Yingxin Lin
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/CiteFuse |
| git_branch: master |
| git_last_commit: 8820225 |
| git_last_commit_date: 2022-02-21 20:07:51 -0400 (Mon, 21 Feb 2022) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:07:11 -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 CiteFuse package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CiteFuse.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 321/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CiteFuse 1.7.0 (landing page) Yingxin Lin
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: CiteFuse |
| Version: 1.7.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CiteFuse.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings CiteFuse_1.7.0.tar.gz |
| StartedAt: 2022-03-17 18:43:55 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 18:47:38 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 222.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: CiteFuse.Rcheck |
| Warnings: 1 |
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CiteFuse.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings CiteFuse_1.7.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/CiteFuse.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 'CiteFuse/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CiteFuse' version '1.7.0'
* 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 'CiteFuse' can be installed ... OK
* checking installed package size ... OK
* 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 ... WARNING
Codoc mismatches from documentation object 'igraphClustering':
igraphClustering
Code: function(sce, metadata = "SNF_W", method = c("louvain",
"leiden", "walktrap", "spinglass", "optimal",
"leading_eigen", "label_prop", "fast_greedy",
"edge_betweenness"), ...)
Docs: function(sce, metadata = "SNF_W", method = c("louvain",
"walktrap", "spinglass", "optimal", "leading_eigen",
"label_prop", "fast_greedy", "edge_betweenness"), ...)
Mismatches in argument default values:
Name: 'method'
Code: c("louvain", "leiden", "walktrap", "spinglass", "optimal", "leading_eigen",
"label_prop", "fast_greedy", "edge_betweenness")
Docs: c("louvain", "walktrap", "spinglass", "optimal", "leading_eigen",
"label_prop", "fast_greedy", "edge_betweenness")
* 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
* 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 WARNING
See
'D:/biocbuild/bbs-3.15-bioc/meat/CiteFuse.Rcheck/00check.log'
for details.
CiteFuse.Rcheck/00install.out
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL CiteFuse
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'CiteFuse' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'CiteFuse'
finding HTML links ... done
CITEseq_example html
CiteFuse html
DEbubblePlot html
DEcomparisonPlot html
DEgenes html
DEgenesCross html
crossSampleDoublets html
geneADTnetwork html
igraphClustering html
importanceADT html
ligandReceptorTest html
lr_pair_subset html
normaliseExprs html
plotHTO html
plotHTOSingle html
preprocessing html
readFrom10X html
reducedDimSNF html
sce_control_subset html
sce_ctcl_subset html
selectDEgenes html
spectralClustering html
visImportance html
visLigandReceptor html
visualiseDim html
visualiseExprs html
visualiseExprsList html
visualiseKNN html
withinSampleDoublets 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 (CiteFuse)
Making 'packages.html' ... done
CiteFuse.Rcheck/CiteFuse-Ex.timings
| name | user | system | elapsed | |
| CiteFuse | 1.89 | 0.09 | 1.99 | |
| DEbubblePlot | 2.86 | 0.17 | 3.03 | |
| DEcomparisonPlot | 2.40 | 0.08 | 2.49 | |
| DEgenes | 1.22 | 0.02 | 1.23 | |
| DEgenesCross | 4.10 | 0.04 | 4.14 | |
| crossSampleDoublets | 0.86 | 0.07 | 0.93 | |
| geneADTnetwork | 0.90 | 0.01 | 0.92 | |
| igraphClustering | 0.60 | 0.02 | 0.61 | |
| importanceADT | 0.93 | 0.04 | 0.98 | |
| ligandReceptorTest | 1.36 | 0.10 | 1.45 | |
| normaliseExprs | 0.61 | 0.00 | 0.61 | |
| plotHTO | 2.31 | 0.08 | 2.39 | |
| preprocessing | 0.46 | 0.00 | 0.46 | |
| readFrom10X | 0 | 0 | 0 | |
| reducedDimSNF | 0.86 | 0.04 | 0.90 | |
| selectDEgenes | 1.15 | 0.02 | 1.18 | |
| spectralClustering | 0.52 | 0.00 | 0.51 | |
| visImportance | 1.39 | 0.01 | 1.41 | |
| visLigandReceptor | 0.92 | 0.05 | 0.97 | |
| visualiseDim | 1.52 | 0.02 | 1.53 | |
| visualiseExprs | 1.12 | 0.01 | 1.14 | |
| visualiseExprsList | 0.75 | 0.05 | 0.80 | |
| visualiseKNN | 0.60 | 0.00 | 0.59 | |
| withinSampleDoublets | 0.82 | 0.00 | 0.83 | |