Lei Huang
| Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022) |
| git_url: https://git.bioconductor.org/packages/GeneAnswers |
| git_branch: RELEASE_3_14 |
| git_last_commit: ada47cb |
| git_last_commit_date: 2021-10-26 11:54:49 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:06:36 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
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? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 717/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Lei Huang
| nebbiolo2 | Linux (Ubuntu 20.04.4 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 | TIMEOUT | OK | |||||||||
| Package: GeneAnswers |
| Version: 2.36.0 |
| Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GeneAnswers.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings GeneAnswers_2.36.0.tar.gz |
| StartedAt: 2022-04-12 20:06:48 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 21:22:31 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 4542.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: GeneAnswers.Rcheck |
| Warnings: 2 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GeneAnswers.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings GeneAnswers_2.36.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/GeneAnswers.Rcheck'
* using R version 4.1.3 (2022-03-10)
* 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 '2.36.0'
* 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: Package 'GeneAnswers' is deprecated and will be removed from
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-3.14-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' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
getConceptTable 289.33 0.86 444.31
groupReport 285.22 0.37 434.27
drawTable 283.03 0.55 436.13
geneAnswersReadable 47.89 0.33 48.23
GeneAnswers-class 35.03 1.98 43.69
geneAnswersSort 31.55 0.09 31.64
geneAnswersConcepts 29.94 0.25 30.42
geneAnswersHeatmap 29.44 0.64 30.08
buildNet 29.25 0.20 29.45
geneAnswersConceptRelation 28.79 0.61 29.40
geneAnswersConceptNet 28.82 0.29 29.11
GeneAnswers-package 28.13 0.83 28.95
getMultiLayerGraphIDs 28.37 0.39 28.77
geneAnswersHomoMapping 27.65 0.30 27.96
geneAnswersBuilder 26.50 0.65 27.15
getConnectedGraph 26.66 0.37 27.06
geneAnswersChartPlots 26.81 0.07 26.88
getGOList 18.38 1.56 670.08
getPATHList 5.22 0.00 9.20
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
drawTable 323.72 0.52 492.13
groupReport 311.47 0.34 471.00
getConceptTable 309.96 0.62 500.28
geneAnswersReadable 49.35 0.25 49.59
GeneAnswers-class 28.53 0.89 29.42
geneAnswersBuilder 28.94 0.28 29.22
geneAnswersSort 28.67 0.03 28.70
buildNet 27.00 0.01 27.03
geneAnswersHomoMapping 26.94 0.05 26.99
geneAnswersHeatmap 26.68 0.02 26.70
getConnectedGraph 26.43 0.25 26.69
geneAnswersConceptRelation 26.53 0.05 26.61
geneAnswersChartPlots 25.69 0.06 25.75
geneAnswersConceptNet 25.30 0.22 25.51
geneAnswersConcepts 25.48 0.01 25.53
getMultiLayerGraphIDs 24.70 0.11 24.84
GeneAnswers-package 24.69 0.11 24.80
getGOList 14.39 0.22 14.63
getPATHList 5.55 0.00 9.96
* 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: 2 WARNINGs, 5 NOTEs
See
'C:/Users/biocbuild/bbs-3.14-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://155.52.207.166/BBS/3.14/bioc/src/contrib/GeneAnswers_2.36.0.tar.gz && rm -rf GeneAnswers.buildbin-libdir && mkdir GeneAnswers.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GeneAnswers.buildbin-libdir GeneAnswers_2.36.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL GeneAnswers_2.36.0.zip && rm GeneAnswers_2.36.0.tar.gz GeneAnswers_2.36.0.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
1 32.6M 1 598k 0 0 997k 0 0:00:33 --:--:-- 0:00:33 997k
7 32.6M 7 2436k 0 0 1551k 0 0:00:21 0:00:01 0:00:20 1551k
15 32.6M 15 5195k 0 0 2021k 0 0:00:16 0:00:02 0:00:14 2021k
26 32.6M 26 8865k 0 0 2483k 0 0:00:13 0:00:03 0:00:10 2483k
40 32.6M 40 13.0M 0 0 2927k 0 0:00:11 0:00:04 0:00:07 2928k
54 32.6M 54 17.6M 0 0 3242k 0 0:00:10 0:00:05 0:00:05 3513k
64 32.6M 64 20.9M 0 0 3265k 0 0:00:10 0:00:06 0:00:04 3804k
77 32.6M 77 25.1M 0 0 3402k 0 0:00:09 0:00:07 0:00:02 4112k
92 32.6M 92 30.2M 0 0 3615k 0 0:00:09 0:00:08 0:00:01 4424k
100 32.6M 100 32.6M 0 0 3723k 0 0:00:08 0:00:08 --:--:-- 4547k
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'
Warning: Package 'GeneAnswers' is deprecated and will be removed from
Bioconductor version 3.15
** 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'
Warning: Package 'GeneAnswers' is deprecated and will be removed from
Bioconductor version 3.15
** 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'
Warning: Package 'GeneAnswers' is deprecated and will be removed from
Bioconductor version 3.15
* MD5 sums
packaged installation of 'GeneAnswers' as GeneAnswers_2.36.0.zip
* DONE (GeneAnswers)
* installing to library 'C:/Users/biocbuild/bbs-3.14-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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