David duVerle
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/cellTree |
| Branch: RELEASE_3_6 |
| Last Commit: 3f63d25 |
| Last Changed Date: 2017-10-30 12:41:12 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:27:20 -0400 (Thu, 12 Apr 2018).
| Package 198/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| cellTree 1.8.0 David duVerle
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ WARNINGS ] | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
| Package: cellTree |
| Version: 1.8.0 |
| Command: rm -rf cellTree.buildbin-libdir cellTree.Rcheck && mkdir cellTree.buildbin-libdir cellTree.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=cellTree.buildbin-libdir cellTree_1.8.0.tar.gz >cellTree.Rcheck\00install.out 2>&1 && cp cellTree.Rcheck\00install.out cellTree-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=cellTree.buildbin-libdir --install="check:cellTree-install.out" --force-multiarch --no-vignettes --timings cellTree_1.8.0.tar.gz |
| StartedAt: 2018-04-11 22:47:07 -0400 (Wed, 11 Apr 2018) |
| EndedAt: 2018-04-11 22:52:59 -0400 (Wed, 11 Apr 2018) |
| EllapsedTime: 351.7 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: cellTree.Rcheck |
| Warnings: 1 |
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### Running command:
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### rm -rf cellTree.buildbin-libdir cellTree.Rcheck && mkdir cellTree.buildbin-libdir cellTree.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=cellTree.buildbin-libdir cellTree_1.8.0.tar.gz >cellTree.Rcheck\00install.out 2>&1 && cp cellTree.Rcheck\00install.out cellTree-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=cellTree.buildbin-libdir --install="check:cellTree-install.out" --force-multiarch --no-vignettes --timings cellTree_1.8.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/cellTree.Rcheck'
* using R version 3.4.4 (2018-03-15)
* 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 '1.8.0'
* 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 ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyWtAvh/R.INSTALL25641945e0/cellTree/man/cell.ordering.table.Rd:10: missing file link 'igraph'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyWtAvh/R.INSTALL25641945e0/cellTree/man/compute.backbone.tree.Rd:34: missing file link 'igraph'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyWtAvh/R.INSTALL25641945e0/cellTree/man/compute.go.enrichment.Rd:30: missing file link 'igraph'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyWtAvh/R.INSTALL25641945e0/cellTree/man/compute.lda.Rd:25: missing file link 'LDA-class'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyWtAvh/R.INSTALL25641945e0/cellTree/man/compute.lda.Rd:69: missing file link 'LDA'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyWtAvh/R.INSTALL25641945e0/cellTree/man/compute.lda.Rd:69: missing file link 'LDA_Gibbscontrol-class'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyWtAvh/R.INSTALL25641945e0/cellTree/man/compute.lda.Rd:69: missing file link 'CTM_VEMcontrol-class'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyWtAvh/R.INSTALL25641945e0/cellTree/man/ct.plot.go.dag.Rd:27: missing file link 'igraph'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyWtAvh/R.INSTALL25641945e0/cellTree/man/ct.plot.grouping.Rd:12: missing file link 'igraph'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyWtAvh/R.INSTALL25641945e0/cellTree/man/ct.plot.grouping.Rd:31: missing file link 'igraph'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyWtAvh/R.INSTALL25641945e0/cellTree/man/ct.plot.topics.Rd:12: missing file link 'igraph'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyWtAvh/R.INSTALL25641945e0/cellTree/man/ct.plot.topics.Rd:27: missing file link 'igraph'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/cellTree.Rcheck/00install.out' for details.
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... 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 'plot'
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 plot 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", "plot")
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 data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
compute.lda 44.45 7.56 55.39
ct.plot.heatmap 25.49 0.28 25.78
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
compute.lda 43.35 9.05 52.55
ct.plot.heatmap 17.66 0.38 18.22
* 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, 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.6-bioc/meat/cellTree.Rcheck/00check.log'
for details.
cellTree.Rcheck/00install.out
install for i386
* installing *source* package 'cellTree' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing 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
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyWtAvh/R.INSTALL25641945e0/cellTree/man/cell.ordering.table.Rd:10: missing file link 'igraph'
cellTree-package html
compute.backbone.tree html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyWtAvh/R.INSTALL25641945e0/cellTree/man/compute.backbone.tree.Rd:34: missing file link 'igraph'
compute.go.enrichment html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyWtAvh/R.INSTALL25641945e0/cellTree/man/compute.go.enrichment.Rd:30: missing file link 'igraph'
compute.lda html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyWtAvh/R.INSTALL25641945e0/cellTree/man/compute.lda.Rd:25: missing file link 'LDA-class'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyWtAvh/R.INSTALL25641945e0/cellTree/man/compute.lda.Rd:69: missing file link 'LDA'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyWtAvh/R.INSTALL25641945e0/cellTree/man/compute.lda.Rd:69: missing file link 'LDA_Gibbscontrol-class'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyWtAvh/R.INSTALL25641945e0/cellTree/man/compute.lda.Rd:69: missing file link 'CTM_VEMcontrol-class'
ct.plot.go.dag html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyWtAvh/R.INSTALL25641945e0/cellTree/man/ct.plot.go.dag.Rd:27: missing file link 'igraph'
ct.plot.grouping html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyWtAvh/R.INSTALL25641945e0/cellTree/man/ct.plot.grouping.Rd:12: missing file link 'igraph'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyWtAvh/R.INSTALL25641945e0/cellTree/man/ct.plot.grouping.Rd:31: missing file link 'igraph'
ct.plot.heatmap html
ct.plot.topics html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyWtAvh/R.INSTALL25641945e0/cellTree/man/ct.plot.topics.Rd:12: missing file link 'igraph'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyWtAvh/R.INSTALL25641945e0/cellTree/man/ct.plot.topics.Rd:27: missing file link 'igraph'
get.cell.dists html
go.results.to.latex html
** building package indices
** installing vignettes
** testing if installed package can be loaded
groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built.
In R CMD INSTALL
install for x64
* installing *source* package 'cellTree' ...
** testing if installed package can be loaded
groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built.
* MD5 sums
packaged installation of 'cellTree' as cellTree_1.8.0.zip
* DONE (cellTree)
In R CMD INSTALL
In R CMD INSTALL
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cellTree.Rcheck/examples_i386/cellTree-Ex.timings
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cellTree.Rcheck/examples_x64/cellTree-Ex.timings
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