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This page was generated on 2023-10-16 11:36:26 -0400 (Mon, 16 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4626
palomino3Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4379
merida1macOS 12.6.4 Montereyx86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4395
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1455/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PAA 1.34.0  (landing page)
Michael Turewicz , Martin Eisenacher
Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/PAA
git_branch: RELEASE_3_17
git_last_commit: 96ceada
git_last_commit_date: 2023-04-25 10:35:23 -0400 (Tue, 25 Apr 2023)
nebbiolo1Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.6.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson2macOS 12.6.1 Monterey / arm64see weekly results here

CHECK results for PAA on palomino3


To the developers/maintainers of the PAA package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/PAA.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: PAA
Version: 1.34.0
Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:PAA.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings PAA_1.34.0.tar.gz
StartedAt: 2023-10-16 05:03:28 -0400 (Mon, 16 Oct 2023)
EndedAt: 2023-10-16 05:07:07 -0400 (Mon, 16 Oct 2023)
EllapsedTime: 218.8 seconds
RetCode: 0
Status:   OK  
CheckDir: PAA.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:PAA.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings PAA_1.34.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.17-bioc/meat/PAA.Rcheck'
* using R version 4.3.1 (2023-06-16 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.2.0
    GNU Fortran (GCC) 12.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'PAA/DESCRIPTION' ... OK
* this is package 'PAA' version '1.34.0'
* 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 'PAA' can be installed ... OK
* used C compiler: 'gcc.exe (GCC) 12.2.0'
* used C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
* checking installed package size ... OK
* 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 '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 '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 '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 '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 '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 '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 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", "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 use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'F:/biocbuild/bbs-3.17-bioc/R/library/PAA/libs/x64/PAA.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
* 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: 3 NOTEs
See
  'F:/biocbuild/bbs-3.17-bioc/meat/PAA.Rcheck/00check.log'
for details.

Installation output

PAA.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL PAA
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library'
* installing *source* package 'PAA' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 12.2.0'
using C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c PAA_init.c -o PAA_init.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c joinMCountResults.cpp -o joinMCountResults.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c mCount.cpp -o mCount.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c mMsMatrix.cpp -o mMsMatrix.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c sampling.cpp -o sampling.o
g++ -std=gnu++17 -shared -s -static-libgcc -o PAA.dll tmp.def PAA_init.o RcppExports.o joinMCountResults.o mCount.o mMsMatrix.o sampling.o -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.17-bioc/R/library/00LOCK-PAA/00new/PAA/libs/x64
** R
** demo
** 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 (PAA)

Tests output

PAA.Rcheck/tests/runTests.Rout


R version 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 F:/biocbuild/bbs-3.17-bioc/R/library/PAA/extdata/dummy_GSM734833_PA41992_-_AD1.gpr 
Read F:/biocbuild/bbs-3.17-bioc/R/library/PAA/extdata/dummy_GSM734834_PA41994_-_AD2.gpr 
Read F:/biocbuild/bbs-3.17-bioc/R/library/PAA/extdata/dummy_GSM734835_PA42006_-AD3.gpr 
Read F:/biocbuild/bbs-3.17-bioc/R/library/PAA/extdata/dummy_GSM734836_PA42005_-_AD4.gpr 
Read F:/biocbuild/bbs-3.17-bioc/R/library/PAA/extdata/dummy_GSM734837_PA41957_-_AD5.gpr 
Read F:/biocbuild/bbs-3.17-bioc/R/library/PAA/extdata/dummy_GSM735203_PA42023_-_CO13.gpr 
Read F:/biocbuild/bbs-3.17-bioc/R/library/PAA/extdata/dummy_GSM735204_PA42025_-_CO14.gpr 
Read F:/biocbuild/bbs-3.17-bioc/R/library/PAA/extdata/dummy_GSM735205_PA42026_-_CO15.gpr 
Read F:/biocbuild/bbs-3.17-bioc/R/library/PAA/extdata/dummy_GSM735206_PA42028_-_CO16.gpr 
Read F:/biocbuild/bbs-3.17-bioc/R/library/PAA/extdata/dummy_GSM735207_PA42029_-_CO17.gpr 
No aggregation performed.


RUNIT TEST PROTOCOL -- Mon Oct 16 05:06:59 2023 
*********************************************** 
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 
   8.21    0.65    8.84

Example timings

PAA.Rcheck/PAA-Ex.timings

nameusersystemelapsed
batchAdjust1.270.033.12
batchFilter0.670.040.72
batchFilter.anova2.490.102.57
diffAnalysis1.090.061.16
loadGPR0.060.020.09
mMsMatrix000
normalizeArrays0.180.000.18
plotArray0.310.000.61
plotFeatures0.280.010.29
plotFeaturesHeatmap.20.250.020.27
plotFeaturesHeatmap0.230.000.23
plotMAPlots0.820.080.89
plotNormMethods0.480.010.50
preselect0.670.050.72
printFeatures0.250.010.27
pvaluePlot0.580.020.59
selectFeatures1.670.001.67
shuffleData0.170.000.18
volcanoPlot0.990.021.00