| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:07:09 -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 cellTree package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/cellTree.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 274/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| cellTree 1.25.0 (landing page) David duVerle
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | ERROR | skipped | skipped | |||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | ERROR | skipped | skipped | |||||||||
| Package: cellTree |
| Version: 1.25.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:cellTree.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings cellTree_1.25.0.tar.gz |
| StartedAt: 2022-03-17 18:41:19 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 19:09:37 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 1698.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: cellTree.Rcheck |
| Warnings: 0 |
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### Running command:
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### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:cellTree.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings cellTree_1.25.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/cellTree.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 'cellTree/DESCRIPTION' ... OK
* this is package 'cellTree' version '1.25.0'
* 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 'cellTree' 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 ... NOTE
Package in Depends field not imported from: 'topGO'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.format.grouping: no visible global function definition for
'colorRampPalette'
.format.grouping: no visible global function definition for 'rainbow'
.merge.backbone.node.to: no visible global function definition for
'nei'
.merge.backbone.node.to: no visible global function definition for
'inc'
.mixrgb : <anonymous>: no visible global function definition for
'col2rgb'
.mixrgb: no visible global function definition for 'rgb'
.normalise.data: no visible binding for global variable 'sd'
.plot.b.tree: no visible global function definition for 'pdf'
.plot.b.tree: no visible global function definition for 'par'
.plot.b.tree: no visible global function definition for 'dev.size'
.plot.b.tree: no visible global function definition for 'legend'
.plot.b.tree: no visible global function definition for 'rainbow'
.plot.b.tree: no visible global function definition for 'dev.off'
.recur.merge.backbone: no visible global function definition for 'nei'
.recur.merge.backbone: no visible global function definition for 'inc'
.recur.ordered.branches: no visible global function definition for
'nei'
.recur.shorten.backbone: no visible global function definition for
'nei'
.recur.shorten.backbone: no visible global function definition for 'to'
.recur.tree.layout: no visible global function definition for 'nei'
cell.ordering.table: no visible global function definition for
'rainbow'
cell.ordering.table: no visible global function definition for
'toLatex'
compute.backbone.tree: no visible global function definition for 'nei'
compute.backbone.tree: no visible global function definition for 'from'
compute.backbone.tree: no visible global function definition for
'density'
compute.go.enrichment: no visible global function definition for 'new'
compute.go.enrichment: no visible global function definition for
'score'
compute.go.enrichment: no visible global function definition for
'getFromNamespace'
compute.go.enrichment: no visible global function definition for
'ontology'
ct.plot.go.dag: no visible global function definition for 'rainbow'
ct.plot.go.dag: no visible global function definition for 'pdf'
ct.plot.go.dag : <anonymous>: no visible global function definition for
'col2rgb'
ct.plot.go.dag: no visible global function definition for 'nei'
ct.plot.go.dag: no visible global function definition for 'par'
ct.plot.go.dag: no visible global function definition for 'legend'
ct.plot.go.dag: no visible global function definition for 'dev.off'
ct.plot.heatmap: no visible global function definition for
'colorRampPalette'
ct.plot.heatmap: no visible global function definition for 'dev.new'
ct.plot.heatmap: no visible binding for global variable
'gene.reordering'
go.results.to.latex: no visible global function definition for
'rainbow'
go.results.to.latex: no visible global function definition for
'toLatex'
order.genes.by.fit : <anonymous>: no visible global function definition
for 'rnorm'
order.genes.by.fit : <anonymous>: no visible global function definition
for 'lm'
save.per.topic.gene.distribution : <anonymous>: no visible global
function definition for 'pdf'
save.per.topic.gene.distribution : <anonymous>: no visible global
function definition for 'barplot'
save.per.topic.gene.distribution : <anonymous>: no visible global
function definition for 'dev.off'
save.per.topic.gene.distribution : <anonymous>: no visible global
function definition for 'write.table'
Undefined global functions or variables:
barplot col2rgb colorRampPalette density dev.new dev.off dev.size
from gene.reordering getFromNamespace inc legend lm nei new ontology
par pdf rainbow rgb rnorm score sd to toLatex write.table
Consider adding
importFrom("grDevices", "col2rgb", "colorRampPalette", "dev.new",
"dev.off", "dev.size", "pdf", "rainbow", "rgb")
importFrom("graphics", "barplot", "legend", "par")
importFrom("methods", "new")
importFrom("stats", "density", "lm", "rnorm", "sd")
importFrom("utils", "getFromNamespace", "toLatex", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 LazyData ... 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
compute.lda 814.72 758.38 1576.67
ct.plot.heatmap 19.69 0.69 20.38
* 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
'D:/biocbuild/bbs-3.15-bioc/meat/cellTree.Rcheck/00check.log'
for details.
cellTree.Rcheck/00install.out
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### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL cellTree
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'cellTree' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built.
** help
*** installing help indices
converting help for package 'cellTree'
finding HTML links ... done
HSMM_lda_model html
cell.ordering.table html
cellTree-package html
compute.backbone.tree html
compute.go.enrichment html
compute.lda html
ct.plot.go.dag html
ct.plot.grouping html
ct.plot.heatmap html
ct.plot.topics html
get.cell.dists html
go.results.to.latex html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built.
** testing if installed package can be loaded from final location
groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built.
** testing if installed package keeps a record of temporary installation path
* DONE (cellTree)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'PAIRADISE' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'universalmotif' is missing or broken
done
cellTree.Rcheck/cellTree-Ex.timings
| name | user | system | elapsed | |
| cell.ordering.table | 0.59 | 0.08 | 0.67 | |
| compute.backbone.tree | 0.66 | 0.02 | 0.69 | |
| compute.go.enrichment | 0.00 | 0.01 | 0.02 | |
| compute.lda | 814.72 | 758.38 | 1576.67 | |
| ct.plot.go.dag | 0.17 | 0.00 | 0.17 | |
| ct.plot.grouping | 0.92 | 0.20 | 1.12 | |
| ct.plot.heatmap | 19.69 | 0.69 | 20.38 | |
| ct.plot.topics | 1.25 | 0.12 | 1.37 | |
| get.cell.dists | 0.31 | 0.02 | 0.33 | |
| go.results.to.latex | 0.01 | 0.00 | 0.02 | |