| Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:08 -0400 (Fri, 15 Oct 2021).
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To the developers/maintainers of the interactiveDisplay package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/interactiveDisplay.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 931/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| interactiveDisplay 1.30.0 (landing page) Shawn Balcome
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS |  | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: interactiveDisplay |
| Version: 1.30.0 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:interactiveDisplay.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings interactiveDisplay_1.30.0.tar.gz |
| StartedAt: 2021-10-15 00:47:46 -0400 (Fri, 15 Oct 2021) |
| EndedAt: 2021-10-15 00:52:04 -0400 (Fri, 15 Oct 2021) |
| EllapsedTime: 257.7 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: interactiveDisplay.Rcheck |
| Warnings: 1 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:interactiveDisplay.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings interactiveDisplay_1.30.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/interactiveDisplay.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'interactiveDisplay/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'interactiveDisplay' version '1.30.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'rstudio'
* 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 'interactiveDisplay' 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
* 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 ... WARNING
'::' or ':::' import not declared from: '.interactiveDisplayBase'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.altgr : <anonymous>: no visible global function definition for
'elementMetadata'
.altgr : <anonymous>: no visible global function definition for
'seqlevels<-'
.bicgo : <anonymous>: no visible binding for global variable 'GO.db'
.bicgo : <anonymous>: no visible global function definition for 'exprs'
.bicgo : <anonymous>: no visible global function definition for
'cutree'
.bicgo : <anonymous>: no visible global function definition for
'hclust'
.bicgo : <anonymous>: no visible global function definition for 'dist'
.bicgo : <anonymous>: no visible global function definition for 'cim'
.choose_gen: no visible global function definition for 'ucscGenomes'
.simplenet : <anonymous>: no visible global function definition for
'cutree'
.simplenet : <anonymous>: no visible global function definition for
'rainbow'
.simplenet : <anonymous> : hc: no visible global function definition
for 'hclust'
.simplenet : <anonymous> : hc: no visible global function definition
for 'dist'
.simplenet : <anonymous> : dm: no visible global function definition
for 'dist'
.usePackage: no visible global function definition for
'installed.packages'
ggheat: no visible global function definition for 'colorRampPalette'
ggheat: no visible binding for global variable 'Var2'
ggheat: no visible binding for global variable 'Var1'
ggheat: no visible binding for global variable 'value'
ggheat: no visible global function definition for 'coord_flip'
grid2jssvg: no visible global function definition for 'png'
grid2jssvg: no visible global function definition for 'dev.off'
subgr: no visible global function definition for 'seqnames'
subgr: no visible global function definition for 'seqlevels<-'
subgr: no visible global function definition for 'ranges'
subgr2: no visible global function definition for 'seqnames'
subgr2: no visible global function definition for 'seqlevels<-'
subgr2: no visible global function definition for 'ranges'
display,ExpressionSet : <anonymous>: no visible global function
definition for 'exprs'
display,ExpressionSet : <anonymous>: no visible global function
definition for 'experimentData'
display,ExpressionSet : <anonymous>: no visible binding for global
variable 'GO.db'
display,ExpressionSet : <anonymous>: no visible global function
definition for 'cutree'
display,ExpressionSet : <anonymous>: no visible global function
definition for 'rainbow'
display,ExpressionSet : <anonymous> : hc: no visible global function
definition for 'hclust'
display,ExpressionSet : <anonymous> : hc: no visible global function
definition for 'dist'
display,ExpressionSet : <anonymous> : dm: no visible global function
definition for 'dist'
display,ExpressionSet : <anonymous>: no visible global function
definition for 'as.dendrogram'
display,ExpressionSet : <anonymous> : <local> : <anonymous>: no visible
global function definition for 'is.leaf'
display,ExpressionSet : <anonymous>: no visible global function
definition for 'dendrapply'
display,GRanges: no visible global function definition for 'mcols'
display,GRanges : <anonymous>: no visible global function definition
for 'AnnotationTrack'
display,GRanges : <anonymous>: no visible global function definition
for 'GenomeAxisTrack'
display,GRanges : <anonymous>: no visible global function definition
for 'IdeogramTrack'
display,GRanges : <anonymous>: no visible global function definition
for 'plotTracks'
display,GRanges : <anonymous>: no visible global function definition
for 'layout_circle'
display,GRanges : <anonymous>: no visible binding for global variable
'seqnames'
display,GRanges : <anonymous>: no visible global function definition
for 'seqnames'
display,GRanges : <anonymous>: no visible global function definition
for 'ranges'
display,GRanges : <anonymous>: no visible global function definition
for 'ucscGenomes'
display,GRanges : <anonymous>: no visible global function definition
for 'GRanges'
display,GRanges : <anonymous>: no visible global function definition
for 'IRanges'
display,GRanges : <anonymous>: no visible global function definition
for 'seqlengths<-'
display,GRanges : <anonymous>: no visible global function definition
for 'seqlengths'
display,GRangesList : <anonymous>: no visible global function
definition for 'mcols'
display,GRangesList : <anonymous>: no visible global function
definition for 'AnnotationTrack'
display,GRangesList : <anonymous>: no visible global function
definition for 'GenomeAxisTrack'
display,GRangesList : <anonymous>: no visible global function
definition for 'IdeogramTrack'
display,GRangesList : <anonymous>: no visible global function
definition for 'plotTracks'
display,GRangesList : <anonymous>: no visible global function
definition for 'layout_circle'
display,GRangesList : <anonymous>: no visible binding for global
variable 'seqnames'
display,GRangesList : <anonymous>: no visible global function
definition for 'seqnames'
display,GRangesList : <anonymous>: no visible global function
definition for 'ranges'
display,GRangesList : <anonymous>: no visible global function
definition for 'ucscGenomes'
display,GRangesList : <anonymous>: no visible global function
definition for 'GRanges'
display,GRangesList : <anonymous>: no visible global function
definition for 'IRanges'
display,GRangesList : <anonymous>: no visible global function
definition for 'seqlengths<-'
display,GRangesList : <anonymous>: no visible global function
definition for 'seqlengths'
display,GRangesList : <anonymous>: no visible global function
definition for 'GRangesList'
display,MRexperiment : <anonymous>: no visible global function
definition for 'MRcounts'
display,MRexperiment : <anonymous>: no visible global function
definition for 'pData'
display,MRexperiment : <anonymous>: no visible global function
definition for 'colorRampPalette'
display,MRexperiment : <anonymous>: no visible global function
definition for 'legend'
display,MRexperiment : <anonymous>: no visible global function
definition for 'plotFeature'
display,MRexperiment : <anonymous>: no visible global function
definition for 'plotOrd'
display,MRexperiment : <anonymous>: no visible global function
definition for 'libSize'
display,MRexperiment : <anonymous>: no visible global function
definition for 'fData'
display,RangedSummarizedExperiment : <anonymous>: no visible global
function definition for 'seqnames'
display,RangedSummarizedExperiment : <anonymous>: no visible global
function definition for 'rowRanges'
display,RangedSummarizedExperiment : <anonymous>: no visible global
function definition for 'assays'
display,RangedSummarizedExperiment : <anonymous>: no visible global
function definition for 'colorRampPalette'
display,RangedSummarizedExperiment : <anonymous>: no visible binding
for global variable 'Var1'
display,RangedSummarizedExperiment : <anonymous>: no visible binding
for global variable 'Var2'
display,RangedSummarizedExperiment : <anonymous>: no visible binding
for global variable 'value'
Undefined global functions or variables:
AnnotationTrack GO.db GRanges GRangesList GenomeAxisTrack IRanges
IdeogramTrack MRcounts Var1 Var2 as.dendrogram assays cim
colorRampPalette coord_flip cutree dendrapply dev.off dist
elementMetadata experimentData exprs fData hclust installed.packages
is.leaf layout_circle legend libSize mcols pData plotFeature plotOrd
plotTracks png rainbow ranges rowRanges seqlengths seqlengths<-
seqlevels<- seqnames ucscGenomes value
Consider adding
importFrom("grDevices", "colorRampPalette", "dev.off", "png",
"rainbow")
importFrom("graphics", "legend")
importFrom("stats", "as.dendrogram", "cutree", "dendrapply", "dist",
"hclust", "is.leaf")
importFrom("utils", "installed.packages")
to your NAMESPACE file.
* 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
** running examples for arch 'x64' ... 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, 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.13-bioc/meat/interactiveDisplay.Rcheck/00check.log'
for details.
interactiveDisplay.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/interactiveDisplay_1.30.0.tar.gz && rm -rf interactiveDisplay.buildbin-libdir && mkdir interactiveDisplay.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=interactiveDisplay.buildbin-libdir interactiveDisplay_1.30.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL interactiveDisplay_1.30.0.zip && rm interactiveDisplay_1.30.0.tar.gz interactiveDisplay_1.30.0.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
20 3186k 20 666k 0 0 1822k 0 0:00:01 --:--:-- 0:00:01 1822k
42 3186k 42 1352k 0 0 1010k 0 0:00:03 0:00:01 0:00:02 1010k
100 3186k 100 3186k 0 0 1538k 0 0:00:02 0:00:02 --:--:-- 1539k
install for i386
* installing *source* package 'interactiveDisplay' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
in method for 'display' with signature 'object="GRanges"': no definition for class "GRanges"
in method for 'display' with signature 'object="GRangesList"': no definition for class "GRangesList"
in method for 'display' with signature 'object="RangedSummarizedExperiment"': no definition for class "RangedSummarizedExperiment"
in method for 'display' with signature 'object="MRexperiment"': no definition for class "MRexperiment"
** help
*** installing help indices
converting help for package 'interactiveDisplay'
finding HTML links ... done
altgr html
bicgo html
expr html
gridsvgjs html
gridtweak html
interactiveDisplay-methods html
mmgr html
mmgrl html
se html
simplenet 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
install for x64
* installing *source* package 'interactiveDisplay' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'interactiveDisplay' as interactiveDisplay_1.30.0.zip
* DONE (interactiveDisplay)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'interactiveDisplay' successfully unpacked and MD5 sums checked
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interactiveDisplay.Rcheck/examples_i386/interactiveDisplay-Ex.timings
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interactiveDisplay.Rcheck/examples_x64/interactiveDisplay-Ex.timings
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