| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-10-19 13:23:46 -0400 (Wed, 19 Oct 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4386 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" | 4138 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4205 |
| 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 | ||||
|
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? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1896/2140 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| spatialHeatmap 2.2.0 (landing page) Jianhai Zhang
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: spatialHeatmap |
| Version: 2.2.0 |
| 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_2.2.0.tar.gz |
| StartedAt: 2022-10-19 08:20:27 -0400 (Wed, 19 Oct 2022) |
| EndedAt: 2022-10-19 08:32:19 -0400 (Wed, 19 Oct 2022) |
| EllapsedTime: 711.5 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_2.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/spatialHeatmap.Rcheck’
* using R version 4.2.1 (2022-06-23)
* 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 ‘2.2.0’
* 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 18.8Mb
sub-directories of 1Mb or more:
extdata 18.0Mb
* 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 ... NOTE
Unknown package ‘BioParallel’ in Rd xrefs
* 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
spatial_hm 45.487 1.776 47.585
read_hdf5 22.963 0.742 23.739
spatialHeatmap-package 19.880 0.797 20.808
write_hdf5 18.670 0.573 19.272
spatial_enrich 8.225 0.209 8.598
* 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: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.15-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/4.2/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)
spatialHeatmap.Rcheck/tests/runTests.Rout
R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 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 -- Wed Oct 19 08:32:05 2022
***********************************************
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
47.438 1.786 49.265
spatialHeatmap.Rcheck/spatialHeatmap-Ex.timings
| name | user | system | elapsed | |
| aSVG.remote.repo | 0.004 | 0.001 | 0.005 | |
| adj_mod | 3.665 | 0.067 | 3.735 | |
| aggr_rep | 0.583 | 0.017 | 0.601 | |
| auc_bar | 0.336 | 0.006 | 0.343 | |
| auc_stat | 0.138 | 0.009 | 0.148 | |
| auc_violin | 0.131 | 0.008 | 0.139 | |
| cluster_cell | 2.901 | 0.134 | 3.037 | |
| coclus_opt | 0.138 | 0.007 | 0.145 | |
| coclus_roc | 1.469 | 0.033 | 1.504 | |
| cocluster | 1.564 | 0.055 | 1.621 | |
| com_factor | 0.022 | 0.001 | 0.023 | |
| custom_shiny | 0.016 | 0.002 | 0.019 | |
| deg.table | 0.030 | 0.001 | 0.032 | |
| deg_ovl | 2.332 | 0.051 | 2.386 | |
| desired_bulk_shiny | 0.000 | 0.001 | 0.001 | |
| edit_tar | 0.007 | 0.001 | 0.008 | |
| filter_cell | 1.522 | 0.051 | 1.575 | |
| filter_data | 2.142 | 0.071 | 2.215 | |
| filter_iter | 0.140 | 0.008 | 0.148 | |
| lis.deg.up.down | 0.002 | 0.002 | 0.003 | |
| matrix_hm | 2.425 | 0.079 | 2.520 | |
| mean_auc_bar | 0.137 | 0.003 | 0.140 | |
| network | 2.644 | 0.048 | 2.696 | |
| norm_data | 0.834 | 0.015 | 0.850 | |
| norm_multi | 1.448 | 0.022 | 1.472 | |
| plot_dim | 2.868 | 0.037 | 2.908 | |
| profile_gene | 0.365 | 0.004 | 0.370 | |
| random_para | 0.015 | 0.000 | 0.016 | |
| read_cache | 2.166 | 0.035 | 2.207 | |
| read_fr | 0.007 | 0.000 | 0.008 | |
| read_hdf5 | 22.963 | 0.742 | 23.739 | |
| reduce_rep | 0.002 | 0.000 | 0.003 | |
| refine_cluster | 2.339 | 0.026 | 2.368 | |
| return_feature | 1.978 | 0.019 | 2.010 | |
| save_cache | 2.141 | 0.059 | 2.203 | |
| shiny_shm | 0 | 0 | 0 | |
| spatialHeatmap-package | 19.880 | 0.797 | 20.808 | |
| spatial_enrich | 8.225 | 0.209 | 8.598 | |
| spatial_hm | 45.487 | 1.776 | 47.585 | |
| spd_auc_violin | 0.142 | 0.002 | 0.144 | |
| sub_asg | 1.399 | 0.009 | 1.410 | |
| sub_data | 1.195 | 0.045 | 1.241 | |
| submatrix | 1.462 | 0.023 | 1.487 | |
| true_bulk | 0.805 | 0.018 | 0.824 | |
| update_feature | 0.002 | 0.002 | 0.004 | |
| write_hdf5 | 18.670 | 0.573 | 19.272 | |