| Back to Build/check report for BioC 3.18: simplified long |
|
This page was generated on 2023-06-06 11:00:42 -0000 (Tue, 06 Jun 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4366 |
| 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: - 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. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 1948/2199 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| spatialHeatmap 2.7.3 (landing page) Jianhai Zhang
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | |||||||||
| Package: spatialHeatmap |
| Version: 2.7.3 |
| Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:spatialHeatmap.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings spatialHeatmap_2.7.3.tar.gz |
| StartedAt: 2023-06-06 07:27:49 -0000 (Tue, 06 Jun 2023) |
| EndedAt: 2023-06-06 07:42:51 -0000 (Tue, 06 Jun 2023) |
| EllapsedTime: 902.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: spatialHeatmap.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:spatialHeatmap.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings spatialHeatmap_2.7.3.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/spatialHeatmap.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘spatialHeatmap/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘spatialHeatmap’ version ‘2.7.3’
* 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 24.2Mb
sub-directories of 1Mb or more:
R 1.2Mb
extdata 22.5Mb
* 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 loading without being on the library search path ... 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
SPHM 23.287 0.507 23.830
covis 21.443 0.481 21.954
cell_group 15.161 0.491 15.676
reduce_dim 9.294 0.527 9.838
process_cell_meta 9.533 0.164 9.711
spatial_hm 6.092 0.298 6.397
SpatialEnrichment 5.045 0.413 5.459
color_svg 4.942 0.222 5.169
* 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 ...
‘covisualize.Rmd’ using ‘UTF-8’... OK
‘spatialHeatmap.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.18-bioc/meat/spatialHeatmap.Rcheck/00check.log’
for details.
spatialHeatmap.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL spatialHeatmap ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.0/site-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 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (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 -- Tue Jun 6 07:36:53 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
36.844 0.939 37.849
spatialHeatmap.Rcheck/spatialHeatmap-Ex.timings
| name | user | system | elapsed | |
| Database | 1.331 | 0.016 | 1.352 | |
| SPHM | 23.287 | 0.507 | 23.830 | |
| SPHMMethods | 2.434 | 0.066 | 2.505 | |
| SVG | 0.749 | 0.135 | 0.879 | |
| SVGMethods | 0.475 | 0.093 | 0.566 | |
| SpatialEnrichment | 5.045 | 0.413 | 5.459 | |
| aSVG.remote.repo | 0.003 | 0.000 | 0.003 | |
| adj_mod | 3.364 | 0.503 | 3.863 | |
| aggr_rep | 1.223 | 0.060 | 1.286 | |
| cell_group | 15.161 | 0.491 | 15.676 | |
| cluster_cell | 1.965 | 0.072 | 2.040 | |
| coclus_opt | 0.315 | 0.004 | 0.323 | |
| cocluster | 0.249 | 0.016 | 0.268 | |
| color_svg | 4.942 | 0.222 | 5.169 | |
| com_factor | 0.223 | 0.012 | 0.236 | |
| covis | 21.443 | 0.481 | 21.954 | |
| custom_shiny | 0.016 | 0.008 | 0.024 | |
| cut_dendro | 0.882 | 0.004 | 0.884 | |
| cvt_id | 0.499 | 0.035 | 0.540 | |
| edit_tar | 0.002 | 0.004 | 0.005 | |
| filter_data | 1.333 | 0.036 | 1.372 | |
| matrix_hm | 3.133 | 0.104 | 3.243 | |
| network | 2.894 | 0.044 | 2.943 | |
| norm_cell | 2.771 | 0.040 | 2.817 | |
| norm_data | 1.240 | 0.016 | 1.259 | |
| norm_srsc | 2.503 | 0.080 | 2.589 | |
| opt_bar | 0.162 | 0.000 | 0.162 | |
| opt_setting | 0.007 | 0.004 | 0.010 | |
| opt_violin | 0.246 | 0.008 | 0.255 | |
| optimal_k | 0.181 | 0.008 | 0.189 | |
| plot_dim | 2.234 | 0.043 | 2.283 | |
| plot_kmeans | 0.888 | 0.016 | 0.905 | |
| plot_meta | 3.279 | 0.092 | 3.377 | |
| process_cell_meta | 9.533 | 0.164 | 9.711 | |
| qc_cell | 1.540 | 0.016 | 1.559 | |
| read_cache | 2.610 | 0.016 | 2.631 | |
| read_fr | 0.005 | 0.000 | 0.005 | |
| read_svg | 0.507 | 0.142 | 0.643 | |
| reduce_dim | 9.294 | 0.527 | 9.838 | |
| reduce_rep | 0.000 | 0.001 | 0.001 | |
| return_feature | 0.973 | 0.041 | 1.032 | |
| save_cache | 2.490 | 0.187 | 2.682 | |
| shiny_shm | 0 | 0 | 0 | |
| shm | 4.167 | 0.233 | 4.402 | |
| spatialHeatmap-package | 0 | 0 | 0 | |
| spatial_hm | 6.092 | 0.298 | 6.397 | |
| submatrix | 3.284 | 0.324 | 3.614 | |
| true_bulk | 0.434 | 0.016 | 0.451 | |
| update_feature | 0.002 | 0.000 | 0.002 | |