | 0.001 | 0.001 | |
| spatial_hm | 4.901 | 0.236 | 5.190 | |
| submatrix | 2.925 | 0.062 | 3.003 | |
| true_bulk | 0.412 | 0.016 | 0.429 | |
| update_feature | 0.001 | 0.002 | 0.003 | |
| write_svg | 2.960 | 0.263 | 3.318 | |