Michael Turewicz
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/PAA |
| Branch: master |
| Last Commit: 93b0745 |
| Last Changed Date: 2018-10-30 11:54:33 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 11:40:04 -0400 (Tue, 09 Apr 2019).
| Package 1136/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| PAA 1.17.0 Michael Turewicz
| 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 | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
| Package: PAA |
| Version: 1.17.0 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:PAA.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings PAA_1.17.0.tar.gz |
| StartedAt: 2019-04-09 02:32:13 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 02:34:58 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 165.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: PAA.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:PAA.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings PAA_1.17.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/PAA.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PAA/DESCRIPTION’ ... OK
* this is package ‘PAA’ version ‘1.17.0’
* 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 ‘PAA’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 6.2Mb
sub-directories of 1Mb or more:
extdata 2.6Mb
libs 2.2Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Authors@R field gives more than one person with maintainer role:
Michael Turewicz <michael.turewicz@rub.de> [aut, cre]
Martin Eisenacher <martin.eisenacher@rub.de> [ctb, cre]
* 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
batchFilter: no visible global function definition for ‘t.test’
batchFilter: no visible global function definition for ‘plot’
batchFilter: no visible global function definition for ‘points’
batchFilter: no visible global function definition for ‘abline’
batchFilter: no visible global function definition for ‘write.table’
batchFilter: no visible global function definition for ‘tiff’
batchFilter: no visible global function definition for ‘dev.off’
batchFilter.anova: no visible global function definition for ‘combn’
batchFilter.anova: no visible global function definition for
‘oneway.test’
batchFilter.anova: no visible global function definition for ‘plot’
batchFilter.anova: no visible global function definition for ‘points’
batchFilter.anova: no visible global function definition for ‘abline’
batchFilter.anova: no visible global function definition for
‘write.table’
batchFilter.anova: no visible global function definition for ‘tiff’
batchFilter.anova: no visible global function definition for ‘dev.off’
classify.svm.ensemble: no visible global function definition for
‘predict’
classify.svm.ensemble: no visible global function definition for ‘tiff’
classify.svm.ensemble: no visible global function definition for
‘dev.off’
diffAnalysis: no visible global function definition for ‘t.test’
diffAnalysis: no visible global function definition for ‘median’
diffAnalysis: no visible global function definition for ‘sd’
diffAnalysis: no visible global function definition for ‘p.adjust’
diffAnalysis: no visible global function definition for ‘write.table’
final.classify.rf: no visible global function definition for ‘predict’
final.classify.rf: no visible global function definition for ‘tiff’
final.classify.rf: no visible global function definition for ‘dev.off’
final.classify.svm: no visible global function definition for ‘predict’
final.classify.svm: no visible global function definition for ‘tiff’
final.classify.svm: no visible global function definition for ‘dev.off’
normalizeRLM: no visible global function definition for ‘rnorm’
normalizeRLM: no visible global function definition for ‘tiff’
normalizeRLM: no visible global function definition for ‘boxplot’
normalizeRLM: no visible global function definition for ‘dev.off’
plotArray: no visible global function definition for ‘par’
plotArrayPng: no visible global function definition for ‘png’
plotArrayPng: no visible global function definition for ‘dev.off’
plotArrayTiff: no visible global function definition for ‘tiff’
plotArrayTiff: no visible global function definition for ‘dev.off’
plotFeatures: no visible global function definition for ‘tiff’
plotFeatures: no visible global function definition for ‘par’
plotFeatures: no visible global function definition for ‘plot’
plotFeatures: no visible global function definition for ‘axis’
plotFeatures: no visible global function definition for ‘box’
plotFeatures: no visible global function definition for ‘points’
plotFeatures: no visible global function definition for ‘legend’
plotFeatures: no visible global function definition for ‘dev.off’
plotFeaturesHeatmap: no visible global function definition for
‘na.exclude’
plotFeaturesHeatmap : my.dist: no visible global function definition
for ‘as.dist’
plotFeaturesHeatmap : my.dist: no visible global function definition
for ‘cor’
plotFeaturesHeatmap : my.hclust: no visible global function definition
for ‘hclust’
plotFeaturesHeatmap: no visible global function definition for ‘tiff’
plotFeaturesHeatmap: no visible global function definition for
‘heatmap’
plotFeaturesHeatmap: no visible global function definition for
‘dev.off’
plotFeaturesHeatmap.2: no visible global function definition for
‘na.exclude’
plotFeaturesHeatmap.2 : my.dist: no visible global function definition
for ‘as.dist’
plotFeaturesHeatmap.2 : my.dist: no visible global function definition
for ‘cor’
plotFeaturesHeatmap.2: no visible global function definition for ‘png’
plotFeaturesHeatmap.2 : <anonymous>: no visible global function
definition for ‘as.dist’
plotFeaturesHeatmap.2 : <anonymous>: no visible global function
definition for ‘cor’
plotFeaturesHeatmap.2: no visible global function definition for ‘par’
plotFeaturesHeatmap.2: no visible global function definition for
‘legend’
plotFeaturesHeatmap.2: no visible global function definition for
‘dev.off’
plotMAPlots: no visible binding for global variable ‘median’
plotMAPlots: no visible global function definition for ‘tiff’
plotMAPlots: no visible global function definition for ‘par’
plotMAPlots: no visible global function definition for ‘plot’
plotMAPlots: no visible global function definition for ‘abline’
plotMAPlots: no visible global function definition for ‘lines’
plotMAPlots: no visible global function definition for ‘lowess’
plotMAPlots: no visible global function definition for ‘dev.off’
plotNormMethods: no visible global function definition for ‘par’
plotNormMethods: no visible global function definition for ‘boxplot’
plotNormMethods: no visible global function definition for ‘dev.off’
plotNormMethods: no visible global function definition for ‘tiff’
printFeatures: no visible global function definition for ‘write.table’
pvaluePlot: no visible global function definition for ‘t.test’
pvaluePlot: no visible global function definition for ‘p.adjust’
pvaluePlot: no visible global function definition for ‘plot’
pvaluePlot: no visible global function definition for ‘abline’
pvaluePlot: no visible global function definition for ‘legend’
pvaluePlot: no visible global function definition for ‘tiff’
pvaluePlot: no visible global function definition for ‘dev.off’
rj.rfe: no visible global function definition for ‘write.table’
rj.rfe: no visible global function definition for ‘read.table’
selectFeatures.ensemble: no visible global function definition for
‘write.table’
selectFeatures.frequency.cv: no visible global function definition for
‘write.table’
selectFeatures.frequency.cv: no visible global function definition for
‘read.table’
selectFeatures.frequency.cv: no visible global function definition for
‘tiff’
selectFeatures.frequency.cv: no visible global function definition for
‘title’
selectFeatures.frequency.cv: no visible global function definition for
‘dev.off’
selectFeatures.frequency.cv: no visible global function definition for
‘na.omit’
svm.rfe: no visible global function definition for ‘predict’
tTest: no visible global function definition for ‘t.test’
tTestFS: no visible global function definition for ‘t.test’
volcanoPlot: no visible global function definition for ‘t.test’
volcanoPlot: no visible global function definition for ‘plot’
volcanoPlot: no visible global function definition for ‘tiff’
volcanoPlot: no visible global function definition for ‘dev.off’
volcanoPlot: no visible global function definition for ‘points’
volcanoPlot: no visible global function definition for ‘abline’
Undefined global functions or variables:
abline as.dist axis box boxplot combn cor dev.off hclust heatmap
legend lines lowess median na.exclude na.omit oneway.test p.adjust
par plot png points predict read.table rnorm sd t.test tiff title
write.table
Consider adding
importFrom("grDevices", "dev.off", "png", "tiff")
importFrom("graphics", "abline", "axis", "box", "boxplot", "legend",
"lines", "par", "plot", "points", "title")
importFrom("stats", "as.dist", "cor", "hclust", "heatmap", "lowess",
"median", "na.exclude", "na.omit", "oneway.test",
"p.adjust", "predict", "rnorm", "sd", "t.test")
importFrom("utils", "combn", "read.table", "write.table")
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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
batchFilter.anova 5.353 0.01 6.973
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’
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: 4 NOTEs
See
‘/home/biocbuild/bbs-3.9-bioc/meat/PAA.Rcheck/00check.log’
for details.
PAA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL PAA ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’ * installing *source* package ‘PAA’ ... ** using staged installation ** libs gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c PAA_init.c -o PAA_init.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c joinMCountResults.cpp -o joinMCountResults.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c mCount.cpp -o mCount.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c mMsMatrix.cpp -o mMsMatrix.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c sampling.cpp -o sampling.o g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o PAA.so PAA_init.o RcppExports.o joinMCountResults.o mCount.o mMsMatrix.o sampling.o -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-PAA/00new/PAA/libs ** R ** demo ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ‘PAA_vignette.Rnw’ ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (PAA)
PAA.Rcheck/tests/runTests.Rout
R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> BiocGenerics:::testPackage("PAA")
Found2batches
Adjusting for1covariate(s) or covariate level(s)
Standardizing Data across genes
Fitting L/S model and finding priors
Finding parametric adjustments
Adjusting the Data
batchFilter - number of features to discard: 0
Read /home/biocbuild/bbs-3.9-bioc/R/library/PAA/extdata/dummy_GSM734833_PA41992_-_AD1.gpr
Read /home/biocbuild/bbs-3.9-bioc/R/library/PAA/extdata/dummy_GSM734834_PA41994_-_AD2.gpr
Read /home/biocbuild/bbs-3.9-bioc/R/library/PAA/extdata/dummy_GSM734835_PA42006_-AD3.gpr
Read /home/biocbuild/bbs-3.9-bioc/R/library/PAA/extdata/dummy_GSM734836_PA42005_-_AD4.gpr
Read /home/biocbuild/bbs-3.9-bioc/R/library/PAA/extdata/dummy_GSM734837_PA41957_-_AD5.gpr
Read /home/biocbuild/bbs-3.9-bioc/R/library/PAA/extdata/dummy_GSM735203_PA42023_-_CO13.gpr
Read /home/biocbuild/bbs-3.9-bioc/R/library/PAA/extdata/dummy_GSM735204_PA42025_-_CO14.gpr
Read /home/biocbuild/bbs-3.9-bioc/R/library/PAA/extdata/dummy_GSM735205_PA42026_-_CO15.gpr
Read /home/biocbuild/bbs-3.9-bioc/R/library/PAA/extdata/dummy_GSM735206_PA42028_-_CO16.gpr
Read /home/biocbuild/bbs-3.9-bioc/R/library/PAA/extdata/dummy_GSM735207_PA42029_-_CO17.gpr
No aggregation performed.
RUNIT TEST PROTOCOL -- Tue Apr 9 02:34:51 2019
***********************************************
Number of test functions: 6
Number of errors: 0
Number of failures: 0
1 Test Suite :
PAA RUnit Tests - 6 test functions, 0 errors, 0 failures
Number of test functions: 6
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
7.992 0.349 11.104
PAA.Rcheck/PAA-Ex.timings
| name | user | system | elapsed | |
| batchAdjust | 0.352 | 0.116 | 0.481 | |
| batchFilter | 1.309 | 0.043 | 1.770 | |
| batchFilter.anova | 5.353 | 0.010 | 6.973 | |
| diffAnalysis | 2.278 | 0.124 | 3.098 | |
| loadGPR | 0.141 | 0.012 | 0.317 | |
| mMsMatrix | 0 | 0 | 0 | |
| normalizeArrays | 0.306 | 0.004 | 0.635 | |
| plotArray | 0.545 | 0.008 | 0.796 | |
| plotFeatures | 0.540 | 0.008 | 0.549 | |
| plotFeaturesHeatmap.2 | 0.554 | 0.004 | 0.637 | |
| plotFeaturesHeatmap | 0.345 | 0.008 | 0.353 | |
| plotMAPlots | 1.328 | 0.028 | 1.356 | |
| plotNormMethods | 0.579 | 0.008 | 0.587 | |
| preselect | 1.105 | 0.032 | 1.137 | |
| printFeatures | 0.488 | 0.012 | 0.500 | |
| pvaluePlot | 0.936 | 0.008 | 0.947 | |
| selectFeatures | 1.629 | 0.008 | 1.638 | |
| shuffleData | 0.211 | 0.012 | 0.224 | |
| volcanoPlot | 1.775 | 0.004 | 2.144 | |