Xin Wang
| Snapshot Date: 2021-01-18 09:00:15 -0500 (Mon, 18 Jan 2021) |
| URL: https://git.bioconductor.org/packages/DeSousa2013 |
| Branch: master |
| Last Commit: bb7af97 |
| Last Changed Date: 2020-10-27 10:02:18 -0500 (Tue, 27 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.13 experimental data |
|
This page was generated on 2021-01-18 15:58:47 -0500 (Mon, 18 Jan 2021).
| TO THE DEVELOPERS/MAINTAINERS OF THE DeSousa2013 PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 92/385 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | ||||||
| DeSousa2013 1.27.0 Xin Wang
| malbec2 | Linux (Ubuntu 20.04.1 LTS) / x86_64 | OK | OK | OK | | |||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | [ OK ] |
| Package: DeSousa2013 |
| Version: 1.27.0 |
| Command: D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DeSousa2013.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings DeSousa2013_1.27.0.tar.gz |
| StartedAt: 2021-01-18 11:18:59 -0500 (Mon, 18 Jan 2021) |
| EndedAt: 2021-01-18 11:23:00 -0500 (Mon, 18 Jan 2021) |
| EllapsedTime: 240.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: DeSousa2013.Rcheck |
| Warnings: 0 |
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### Running command:
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### D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DeSousa2013.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings DeSousa2013_1.27.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.13-data-experiment/meat/DeSousa2013.Rcheck'
* using R Under development (unstable) (2020-12-30 r79736)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'DeSousa2013/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'DeSousa2013' version '1.27.0'
* 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 'DeSousa2013' can be installed ... OK
* checking installed package size ... NOTE
installed size is 44.0Mb
sub-directories of 1Mb or more:
data 43.7Mb
* 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 ... NOTE
Namespaces in Imports field not imported from:
'frmaTools' 'hgu133plus2frmavecs' 'rgl'
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
CRCPipeLine: no visible global function definition for 'data'
CRCPipeLine: no visible global function definition for 'pdf'
CRCPipeLine: no visible global function definition for 'graphics.off'
compGapStats: no visible binding for global variable 'mad'
compGapStats : fun: no visible global function definition for 'hclust'
compGapStats : fun: no visible global function definition for 'as.dist'
compGapStats : fun: no visible global function definition for 'cor'
compGapStats : fun: no visible global function definition for 'cutree'
compGapStats: no visible binding for global variable 'median'
figClassify: no visible global function definition for 'layout'
figClassify: no visible global function definition for 'par'
figClassify: no visible global function definition for 'image'
figClassify: no visible global function definition for 'axis'
figClassify: no visible global function definition for 'box'
figClassify: no visible global function definition for 'gray'
figClassify: no visible global function definition for 'mtext'
figClassify: no visible global function definition for 'barplot'
figClassify: no visible global function definition for 'grid'
figGAP: no visible global function definition for 'par'
figGAP: no visible global function definition for 'lines'
figGAP: no visible global function definition for 'title'
figKM: no visible global function definition for 'axis'
figKM: no visible global function definition for 'box'
figKM: no visible global function definition for 'text'
figKM: no visible global function definition for 'legend'
figPAMCV: no visible global function definition for 'boxplot'
filterSamples: no visible global function definition for 'as.dist'
filterSamples: no visible global function definition for 'cor'
pamClassify: no visible global function definition for 'hclust'
pamClassify: no visible global function definition for 'as.dist'
pamClassify: no visible global function definition for 'cor'
pbs2unigenes: no visible global function definition for 'mappedkeys'
progAMC: no visible global function definition for 'pchisq'
selTopVarGenes: no visible binding for global variable 'mad'
selTopVarGenes: no visible binding for global variable 'median'
Undefined global functions or variables:
as.dist axis barplot box boxplot cor cutree data graphics.off gray
grid hclust image layout legend lines mad mappedkeys median mtext par
pchisq pdf text title
Consider adding
importFrom("grDevices", "graphics.off", "gray", "pdf")
importFrom("graphics", "axis", "barplot", "box", "boxplot", "grid",
"image", "layout", "legend", "lines", "mtext", "par",
"text", "title")
importFrom("stats", "as.dist", "cor", "cutree", "hclust", "mad",
"median", "pchisq")
importFrom("utils", "data")
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
compGapStats 10.04 0.19 10.24
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
compGapStats 10.18 0.22 10.39
* 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: 3 NOTEs
See
'D:/biocbuild/bbs-3.13-data-experiment/meat/DeSousa2013.Rcheck/00check.log'
for details.
DeSousa2013.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://172.29.0.4/BBS/3.13/data-experiment/src/contrib/DeSousa2013_1.27.0.tar.gz && rm -rf DeSousa2013.buildbin-libdir && mkdir DeSousa2013.buildbin-libdir && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DeSousa2013.buildbin-libdir DeSousa2013_1.27.0.tar.gz && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL DeSousa2013_1.27.0.zip && rm DeSousa2013_1.27.0.tar.gz DeSousa2013_1.27.0.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
39 44.0M 39 17.1M 0 0 45.1M 0 --:--:-- --:--:-- --:--:-- 44.9M
100 44.0M 100 44.0M 0 0 66.6M 0 --:--:-- --:--:-- --:--:-- 66.6M
install for i386
* installing *source* package 'DeSousa2013' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'DeSousa2013'
finding HTML links ... done
CRCPipeLine html
REDIRECT:topic CRCPipeLine -> CRCPipeLine.html [ SUCCESS ]
REDIRECT:topic DeSousa2013 -> CRCPipeLine.html [ SUCCESS ]
buildClassifier html
REDIRECT:topic buildClassifier -> buildClassifier.html [ SUCCESS ]
REDIRECT:topic figPAMCV -> buildClassifier.html [ SUCCESS ]
compGapStats html
REDIRECT:topic compGapStats -> compGapStats.html [ SUCCESS ]
REDIRECT:topic figGAP -> compGapStats.html [ SUCCESS ]
conClust html
REDIRECT:topic conClust -> conClust.html [ SUCCESS ]
data-AMC html
REDIRECT:topic AMC_CRC_clinical -> data-AMC.html [ SUCCESS ]
REDIRECT:topic AMC_sample_head -> data-AMC.html [ SUCCESS ]
REDIRECT:topic ge.all -> data-AMC.html [ SUCCESS ]
REDIRECT:topic selPbs -> data-AMC.html [ SUCCESS ]
REDIRECT:topic gapsmat -> data-AMC.html [ SUCCESS ]
REDIRECT:topic gapsSE -> data-AMC.html [ SUCCESS ]
REDIRECT:topic sdat -> data-AMC.html [ SUCCESS ]
REDIRECT:topic uniGenes -> data-AMC.html [ SUCCESS ]
REDIRECT:topic clus -> data-AMC.html [ SUCCESS ]
REDIRECT:topic clus.f -> data-AMC.html [ SUCCESS ]
REDIRECT:topic sdat.f -> data-AMC.html [ SUCCESS ]
REDIRECT:topic silh -> data-AMC.html [ SUCCESS ]
REDIRECT:topic diffGenes -> data-AMC.html [ SUCCESS ]
REDIRECT:topic diffGenes.f -> data-AMC.html [ SUCCESS ]
REDIRECT:topic pam.rslt -> data-AMC.html [ SUCCESS ]
REDIRECT:topic signature -> data-AMC.html [ SUCCESS ]
REDIRECT:topic thresh -> data-AMC.html [ SUCCESS ]
REDIRECT:topic err -> data-AMC.html [ SUCCESS ]
REDIRECT:topic cents -> data-AMC.html [ SUCCESS ]
REDIRECT:topic clu.pred -> data-AMC.html [ SUCCESS ]
REDIRECT:topic sdat.sig -> data-AMC.html [ SUCCESS ]
REDIRECT:topic pred -> data-AMC.html [ SUCCESS ]
REDIRECT:topic gclu.f -> data-AMC.html [ SUCCESS ]
REDIRECT:topic nam.ord -> data-AMC.html [ SUCCESS ]
REDIRECT:topic surv -> data-AMC.html [ SUCCESS ]
REDIRECT:topic survstats -> data-AMC.html [ SUCCESS ]
REDIRECT:topic data4surv -> data-AMC.html [ SUCCESS ]
REDIRECT:file data-AMC.html -> data-AMC.html [ SUCCESS ]
filterDiffGenes html
REDIRECT:topic filterDiffGenes -> filterDiffGenes.html [ SUCCESS ]
filterSamples html
REDIRECT:topic filterSamples -> filterSamples.html [ SUCCESS ]
REDIRECT:topic figSilh -> filterSamples.html [ SUCCESS ]
findDiffGenes html
REDIRECT:topic findDiffGenes -> findDiffGenes.html [ SUCCESS ]
geneExpPre html
REDIRECT:topic geneExpPre -> geneExpPre.html [ SUCCESS ]
getCentroids html
REDIRECT:topic getCentroids -> getCentroids.html [ SUCCESS ]
pamClassify html
REDIRECT:topic pamClassify -> pamClassify.html [ SUCCESS ]
REDIRECT:topic figClassify -> pamClassify.html [ SUCCESS ]
pbs2unigenes html
REDIRECT:topic pbs2unigenes -> pbs2unigenes.html [ SUCCESS ]
progAMC html
REDIRECT:topic progAMC -> progAMC.html [ SUCCESS ]
REDIRECT:topic figKM -> progAMC.html [ SUCCESS ]
selTopVarGenes html
REDIRECT:topic selTopVarGenes -> selTopVarGenes.html [ SUCCESS ]
** building package indices
** installing vignettes
** 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 'DeSousa2013' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DeSousa2013' as DeSousa2013_1.27.0.zip
* DONE (DeSousa2013)
* installing to library 'D:/biocbuild/bbs-3.13-bioc/R/library'
package 'DeSousa2013' successfully unpacked and MD5 sums checked
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DeSousa2013.Rcheck/examples_i386/DeSousa2013-Ex.timings
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DeSousa2013.Rcheck/examples_x64/DeSousa2013-Ex.timings
|