David duVerle
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/cellTree |
| Branch: master |
| Last Commit: a60a308 |
| Last Changed Date: 2019-01-04 13:25:01 -0400 (Fri, 04 Jan 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 12:25:31 -0400 (Tue, 09 Apr 2019).
| Package 231/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| cellTree 1.13.1 David duVerle
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
| Package: cellTree |
| Version: 1.13.1 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:cellTree.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings cellTree_1.13.1.tar.gz |
| StartedAt: 2019-04-09 01:38:53 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 01:43:25 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 272.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: cellTree.Rcheck |
| Warnings: 1 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:cellTree.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings cellTree_1.13.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/cellTree.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* 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 '1.13.1'
* 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-3.9-bioc/tmpdir/RtmpoVjB7Z/R.INSTALL128c6a9630d5/cellTree/man/cell.ordering.table.Rd:10: file link 'igraph' in package 'igraph' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpoVjB7Z/R.INSTALL128c6a9630d5/cellTree/man/compute.backbone.tree.Rd:34: file link 'igraph' in package 'igraph' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpoVjB7Z/R.INSTALL128c6a9630d5/cellTree/man/compute.go.enrichment.Rd:30: file link 'igraph' in package 'igraph' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpoVjB7Z/R.INSTALL128c6a9630d5/cellTree/man/compute.lda.Rd:25: file link 'LDA-class' in package 'topicmodels' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpoVjB7Z/R.INSTALL128c6a9630d5/cellTree/man/compute.lda.Rd:69: file link 'LDA' in package 'topicmodels' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpoVjB7Z/R.INSTALL128c6a9630d5/cellTree/man/compute.lda.Rd:69: file link 'LDA_Gibbscontrol-class' in package 'topicmodels' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpoVjB7Z/R.INSTALL128c6a9630d5/cellTree/man/compute.lda.Rd:69: file link 'CTM_VEMcontrol-class' in package 'topicmodels' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpoVjB7Z/R.INSTALL128c6a9630d5/cellTree/man/ct.plot.go.dag.Rd:27: file link 'igraph' in package 'igraph' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpoVjB7Z/R.INSTALL128c6a9630d5/cellTree/man/ct.plot.grouping.Rd:12: file link 'igraph' in package 'igraph' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpoVjB7Z/R.INSTALL128c6a9630d5/cellTree/man/ct.plot.grouping.Rd:31: file link 'igraph' in package 'igraph' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpoVjB7Z/R.INSTALL128c6a9630d5/cellTree/man/ct.plot.topics.Rd:12: file link 'igraph' in package 'igraph' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpoVjB7Z/R.INSTALL128c6a9630d5/cellTree/man/ct.plot.topics.Rd:27: file link 'igraph' in package 'igraph' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.9-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
* 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 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
compute.lda 36.15 8.16 44.38
ct.plot.heatmap 21.95 0.42 22.43
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
compute.lda 36.37 9.03 45.61
ct.plot.heatmap 24.51 0.28 25.77
* 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-3.9-bioc/meat/cellTree.Rcheck/00check.log'
for details.
cellTree.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/cellTree_1.13.1.tar.gz && rm -rf cellTree.buildbin-libdir && mkdir cellTree.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=cellTree.buildbin-libdir cellTree_1.13.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL cellTree_1.13.1.zip && rm cellTree_1.13.1.tar.gz cellTree_1.13.1.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 499k 100 499k 0 0 3222k 0 --:--:-- --:--:-- --:--:-- 3375k
install for i386
* installing *source* package 'cellTree' ...
** 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
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpoVjB7Z/R.INSTALL128c6a9630d5/cellTree/man/cell.ordering.table.Rd:10: file link 'igraph' in package 'igraph' does not exist and so has been treated as a topic
cellTree-package html
compute.backbone.tree html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpoVjB7Z/R.INSTALL128c6a9630d5/cellTree/man/compute.backbone.tree.Rd:34: file link 'igraph' in package 'igraph' does not exist and so has been treated as a topic
compute.go.enrichment html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpoVjB7Z/R.INSTALL128c6a9630d5/cellTree/man/compute.go.enrichment.Rd:30: file link 'igraph' in package 'igraph' does not exist and so has been treated as a topic
compute.lda html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpoVjB7Z/R.INSTALL128c6a9630d5/cellTree/man/compute.lda.Rd:25: file link 'LDA-class' in package 'topicmodels' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpoVjB7Z/R.INSTALL128c6a9630d5/cellTree/man/compute.lda.Rd:69: file link 'LDA' in package 'topicmodels' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpoVjB7Z/R.INSTALL128c6a9630d5/cellTree/man/compute.lda.Rd:69: file link 'LDA_Gibbscontrol-class' in package 'topicmodels' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpoVjB7Z/R.INSTALL128c6a9630d5/cellTree/man/compute.lda.Rd:69: file link 'CTM_VEMcontrol-class' in package 'topicmodels' does not exist and so has been treated as a topic
ct.plot.go.dag html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpoVjB7Z/R.INSTALL128c6a9630d5/cellTree/man/ct.plot.go.dag.Rd:27: file link 'igraph' in package 'igraph' does not exist and so has been treated as a topic
ct.plot.grouping html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpoVjB7Z/R.INSTALL128c6a9630d5/cellTree/man/ct.plot.grouping.Rd:12: file link 'igraph' in package 'igraph' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpoVjB7Z/R.INSTALL128c6a9630d5/cellTree/man/ct.plot.grouping.Rd:31: file link 'igraph' in package 'igraph' does not exist and so has been treated as a topic
ct.plot.heatmap html
ct.plot.topics html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpoVjB7Z/R.INSTALL128c6a9630d5/cellTree/man/ct.plot.topics.Rd:12: file link 'igraph' in package 'igraph' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpoVjB7Z/R.INSTALL128c6a9630d5/cellTree/man/ct.plot.topics.Rd:27: file link 'igraph' in package 'igraph' does not exist and so has been treated as a topic
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
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_1.13.1.zip
* DONE (cellTree)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'cellTree' successfully unpacked and MD5 sums checked
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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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