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This page was generated on 2021-10-15 15:06:05 -0400 (Fri, 15 Oct 2021).
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To the developers/maintainers of the GeneAnswers package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GeneAnswers.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 708/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GeneAnswers 2.34.0 (landing page) Lei Huang
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | TIMEOUT | OK | |||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | ERROR | OK | |||||||||
| Package: GeneAnswers |
| Version: 2.34.0 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GeneAnswers.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings GeneAnswers_2.34.0.tar.gz |
| StartedAt: 2021-10-14 23:28:39 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-15 00:08:55 -0400 (Fri, 15 Oct 2021) |
| EllapsedTime: 2416.7 seconds |
| RetCode: None |
| Status: TIMEOUT |
| CheckDir: GeneAnswers.Rcheck |
| Warnings: NA |
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### Running command:
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### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GeneAnswers.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings GeneAnswers_2.34.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/GeneAnswers.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 'GeneAnswers/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GeneAnswers' version '2.34.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'igraph', 'KEGGREST', '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-3.13-bioc/meat/GeneAnswers.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
installed size is 34.7Mb
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' 'KEGGREST' 'MASS' 'RColorBrewer' 'XML' 'igraph'
Please remove these calls from your code.
'library' or 'require' calls in package code:
'GO.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'.
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'
Undefined global functions or variables:
count.mappedkeys getLDS reactomePATHNAME2ID useMart
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
'queryKegg'
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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' ... ERROR
Running examples in 'GeneAnswers-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getPATHTerms
> ### Title: Get Pathway names of given KEGG IDs
> ### Aliases: getPATHTerms
> ### Keywords: methods
>
> ### ** Examples
>
> getPATHTerms(c('04916', '05221'))
Error in names(temp) <- sapply(temp, function(x) return(x$ENTRY)) :
attempt to set an attribute on NULL
Calls: getPATHTerms -> lapply -> queryKegg
Execution halted
** running examples for arch 'x64' ...
GeneAnswers.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/GeneAnswers_2.34.0.tar.gz && rm -rf GeneAnswers.buildbin-libdir && mkdir GeneAnswers.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GeneAnswers.buildbin-libdir GeneAnswers_2.34.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL GeneAnswers_2.34.0.zip && rm GeneAnswers_2.34.0.tar.gz GeneAnswers_2.34.0.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
3 32.6M 3 1038k 0 0 1529k 0 0:00:21 --:--:-- 0:00:21 1529k
10 32.6M 10 3634k 0 0 2148k 0 0:00:15 0:00:01 0:00:14 2149k
21 32.6M 21 7062k 0 0 2643k 0 0:00:12 0:00:02 0:00:10 2644k
24 32.6M 24 8305k 0 0 2254k 0 0:00:14 0:00:03 0:00:11 2254k
24 32.6M 24 8341k 0 0 1782k 0 0:00:18 0:00:04 0:00:14 1781k
27 32.6M 27 9237k 0 0 1619k 0 0:00:20 0:00:05 0:00:15 1631k
35 32.6M 35 11.6M 0 0 1793k 0 0:00:18 0:00:06 0:00:12 1672k
46 32.6M 46 15.2M 0 0 2034k 0 0:00:16 0:00:07 0:00:09 1708k
59 32.6M 59 19.5M 0 0 2311k 0 0:00:14 0:00:08 0:00:06 2352k
75 32.6M 75 24.4M 0 0 2590k 0 0:00:12 0:00:09 0:00:03 3346k
91 32.6M 91 29.8M 0 0 2858k 0 0:00:11 0:00:10 0:00:01 4275k
100 32.6M 100 32.6M 0 0 3011k 0 0:00:11 0:00:11 --:--:-- 4849k
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_2.34.0.zip
* DONE (GeneAnswers)
* installing to library 'C:/Users/biocbuild/bbs-3.13-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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