Lei Huang
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/GeneAnswers |
| Branch: RELEASE_3_12 |
| Last Commit: a310951 |
| Last Changed Date: 2020-10-27 10:36:41 -0400 (Tue, 27 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:31:25 -0400 (Thu, 06 May 2021).
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To the developers/maintainers of the GeneAnswers package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 682/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GeneAnswers 2.32.0 (landing page) Lei Huang
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: GeneAnswers |
| Version: 2.32.0 |
| Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GeneAnswers.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings GeneAnswers_2.32.0.tar.gz |
| StartedAt: 2021-05-06 03:00:18 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 03:26:24 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 1566.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: GeneAnswers.Rcheck |
| Warnings: 1 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GeneAnswers.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings GeneAnswers_2.32.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/GeneAnswers.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GeneAnswers/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GeneAnswers' version '2.32.0'
* 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 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 'C:/Users/biocbuild/bbs-3.12-bioc/meat/GeneAnswers.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
installed size is 34.5Mb
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
* 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
'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'.
.defaultHeatmapColors: no visible global function definition for 'rgb'
.drawHTMLtable: no visible global function definition for
'colorRampPalette'
.heatmap.mds: no visible global function definition for
'colorRampPalette'
buildNet: no visible global function definition for 'colorRampPalette'
chartPlots: no visible global function definition for 'x11'
chartPlots: no visible global function definition for 'rainbow'
drawTable: no visible global function definition for 'colorRampPalette'
drawTable: no visible global function definition for 'x11'
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'
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 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:
col2rgb colorRampPalette count.mappedkeys dev.off dev.prev dev.set
getLDS png rainbow reactomePATHNAME2ID rgb useMart x11
Consider adding
importFrom("grDevices", "col2rgb", "colorRampPalette", "dev.off",
"dev.prev", "dev.set", "png", "rainbow", "rgb", "x11")
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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
geneAnswersReadable 70.03 1.23 71.30
GeneAnswers-class 49.14 3.64 61.05
buildNet 44.84 0.53 45.38
getMultiLayerGraphIDs 40.92 0.06 40.99
getConnectedGraph 40.32 0.50 40.83
GeneAnswers-package 39.19 1.38 40.56
geneAnswersSort 39.25 0.63 39.89
geneAnswersBuilder 39.14 0.42 39.57
geneAnswersHeatmap 35.25 0.27 35.51
geneAnswersConceptRelation 34.67 0.19 34.87
geneAnswersHomoMapping 34.36 0.22 34.58
geneAnswersChartPlots 33.15 0.41 33.57
geneAnswersConcepts 32.82 0.28 33.09
geneAnswersConceptNet 32.34 0.39 32.74
getGOList 21.25 0.90 180.98
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
geneAnswersReadable 75.63 0.32 75.94
geneAnswersConceptRelation 47.29 0.61 48.05
geneAnswersHeatmap 43.53 0.17 44.00
geneAnswersConcepts 42.39 0.52 42.90
geneAnswersSort 41.39 0.23 41.62
geneAnswersChartPlots 40.65 0.33 40.98
getConnectedGraph 39.84 0.16 40.03
geneAnswersHomoMapping 39.31 0.15 39.47
buildNet 38.84 0.22 39.06
GeneAnswers-class 37.91 0.92 38.84
getMultiLayerGraphIDs 37.94 0.08 38.01
geneAnswersConceptNet 37.46 0.31 37.77
GeneAnswers-package 36.59 0.29 36.89
geneAnswersBuilder 31.94 0.27 32.20
getGOList 17.86 0.11 17.99
* 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
'C:/Users/biocbuild/bbs-3.12-bioc/meat/GeneAnswers.Rcheck/00check.log'
for details.
GeneAnswers.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/GeneAnswers_2.32.0.tar.gz && rm -rf GeneAnswers.buildbin-libdir && mkdir GeneAnswers.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GeneAnswers.buildbin-libdir GeneAnswers_2.32.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL GeneAnswers_2.32.0.zip && rm GeneAnswers_2.32.0.tar.gz GeneAnswers_2.32.0.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
100 32.6M 100 32.6M 0 0 92.2M 0 --:--:-- --:--:-- --:--:-- 92.4M
install for i386
* 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
converting help for package 'GeneAnswers'
finding HTML links ... done
DO html
DOLite html
DOLiteTerm html
DmIALite html
GeneAnswers-class html
GeneAnswers-package html
HsIALite html
MmIALite html
RnIALite html
buildNet html
caBIO.PATHGenes html
caBIO2entrez html
categoryNet html
chartPlots html
drawTable html
entrez2caBIO html
geneAnnotationHeatmap html
geneAnswersBuilder html
geneAnswersChartPlots html
geneAnswersConceptNet html
geneAnswersConceptRelation html
geneAnswersConcepts html
geneAnswersHeatmap html
geneAnswersHomoMapping html
geneAnswersReadable html
geneAnswersSort html
geneConceptNet html
getCategoryList html
getCategoryTerms html
getConceptTable html
getConnectedGraph html
getDOLiteTerms html
getGOList html
getHomoGeneIDs html
getListGIF html
getMultiLayerGraphIDs html
getNextGOIDs html
getPATHList html
getPATHTerms html
getREACTOMEPATHList html
getREACTOMEPATHTerms html
getSingleLayerGraphIDs html
getSymbols html
getTotalGeneNumber html
getcaBIOPATHList html
getcaBIOPATHTerms html
groupReport html
humanExpr html
humanGeneInput html
mouseExpr html
mouseGeneInput html
sampleGroupsData html
searchEntrez html
topCategory html
topCategoryGenes html
topDOLITE html
topDOLITEGenes html
topGO html
topGOGenes html
topPATH html
topPATHGenes html
topREACTOME.PATH html
topREACTOME.PATHGenes html
topcaBIO.PATH html
** 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
install for x64
* installing *source* package 'GeneAnswers' ...
** testing if installed package can be loaded
Warning: replacing previous import 'stats::decompose' by 'igraph::decompose' when loading 'GeneAnswers'
Warning: replacing previous import 'stats::spectrum' by 'igraph::spectrum' when loading 'GeneAnswers'
* MD5 sums
packaged installation of 'GeneAnswers' as GeneAnswers_2.32.0.zip
* DONE (GeneAnswers)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'GeneAnswers' successfully unpacked and MD5 sums checked
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GeneAnswers.Rcheck/examples_i386/GeneAnswers-Ex.timings
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GeneAnswers.Rcheck/examples_x64/GeneAnswers-Ex.timings
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