Charlotte Soneson
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/compcodeR |
| Branch: RELEASE_3_9 |
| Last Commit: 9f60a50 |
| Last Changed Date: 2019-07-31 11:25:40 -0400 (Wed, 31 Jul 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:29:54 -0400 (Wed, 16 Oct 2019).
| Package 328/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| compcodeR 1.20.1 Charlotte Soneson
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: compcodeR |
| Version: 1.20.1 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:compcodeR.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings compcodeR_1.20.1.tar.gz |
| StartedAt: 2019-10-16 02:51:40 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 03:05:55 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 855.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: compcodeR.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:compcodeR.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings compcodeR_1.20.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/compcodeR.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'compcodeR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'compcodeR' version '1.20.1'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'rpanel'
* 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 'compcodeR' 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 ... NOTE
'library' or 'require' call to 'rpanel' in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: 'sm'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
DESeq.GLM.createRmd: no visible global function definition for
'packageVersion'
DESeq.nbinom.createRmd: no visible global function definition for
'packageVersion'
DESeq2.createRmd: no visible global function definition for
'packageVersion'
DSS.createRmd: no visible global function definition for
'packageVersion'
EBSeq.createRmd: no visible global function definition for
'packageVersion'
NBPSeq.createRmd: no visible global function definition for
'packageVersion'
NOISeq.prenorm.createRmd: no visible global function definition for
'packageVersion'
TCC.createRmd: no visible global function definition for
'packageVersion'
baySeq.createRmd: no visible global function definition for
'packageVersion'
computeCorrelation: no visible global function definition for 'cor'
computeCorrelation: no visible global function definition for 'hclust'
computeCorrelation: no visible global function definition for 'as.dist'
computeCorrelation: no visible global function definition for
'heat.colors'
computeOverlap: no visible global function definition for 'hclust'
computeOverlap: no visible global function definition for 'as.dist'
computeOverlap: no visible global function definition for 'heat.colors'
computeSignal: no visible binding for global variable 'sd'
createResultsRmdFile: no visible global function definition for
'packageVersion'
edgeR.GLM.createRmd: no visible global function definition for
'packageVersion'
edgeR.exact.createRmd: no visible global function definition for
'packageVersion'
generateSyntheticData: no visible global function definition for
'runif'
generateSyntheticData: no visible global function definition for 'rexp'
generateSyntheticData: no visible global function definition for
'rnbinom'
generateSyntheticData: no visible global function definition for
'rpois'
generateSyntheticData: no visible binding for global variable 'median'
logcpm.limma.createRmd: no visible global function definition for
'packageVersion'
makeFalseDiscoveryCurves: no visible global function definition for
'par'
makeFalseDiscoveryCurves: no visible global function definition for
'lines'
makeFalseDiscoveryCurves: no visible global function definition for
'legend'
makeROCcurves: no visible global function definition for 'par'
makeROCcurves: no visible global function definition for 'lines'
makeROCcurves: no visible global function definition for 'legend'
plotMASignificant: no visible global function definition for 'par'
plotResultTable: no visible global function definition for 'par'
plotScoreVsExpr: no visible global function definition for 'par'
plotScoreVsExpr: no visible global function definition for 'loess'
plotScoreVsExpr: no visible global function definition for 'lines'
plotScoreVsExpr: no visible global function definition for 'predict'
plotScoreVsOutlierEvidence: no visible global function definition for
'par'
plotScoreVsOutlierEvidence: no visible global function definition for
'loess'
plotScoreVsOutlierEvidence: no visible global function definition for
'lines'
plotScoreVsOutlierEvidence: no visible global function definition for
'predict'
plotScoreVsOutliers: no visible global function definition for 'par'
plotScoreVsOutliers: no visible binding for global variable 'na.omit'
plotScoreVsOutliers: no visible global function definition for 'title'
plotScoreVsOutliers: no visible global function definition for 'axis'
plotSignalForZeroCounts: no visible global function definition for
'par'
sqrtcpm.limma.createRmd: no visible global function definition for
'packageVersion'
ttest.createRmd: no visible global function definition for
'packageVersion'
voom.limma.createRmd: no visible global function definition for
'packageVersion'
voom.ttest.createRmd: no visible global function definition for
'packageVersion'
vst.limma.createRmd: no visible global function definition for
'packageVersion'
vst.ttest.createRmd: no visible global function definition for
'packageVersion'
show,compData: no visible global function definition for 'head'
Undefined global functions or variables:
as.dist axis cor hclust head heat.colors legend lines loess median
na.omit packageVersion par predict rexp rnbinom rpois runif sd title
Consider adding
importFrom("grDevices", "heat.colors")
importFrom("graphics", "axis", "legend", "lines", "par", "title")
importFrom("stats", "as.dist", "cor", "hclust", "loess", "median",
"na.omit", "predict", "rexp", "rnbinom", "rpois", "runif",
"sd")
importFrom("utils", "head", "packageVersion")
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
DESeq.nbinom.createRmd 88.59 1.83 90.44
convertcompDataToList 54.75 3.67 58.42
NBPSeq.createRmd 56.92 0.46 57.56
show-compData-method 45.64 2.60 48.25
EBSeq.createRmd 17.00 0.11 17.27
DESeq.GLM.createRmd 8.28 0.23 8.62
DESeq2.createRmd 7.59 0.47 8.06
DSS.createRmd 5.42 0.59 6.08
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
DESeq.nbinom.createRmd 73.45 1.64 75.09
NBPSeq.createRmd 55.42 1.03 56.56
show-compData-method 51.60 1.39 53.01
convertcompDataToList 50.47 0.00 50.47
EBSeq.createRmd 13.33 0.10 13.43
DESeq2.createRmd 8.98 0.16 9.16
DESeq.GLM.createRmd 8.15 0.09 8.25
DSS.createRmd 7.12 0.40 7.59
baySeq.createRmd 5.80 0.04 5.85
runComparison 4.83 0.17 7.46
* 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
'C:/Users/biocbuild/bbs-3.9-bioc/meat/compcodeR.Rcheck/00check.log'
for details.
compcodeR.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/compcodeR_1.20.1.tar.gz && rm -rf compcodeR.buildbin-libdir && mkdir compcodeR.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=compcodeR.buildbin-libdir compcodeR_1.20.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL compcodeR_1.20.1.zip && rm compcodeR_1.20.1.tar.gz compcodeR_1.20.1.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
88 2345k 88 2064k 0 0 3828k 0 --:--:-- --:--:-- --:--:-- 3872k
100 2345k 100 2345k 0 0 4314k 0 --:--:-- --:--:-- --:--:-- 4367k
install for i386
* installing *source* package 'compcodeR' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'compcodeR'
finding HTML links ... done
DESeq.GLM.createRmd html
DESeq.nbinom.createRmd html
DESeq2.createRmd html
DSS.createRmd html
EBSeq.createRmd html
NBPSeq.createRmd html
NOISeq.prenorm.createRmd html
TCC.createRmd html
baySeq.createRmd html
checkDataObject html
checkTableConsistency html
check_compData html
check_compData_results html
compData-class html
compData html
compcodeR-package html
convertListTocompData html
convertcompDataToList html
edgeR.GLM.createRmd html
edgeR.exact.createRmd html
generateCodeHTMLs html
generateSyntheticData html
listcreateRmd html
logcpm.limma.createRmd html
runComparison html
runComparisonGUI html
runDiffExp html
show-compData-method html
sqrtcpm.limma.createRmd html
summarizeSyntheticDataSet html
ttest.createRmd html
voom.limma.createRmd html
voom.ttest.createRmd html
vst.limma.createRmd html
vst.ttest.createRmd html
** 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 'compcodeR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'compcodeR' as compcodeR_1.20.1.zip
* DONE (compcodeR)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'compcodeR' successfully unpacked and MD5 sums checked
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compcodeR.Rcheck/examples_i386/compcodeR-Ex.timings
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compcodeR.Rcheck/examples_x64/compcodeR-Ex.timings
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