Xiaoyuan Zhou
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/eegc |
| Branch: RELEASE_3_11 |
| Last Commit: fdd5e15 |
| Last Changed Date: 2020-04-27 15:01:05 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:56:30 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE eegc PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 530/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| eegc 1.14.0 Xiaoyuan Zhou
| malbec2 | Linux (Ubuntu 18.04.4 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: eegc |
| Version: 1.14.0 |
| Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:eegc.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings eegc_1.14.0.tar.gz |
| StartedAt: 2020-10-17 03:39:10 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 03:55:58 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 1007.9 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: eegc.Rcheck |
| Warnings: 2 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:eegc.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings eegc_1.14.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/eegc.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'eegc/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'eegc' version '1.14.0'
* 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 'eegc' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpKWBNzg/R.INSTALL25c86b475861/eegc/man/barplotEnrich.Rd:29: missing file link 'barplot.enrichResult'
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpKWBNzg/R.INSTALL25c86b475861/eegc/man/densityPlot.Rd:29: file link 'plot' in package 'graphics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpKWBNzg/R.INSTALL25c86b475861/eegc/man/dotPercentage.Rd:32: file link 'plot' in package 'graphics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpKWBNzg/R.INSTALL25c86b475861/eegc/man/functionEnrich.Rd:17: file link 'org.Hs.eg.db' in package 'org.Hs.eg.db' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpKWBNzg/R.INSTALL25c86b475861/eegc/man/grnPlot.Rd:33: file link 'igraph.plotting' in package 'igraph' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpKWBNzg/R.INSTALL25c86b475861/eegc/man/grnPlot.Rd:36: file link 'igraph.plotting' in package 'igraph' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpKWBNzg/R.INSTALL25c86b475861/eegc/man/grnPlot.Rd:38: file link 'layout' in package 'igraph' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpKWBNzg/R.INSTALL25c86b475861/eegc/man/grnPlot.Rd:42: file link 'igraph.plotting' in package 'igraph' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpKWBNzg/R.INSTALL25c86b475861/eegc/man/markerScatter.Rd:30: file link 'plot' in package 'graphics' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.11-bioc/meat/eegc.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
installed size is 11.2Mb
sub-directories of 1Mb or more:
data 10.5Mb
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
categorizeGene : <anonymous>: no visible global function definition for
'quantile'
densityPlot: no visible binding for global variable 'density'
densityPlot: no visible global function definition for 'lines'
densityPlot: no visible global function definition for 'axis'
densityPlot: no visible global function definition for 'adjustcolor'
densityPlot: no visible global function definition for 'legend'
densityPlot : <anonymous>: no visible global function definition for
'quantile'
densityPlot: no visible global function definition for 'text'
densityPlot: no visible global function definition for 'dev.copy2pdf'
diffGene: no visible global function definition for 'model.matrix'
diffGene: no visible binding for global variable 'treat'
diffGene: no visible binding for global variable 'control'
diffGene: no visible global function definition for 'results'
diffGene: no visible global function definition for 'p.adjust'
dotPercentage: no visible global function definition for 'lines'
dotPercentage: no visible global function definition for 'axis'
dotPercentage: no visible global function definition for 'text'
dotPercentage: no visible global function definition for 'par'
enrichment : enrichment : <anonymous>: no visible global function
definition for 'phyper'
enrichment : enrichment: no visible global function definition for
'p.adjust'
grnPlot: no visible global function definition for 'title'
grnPlot: no visible global function definition for 'legend'
markerScatter: no visible global function definition for
'colorRampPalette'
markerScatter: no visible global function definition for 'points'
markerScatter: no visible global function definition for 'lm'
markerScatter: no visible global function definition for 'abline'
markerScatter: no visible global function definition for 'text'
markerScatter: no visible global function definition for 'legend'
Undefined global functions or variables:
abline adjustcolor axis colorRampPalette control density dev.copy2pdf
legend lines lm model.matrix p.adjust par phyper points quantile
results text title treat
Consider adding
importFrom("grDevices", "adjustcolor", "colorRampPalette",
"dev.copy2pdf")
importFrom("graphics", "abline", "axis", "legend", "lines", "par",
"points", "text", "title")
importFrom("stats", "density", "lm", "model.matrix", "p.adjust",
"phyper", "quantile")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'barplotEnrich.Rd':
'[DOSE]{barplot.enrichResult}'
See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 (user + system) or elapsed time > 5s
user system elapsed
functionEnrich 279.06 11.52 312.44
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
functionEnrich 220.61 4.04 281.98
heatmapPlot 0.35 0.00 15.81
* checking for unstated dependencies in vignettes ... NOTE
'::' or ':::' import not declared from: 'BiocStyle'
* 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 WARNINGs, 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.11-bioc/meat/eegc.Rcheck/00check.log'
for details.
eegc.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/eegc_1.14.0.tar.gz && rm -rf eegc.buildbin-libdir && mkdir eegc.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=eegc.buildbin-libdir eegc_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL eegc_1.14.0.zip && rm eegc_1.14.0.tar.gz eegc_1.14.0.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
0 9085k 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 9085k 100 9085k 0 0 39.2M 0 --:--:-- --:--:-- --:--:-- 40.1M
install for i386
* installing *source* package 'eegc' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'eegc'
finding HTML links ... done
SandlerFPKM html
barplotEnrich html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpKWBNzg/R.INSTALL25c86b475861/eegc/man/barplotEnrich.Rd:29: missing file link 'barplot.enrichResult'
cate.gene html
cate.ratio html
categorizeGene html
densityPlot html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpKWBNzg/R.INSTALL25c86b475861/eegc/man/densityPlot.Rd:29: file link 'plot' in package 'graphics' does not exist and so has been treated as a topic
diffGene html
diffgene.genes html
dotPercentage html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpKWBNzg/R.INSTALL25c86b475861/eegc/man/dotPercentage.Rd:32: file link 'plot' in package 'graphics' does not exist and so has been treated as a topic
eegc html
enrichment html
expr.filter html
functionEnrich html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpKWBNzg/R.INSTALL25c86b475861/eegc/man/functionEnrich.Rd:17: file link 'org.Hs.eg.db' in package 'org.Hs.eg.db' does not exist and so has been treated as a topic
goenrich html
grnPlot html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpKWBNzg/R.INSTALL25c86b475861/eegc/man/grnPlot.Rd:33: file link 'igraph.plotting' in package 'igraph' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpKWBNzg/R.INSTALL25c86b475861/eegc/man/grnPlot.Rd:36: file link 'igraph.plotting' in package 'igraph' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpKWBNzg/R.INSTALL25c86b475861/eegc/man/grnPlot.Rd:38: file link 'layout' in package 'igraph' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpKWBNzg/R.INSTALL25c86b475861/eegc/man/grnPlot.Rd:42: file link 'igraph.plotting' in package 'igraph' does not exist and so has been treated as a topic
heatmapPlot html
human.gene html
human.grn html
human.tf html
markerScatter html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpKWBNzg/R.INSTALL25c86b475861/eegc/man/markerScatter.Rd:30: file link 'plot' in package 'graphics' does not exist and so has been treated as a topic
markers html
mouse.gene html
mouse.grn html
mouse.tf html
networkAnalyze html
tissueGenes html
tissueGroup html
** building package indices
** installing vignettes
'eegc.Rnw'
** 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 'eegc' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'eegc' as eegc_1.14.0.zip
* DONE (eegc)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'eegc' successfully unpacked and MD5 sums checked
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eegc.Rcheck/examples_i386/eegc-Ex.timings
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eegc.Rcheck/examples_x64/eegc-Ex.timings
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