Bernd Fischer
| Snapshot Date: 2020-04-14 09:30:11 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/DmelSGI |
| Branch: RELEASE_3_10 |
| Last Commit: f7ead31 |
| Last Changed Date: 2019-10-29 13:29:43 -0400 (Tue, 29 Oct 2019) |
| Back to Build/check report for BioC 3.10 experimental data |
This page was generated on 2020-04-14 17:46:23 -0400 (Tue, 14 Apr 2020).
| Package 95/384 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | ||||||
| DmelSGI 1.18.0 Bernd Fischer
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ OK ] | |
| Package: DmelSGI |
| Version: 1.18.0 |
| Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:DmelSGI.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings DmelSGI_1.18.0.tar.gz |
| StartedAt: 2020-04-14 13:24:02 -0400 (Tue, 14 Apr 2020) |
| EndedAt: 2020-04-14 13:24:58 -0400 (Tue, 14 Apr 2020) |
| EllapsedTime: 56.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: DmelSGI.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:DmelSGI.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings DmelSGI_1.18.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-data-experiment/meat/DmelSGI.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DmelSGI/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DmelSGI’ version ‘1.18.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘DmelSGI’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 139.3Mb
sub-directories of 1Mb or more:
Rscripts 1.7Mb
data 137.3Mb
* 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
* 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
callInteractions: no visible global function definition for ‘p.adjust’
fitMatrices: no visible global function definition for ‘png’
fitMatrices: no visible global function definition for ‘dev.off’
makeDall: no visible global function definition for ‘mad’
mymedpolish: no visible binding for global variable ‘median’
mymedpolish : <anonymous>: no visible binding for global variable
‘median’
mymedpolish: no visible global function definition for ‘median’
orderDim: no visible global function definition for ‘cor’
orderDim: no visible global function definition for ‘hclust’
orderDim: no visible global function definition for ‘as.dist’
orderSpiderAxis: no visible global function definition for ‘dist’
plot2Phenotypes: no visible global function definition for ‘layout’
plot2Phenotypes: no visible global function definition for ‘par’
plot2Phenotypes: no visible global function definition for ‘plot’
plot2Phenotypes: no visible global function definition for ‘points’
plot2Phenotypes: no visible global function definition for ‘arrows’
plot2Phenotypes: no visible global function definition for ‘segments’
plot2Phenotypes: no visible global function definition for ‘abline’
plot2Phenotypes: no visible global function definition for ‘text’
plotHairballLabels: no visible global function definition for ‘text’
plotHairballLabels: no visible global function definition for ‘lines’
plotPIdata: no visible global function definition for ‘par’
plotPIdata: no visible global function definition for ‘plot’
plotPIdata: no visible global function definition for ‘abline’
saveHeatmapFile: no visible global function definition for ‘png’
saveHeatmapFile: no visible global function definition for ‘dev.off’
saveHeatmapFile: no visible global function definition for ‘cairo_pdf’
selectByStability: no visible global function definition for ‘lm’
selectByStability : <anonymous>: no visible global function definition
for ‘cor’
subSampleForStabilitySelectionFct : <anonymous>: no visible global
function definition for ‘median’
subSampleForStabilitySelectionFct : <anonymous>: no visible global
function definition for ‘mad’
Undefined global functions or variables:
abline arrows as.dist cairo_pdf cor dev.off dist hclust layout lines
lm mad median p.adjust par plot png points segments text
Consider adding
importFrom("grDevices", "cairo_pdf", "dev.off", "png")
importFrom("graphics", "abline", "arrows", "layout", "lines", "par",
"plot", "points", "segments", "text")
importFrom("stats", "as.dist", "cor", "dist", "hclust", "lm", "mad",
"median", "p.adjust")
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 ... OK
* 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 NOTEs
See
‘/home/biocbuild/bbs-3.10-data-experiment/meat/DmelSGI.Rcheck/00check.log’
for details.
DmelSGI.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL DmelSGI ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’ * installing *source* package ‘DmelSGI’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 * DONE (DmelSGI)
DmelSGI.Rcheck/DmelSGI-Ex.timings
| name | user | system | elapsed | |
| ChromatinSet-package | 3.776 | 0.056 | 3.833 | |
| DPiM | 0.016 | 0.000 | 0.016 | |
| FBgn2anno | 0.324 | 0.008 | 0.332 | |
| Features | 0.000 | 0.004 | 0.007 | |
| Interactions | 1.848 | 0.024 | 1.874 | |
| Intogen | 0.008 | 0.000 | 0.010 | |
| RohnEtAl | 0.000 | 0.000 | 0.002 | |
| SKDdata | 0.352 | 0.008 | 0.362 | |
| SelectedClusters | 0.000 | 0.000 | 0.001 | |
| SelectedClustersComplexes | 0.004 | 0.000 | 0.001 | |
| TID2HUGO | 0.004 | 0.004 | 0.010 | |
| applyDimensionReduction | 0.004 | 0.000 | 0.001 | |
| callInteractions | 0.000 | 0.000 | 0.001 | |
| datamatrix | 3.684 | 0.076 | 3.761 | |
| estimatePairwiseInteractions | 0.000 | 0.004 | 0.001 | |
| fitepistasis | 0.136 | 0.012 | 0.147 | |
| getBaseDir | 0 | 0 | 0 | |
| grid.spider | 0.004 | 0.000 | 0.001 | |
| hrNames | 0 | 0 | 0 | |
| learnCoComplexityFct | 0.000 | 0.000 | 0.001 | |
| mainEffects | 0.076 | 0.000 | 0.077 | |
| myHeatmap | 0.000 | 0.000 | 0.001 | |
| mymedpolish | 0.000 | 0.000 | 0.001 | |
| orderDim | 0 | 0 | 0 | |
| orderSpiderAxis | 0.000 | 0.000 | 0.001 | |
| pimatrix | 0.600 | 0.044 | 0.645 | |
| plot2Phenotypes | 0.000 | 0.000 | 0.002 | |
| plotHairballLabels | 0.004 | 0.000 | 0.001 | |
| qualityControlFeature | 0.000 | 0.000 | 0.003 | |
| qualityControlGene | 0.012 | 0.000 | 0.015 | |
| selectByStability | 0.000 | 0.000 | 0.001 | |
| stabilitySelection | 0.152 | 0.004 | 0.157 | |
| subSampleForStabilitySelection | 0.068 | 0.004 | 0.070 | |
| subSampleForStabilitySelectionFct | 0.000 | 0.000 | 0.001 | |
| toMatrix | 0.000 | 0.000 | 0.001 | |
| toRaster | 0 | 0 | 0 | |
| trsf | 0 | 0 | 0 | |