Lei Huang
| Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020) |
| URL: https://git.bioconductor.org/packages/GeneAnswers |
| Branch: master |
| Last Commit: 8c1aa26 |
| Last Changed Date: 2019-12-23 18:27:52 -0500 (Mon, 23 Dec 2019) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-01-16 13:32:13 -0500 (Thu, 16 Jan 2020).
| Package 646/1818 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| GeneAnswers 2.29.0 Lei Huang
| malbec2 | Linux (Ubuntu 18.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK | |
| Package: GeneAnswers |
| Version: 2.29.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GeneAnswers.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GeneAnswers_2.29.0.tar.gz |
| StartedAt: 2020-01-16 04:43:14 -0500 (Thu, 16 Jan 2020) |
| EndedAt: 2020-01-16 05:00:26 -0500 (Thu, 16 Jan 2020) |
| EllapsedTime: 1032.2 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: GeneAnswers.Rcheck |
| Warnings: 1 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GeneAnswers.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GeneAnswers_2.29.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/GeneAnswers.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GeneAnswers/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GeneAnswers’ version ‘2.29.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'igraph', 'RCurl', 'annotate', 'Biobase', 'XML', 'RSQLite', 'MASS',
'Heatplus', 'RColorBrewer'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘GeneAnswers’ can be installed ... WARNING
Found the following significant warnings:
Warning: replacing previous import ‘stats::decompose’ by ‘igraph::decompose’ when loading ‘GeneAnswers’
Warning: replacing previous import ‘stats::spectrum’ by ‘igraph::spectrum’ when loading ‘GeneAnswers’
See ‘/Users/biocbuild/bbs-3.11-bioc/meat/GeneAnswers.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
installed size is 34.2Mb
sub-directories of 1Mb or more:
External 32.4Mb
data 1.0Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘annotate’
A package should be listed in only one of these fields.
* 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
'library' or 'require' calls to packages already attached by Depends:
‘Biobase’ ‘Heatplus’ ‘MASS’ ‘RColorBrewer’ ‘XML’ ‘igraph’
Please remove these calls from your code.
'library' or 'require' calls in package code:
‘GO.db’ ‘KEGG.db’ ‘biomaRt’ ‘reactome.db’
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
File ‘GeneAnswers/R/zzz.R’:
.onLoad calls:
require(Biobase)
Package startup functions should not change the search path.
See section ‘Good practice’ in '?.onAttach'.
.catsCluster: no visible global function definition for ‘par’
.catsCluster: no visible global function definition for ‘plot’
.defaultHeatmapColors: no visible global function definition for ‘rgb’
.drawHTMLtable: no visible global function definition for
‘colorRampPalette’
.drawTable: no visible global function definition for ‘par’
.drawTable: no visible global function definition for ‘image’
.drawTable: no visible global function definition for ‘abline’
.drawTable: no visible global function definition for ‘axis’
.drawTable: no visible global function definition for ‘points’
.heatmap.mds: no visible global function definition for
‘colorRampPalette’
.heatmap.mds: no visible global function definition for ‘layout’
.heatmap.mds: no visible global function definition for ‘par’
.heatmap.mds: no visible global function definition for ‘image’
.heatmap.mds: no visible global function definition for ‘axis’
.heatmap.mds: no visible global function definition for ‘box’
buildNet: no visible global function definition for ‘colorRampPalette’
buildNet: no visible global function definition for ‘plot’
chartPlots: no visible global function definition for ‘x11’
chartPlots: no visible global function definition for ‘pie’
chartPlots: no visible global function definition for ‘rainbow’
chartPlots: no visible global function definition for ‘barplot’
drawTable: no visible global function definition for ‘colorRampPalette’
drawTable: no visible global function definition for ‘x11’
drawTable: no visible global function definition for ‘par’
drawTable: no visible global function definition for ‘image’
drawTable: no visible global function definition for ‘abline’
drawTable: no visible global function definition for ‘axis’
drawTable: no visible global function definition for ‘text’
drawTable: no visible global function definition for ‘box’
drawTable: no visible global function definition for ‘dev.set’
drawTable: no visible global function definition for ‘dev.prev’
geneAnnotationHeatmap: no visible global function definition for
‘colorRampPalette’
geneAnnotationHeatmap: no visible global function definition for
‘layout’
geneConceptNet: no visible global function definition for
‘colorRampPalette’
getHomoGeneIDs: no visible global function definition for ‘useMart’
getHomoGeneIDs: no visible global function definition for ‘getLDS’
getTotalGeneNumber: no visible global function definition for
‘count.mappedkeys’
getTotalGeneNumber: no visible global function definition for ‘toTable’
getTotalGeneNumber: no visible binding for global variable
‘reactomePATHNAME2ID’
groupReport: no visible global function definition for ‘png’
groupReport: no visible global function definition for ‘dev.off’
groupReport: no visible global function definition for ‘rgb’
groupReport: no visible global function definition for ‘col2rgb’
Undefined global functions or variables:
abline axis barplot box col2rgb colorRampPalette count.mappedkeys
dev.off dev.prev dev.set getLDS image layout par pie plot png points
rainbow reactomePATHNAME2ID rgb text toTable useMart x11
Consider adding
importFrom("grDevices", "col2rgb", "colorRampPalette", "dev.off",
"dev.prev", "dev.set", "png", "rainbow", "rgb", "x11")
importFrom("graphics", "abline", "axis", "barplot", "box", "image",
"layout", "par", "pie", "plot", "points", "text")
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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
geneAnswersReadable 97.017 8.950 106.152
GeneAnswers-class 50.114 5.557 55.985
geneAnswersHeatmap 50.612 3.935 55.090
geneAnswersConceptRelation 50.440 3.851 54.303
geneAnswersChartPlots 49.195 5.002 54.198
geneAnswersConceptNet 49.785 4.023 53.811
getMultiLayerGraphIDs 50.283 2.988 53.619
geneAnswersConcepts 48.290 4.699 53.032
geneAnswersHomoMapping 48.678 4.109 53.208
getConnectedGraph 49.493 2.765 52.347
GeneAnswers-package 47.393 3.364 50.763
buildNet 46.130 4.401 50.537
geneAnswersBuilder 46.073 3.504 49.582
geneAnswersSort 42.295 3.210 45.534
getGOList 25.067 4.035 33.825
* 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, 5 NOTEs
See
‘/Users/biocbuild/bbs-3.11-bioc/meat/GeneAnswers.Rcheck/00check.log’
for details.
GeneAnswers.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL GeneAnswers ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’ * installing *source* package ‘GeneAnswers’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading Warning: replacing previous import ‘stats::decompose’ by ‘igraph::decompose’ when loading ‘GeneAnswers’ Warning: replacing previous import ‘stats::spectrum’ by ‘igraph::spectrum’ when loading ‘GeneAnswers’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: replacing previous import ‘stats::decompose’ by ‘igraph::decompose’ when loading ‘GeneAnswers’ Warning: replacing previous import ‘stats::spectrum’ by ‘igraph::spectrum’ when loading ‘GeneAnswers’ ** testing if installed package can be loaded from final location Warning: replacing previous import ‘stats::decompose’ by ‘igraph::decompose’ when loading ‘GeneAnswers’ Warning: replacing previous import ‘stats::spectrum’ by ‘igraph::spectrum’ when loading ‘GeneAnswers’ ** testing if installed package keeps a record of temporary installation path * DONE (GeneAnswers)
GeneAnswers.Rcheck/GeneAnswers-Ex.timings
| name | user | system | elapsed | |
| DO | 0.443 | 0.044 | 0.486 | |
| DOLite | 0.026 | 0.015 | 0.041 | |
| DOLiteTerm | 0.004 | 0.004 | 0.009 | |
| DmIALite | 0.076 | 0.019 | 0.095 | |
| GeneAnswers-class | 50.114 | 5.557 | 55.985 | |
| GeneAnswers-package | 47.393 | 3.364 | 50.763 | |
| HsIALite | 0.497 | 0.066 | 0.563 | |
| MmIALite | 0.021 | 0.011 | 0.032 | |
| RnIALite | 0.010 | 0.010 | 0.021 | |
| buildNet | 46.130 | 4.401 | 50.537 | |
| caBIO.PATHGenes | 0.000 | 0.000 | 0.001 | |
| caBIO2entrez | 0.000 | 0.001 | 0.000 | |
| categoryNet | 0.000 | 0.000 | 0.001 | |
| chartPlots | 0.091 | 0.064 | 0.199 | |
| drawTable | 0.912 | 0.039 | 0.952 | |
| entrez2caBIO | 0.000 | 0.000 | 0.001 | |
| geneAnnotationHeatmap | 0.002 | 0.000 | 0.002 | |
| geneAnswersBuilder | 46.073 | 3.504 | 49.582 | |
| geneAnswersChartPlots | 49.195 | 5.002 | 54.198 | |
| geneAnswersConceptNet | 49.785 | 4.023 | 53.811 | |
| geneAnswersConceptRelation | 50.440 | 3.851 | 54.303 | |
| geneAnswersConcepts | 48.290 | 4.699 | 53.032 | |
| geneAnswersHeatmap | 50.612 | 3.935 | 55.090 | |
| geneAnswersHomoMapping | 48.678 | 4.109 | 53.208 | |
| geneAnswersReadable | 97.017 | 8.950 | 106.152 | |
| geneAnswersSort | 42.295 | 3.210 | 45.534 | |
| geneConceptNet | 0.000 | 0.000 | 0.001 | |
| getCategoryList | 0.306 | 0.027 | 0.336 | |
| getCategoryTerms | 0.065 | 0.006 | 0.071 | |
| getConceptTable | 1.009 | 0.101 | 1.111 | |
| getConnectedGraph | 49.493 | 2.765 | 52.347 | |
| getDOLiteTerms | 0.006 | 0.003 | 0.009 | |
| getGOList | 25.067 | 4.035 | 33.825 | |
| getHomoGeneIDs | 0.299 | 0.020 | 0.319 | |
| getListGIF | 0.000 | 0.001 | 0.000 | |
| getMultiLayerGraphIDs | 50.283 | 2.988 | 53.619 | |
| getNextGOIDs | 0.144 | 0.004 | 0.149 | |
| getPATHList | 0.065 | 0.004 | 0.071 | |
| getPATHTerms | 0.039 | 0.002 | 0.040 | |
| getREACTOMEPATHList | 0.001 | 0.000 | 0.001 | |
| getREACTOMEPATHTerms | 0 | 0 | 0 | |
| getSingleLayerGraphIDs | 0.003 | 0.000 | 0.004 | |
| getSymbols | 0.044 | 0.003 | 0.047 | |
| getTotalGeneNumber | 0.435 | 0.032 | 0.480 | |
| getcaBIOPATHList | 0 | 0 | 0 | |
| getcaBIOPATHTerms | 0.001 | 0.000 | 0.000 | |
| groupReport | 1.087 | 0.049 | 1.175 | |
| humanExpr | 0.010 | 0.006 | 0.017 | |
| humanGeneInput | 0.006 | 0.006 | 0.013 | |
| mouseExpr | 0.009 | 0.006 | 0.017 | |
| mouseGeneInput | 0.006 | 0.005 | 0.011 | |
| sampleGroupsData | 0.195 | 0.134 | 0.342 | |
| searchEntrez | 0.001 | 0.000 | 0.001 | |
| topCategory | 0.001 | 0.000 | 0.001 | |
| topCategoryGenes | 0.000 | 0.000 | 0.001 | |
| topDOLITE | 0 | 0 | 0 | |
| topDOLITEGenes | 0.001 | 0.001 | 0.001 | |
| topGO | 0.001 | 0.000 | 0.000 | |
| topGOGenes | 0.001 | 0.000 | 0.003 | |
| topPATH | 0.001 | 0.000 | 0.000 | |
| topPATHGenes | 0.000 | 0.000 | 0.001 | |
| topREACTOME.PATH | 0.000 | 0.000 | 0.001 | |
| topREACTOME.PATHGenes | 0.001 | 0.000 | 0.001 | |
| topcaBIO.PATH | 0.001 | 0.000 | 0.001 | |