Daniel Castillo Secilla
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/KnowSeq |
| Branch: RELEASE_3_10 |
| Last Commit: 9f19e01 |
| Last Changed Date: 2020-02-13 15:39:36 -0400 (Thu, 13 Feb 2020) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:32:43 -0400 (Wed, 15 Apr 2020).
| Package 894/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| KnowSeq 1.0.0 Daniel Castillo Secilla
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: KnowSeq |
| Version: 1.0.0 |
| Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:KnowSeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings KnowSeq_1.0.0.tar.gz |
| StartedAt: 2020-04-15 04:16:04 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 04:29:43 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 819.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: KnowSeq.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:KnowSeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings KnowSeq_1.0.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/KnowSeq.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'KnowSeq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'KnowSeq' version '1.0.0'
* package encoding: UTF-8
* 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 'KnowSeq' can be installed ... OK
* checking installed package size ... OK
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
limmaDEGsExtraction: warning in topTable(fit, number = number, coef =
2, sort.by = "logFC", p.value = pvalue, adjust = "fdr", lfc = lfc):
partial argument match of 'adjust' to 'adjust.method'
dataPlot: no visible binding for global variable 'Classes'
dataPlot: no visible binding for global variable 'Value'
dataPlot: no visible global function definition for 'grid'
Undefined global functions or variables:
Classes Value grid
Consider adding
importFrom("graphics", "grid")
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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
svm_CV 53.51 0.00 53.51
knn_CV 22.80 0.02 22.89
geneOntologyEnrichment 15.22 0.28 21.07
svm_test 14.38 0.00 14.39
rf_CV 7.75 0.00 7.75
RNAseqQA 6.67 0.25 9.92
downloadPublicSeries 1.99 0.51 26.64
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
svm_CV 85.08 0.06 85.74
knn_CV 35.31 0.04 35.68
geneOntologyEnrichment 20.86 0.14 26.03
svm_test 16.26 0.02 16.28
rf_CV 11.67 0.00 11.69
RNAseqQA 8.11 0.31 8.42
knn_test 6.33 0.00 6.33
dataPlot 4.67 0.34 5.01
downloadPublicSeries 2.89 0.23 22.77
* 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 NOTE
See
'C:/Users/biocbuild/bbs-3.10-bioc/meat/KnowSeq.Rcheck/00check.log'
for details.
KnowSeq.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/KnowSeq_1.0.0.tar.gz && rm -rf KnowSeq.buildbin-libdir && mkdir KnowSeq.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=KnowSeq.buildbin-libdir KnowSeq_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL KnowSeq_1.0.0.zip && rm KnowSeq_1.0.0.tar.gz KnowSeq_1.0.0.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 2132k 100 2132k 0 0 9364k 0 --:--:-- --:--:-- --:--:-- 9479k
install for i386
* installing *source* package 'KnowSeq' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built.
** help
*** installing help indices
converting help for package 'KnowSeq'
finding HTML links ... done
DEGsPathwayVisualization html
finding level-2 HTML links ... done
DEGsToDiseases html
RNAseqQA html
batchEffectRemoval html
calculateGeneExpressionValues html
countsToMatrix html
dataPlot html
downloadPublicSeries html
featureSelection html
fileMove html
gdcClientDownload html
geneOntologyEnrichment html
getAnnotationFromEnsembl html
hisatAlignment html
kallistoAlignment html
knn_CV html
knn_test html
limmaDEGsExtraction html
plotConfMatrix html
rawAlignment html
rf_CV html
rf_test html
salmonAlignment html
sraToFastq html
svm_CV html
svm_test html
tophatAlignment html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built.
** testing if installed package can be loaded from final location
groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built.
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'KnowSeq' ...
** testing if installed package can be loaded
groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built.
* MD5 sums
packaged installation of 'KnowSeq' as KnowSeq_1.0.0.zip
* DONE (KnowSeq)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'KnowSeq' successfully unpacked and MD5 sums checked
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KnowSeq.Rcheck/examples_i386/KnowSeq-Ex.timings
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KnowSeq.Rcheck/examples_x64/KnowSeq-Ex.timings
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