Jianhai Zhang
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/spatialHeatmap |
| git_branch: master |
| git_last_commit: 32d285c |
| git_last_commit_date: 2021-10-26 13:03:26 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:08:45 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1855/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| spatialHeatmap 2.1.0 (landing page) Jianhai Zhang
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | 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: 2.1.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:spatialHeatmap.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings spatialHeatmap_2.1.0.tar.gz |
| StartedAt: 2022-03-17 20:21:45 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 20:26:47 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 301.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: spatialHeatmap.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:spatialHeatmap.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings spatialHeatmap_2.1.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/spatialHeatmap.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'spatialHeatmap/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'spatialHeatmap' version '2.1.0'
* 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 whether package 'spatialHeatmap' can be installed ... OK
* checking installed package size ... NOTE
installed size is 13.4Mb
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 13.63 1.69 15.31
spatial_hm 7.96 0.14 10.64
spatialHeatmap-package 7.65 0.27 10.28
* 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
'D:/biocbuild/bbs-3.15-bioc/meat/spatialHeatmap.Rcheck/00check.log'
for details.
spatialHeatmap.Rcheck/00install.out
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL spatialHeatmap
###
##############################################################################
##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'spatialHeatmap' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'spatialHeatmap'
finding HTML links ... done
aSVG.remote.repo html
adj_mod html
aggr_rep html
com_factor html
custom_shiny html
deg.table html
deg_ovl html
edit_tar html
filter_data html
lis.deg.up.down html
matrix_hm html
network html
norm_data html
profile_gene html
read_cache html
read_fr html
read_hdf5 html
return_feature html
save_cache html
shiny_shm html
spatialHeatmap-package html
spatial_enrich html
spatial_hm html
sub_data html
submatrix html
update_feature html
write_hdf5 html
** 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)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'TEKRABber' is missing or broken
done
spatialHeatmap.Rcheck/tests/runTests.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
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 -- Thu Mar 17 20:26:33 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
22.67 1.82 24.48
spatialHeatmap.Rcheck/spatialHeatmap-Ex.timings
| name | user | system | elapsed | |
| aSVG.remote.repo | 0 | 0 | 0 | |
| adj_mod | 1.42 | 0.09 | 1.52 | |
| aggr_rep | 0.20 | 0.01 | 0.22 | |
| com_factor | 0 | 0 | 0 | |
| custom_shiny | 0.02 | 0.00 | 0.02 | |
| deg.table | 0.01 | 0.00 | 0.01 | |
| deg_ovl | 1.21 | 0.08 | 1.28 | |
| edit_tar | 0.01 | 0.00 | 0.02 | |
| filter_data | 0.74 | 0.05 | 0.78 | |
| lis.deg.up.down | 0.00 | 0.02 | 0.02 | |
| matrix_hm | 0.98 | 0.09 | 1.07 | |
| network | 1.31 | 0.01 | 1.33 | |
| norm_data | 0.33 | 0.04 | 0.36 | |
| profile_gene | 0.15 | 0.00 | 0.15 | |
| read_cache | 1.41 | 0.04 | 1.47 | |
| read_fr | 0.01 | 0.00 | 0.02 | |
| read_hdf5 | 0 | 0 | 0 | |
| return_feature | 0.71 | 0.02 | 0.72 | |
| save_cache | 1.47 | 0.01 | 1.48 | |
| shiny_shm | 0 | 0 | 0 | |
| spatialHeatmap-package | 7.65 | 0.27 | 10.28 | |
| spatial_enrich | 3.67 | 0.05 | 4.33 | |
| spatial_hm | 7.96 | 0.14 | 10.64 | |
| sub_data | 0.44 | 0.03 | 0.47 | |
| submatrix | 0.53 | 0.03 | 0.56 | |
| update_feature | 0 | 0 | 0 | |
| write_hdf5 | 13.63 | 1.69 | 15.31 | |