Back to Mac ARM64 build report for BioC 3.17
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This page was generated on 2023-10-20 09:38:10 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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 1723/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Ringo 1.64.0  (landing page)
J. Toedling
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/Ringo
git_branch: RELEASE_3_17
git_last_commit: 3553a20
git_last_commit_date: 2023-04-25 09:45:07 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for Ringo on kjohnson2


To the developers/maintainers of the Ringo package:
- 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: Ringo
Version: 1.64.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Ringo.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Ringo_1.64.0.tar.gz
StartedAt: 2023-10-18 19:23:24 -0400 (Wed, 18 Oct 2023)
EndedAt: 2023-10-18 19:28:28 -0400 (Wed, 18 Oct 2023)
EllapsedTime: 303.5 seconds
RetCode: 0
Status:   OK  
CheckDir: Ringo.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Ringo.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Ringo_1.64.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/Ringo.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Ringo/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Ringo’ version ‘1.64.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'Biobase', 'RColorBrewer', 'limma', 'Matrix', 'grid', 'lattice'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘Ringo’ can be installed ... OK
* used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘limma’
A package should be listed in only one of these fields.
* 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 startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to ‘grid’ which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  ‘mclust’ ‘rtracklayer’ ‘topGO’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespace in Imports field not imported from: ‘limma’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘Biobase’ ‘Matrix’ ‘RColorBrewer’ ‘grid’ ‘lattice’ ‘limma’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘clusters’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.onAttach: no visible global function definition for ‘addVigs2WinMenu’
asExprSet: no visible global function definition for ‘featureNames<-’
asExprSet: no visible global function definition for ‘featureData<-’
autocor: no visible global function definition for ‘featureNames’
autocor: no visible global function definition for ‘exprs’
autocor : <anonymous>: no visible global function definition for
  ‘matchpt’
autocor: no visible global function definition for ‘cor’
chersToBED: no visible global function definition for ‘write.table’
chipAlongChrom: no visible global function definition for
  ‘featureNames’
chipAlongChrom: no visible global function definition for ‘exprs’
chipAlongChrom: no visible global function definition for ‘brewer.pal’
chipAlongChrom: no visible global function definition for
  ‘pushViewport’
chipAlongChrom: no visible global function definition for ‘viewport’
chipAlongChrom: no visible global function definition for ‘grid.layout’
chipAlongChrom: no visible global function definition for
  ‘dataViewport’
chipAlongChrom: no visible global function definition for ‘grid.yaxis’
chipAlongChrom: no visible global function definition for ‘gpar’
chipAlongChrom: no visible global function definition for ‘grid.text’
chipAlongChrom: no visible global function definition for ‘unit’
chipAlongChrom: no visible global function definition for ‘draw.key’
chipAlongChrom: no visible global function definition for ‘sampleNames’
chipAlongChrom: no visible global function definition for ‘strwidth’
chipAlongChrom: no visible global function definition for ‘strheight’
chipAlongChrom: no visible global function definition for ‘popViewport’
chipAlongChrom: no visible global function definition for ‘grid.lines’
chipAlongChrom: no visible global function definition for
  ‘grid.segments’
chipAlongChrom: no visible global function definition for ‘arrow’
chipAlongChrom1: no visible global function definition for
  ‘featureNames’
chipAlongChrom1: no visible global function definition for ‘exprs’
chipAlongChrom1: no visible global function definition for ‘colors’
chipAlongChrom1: no visible global function definition for ‘brewer.pal’
chipAlongChrom1: no visible global function definition for ‘axis’
chipAlongChrom1: no visible global function definition for ‘mtext’
chipAlongChrom1: no visible global function definition for ‘abline’
chipAlongChrom1: no visible global function definition for ‘lines’
chipAlongChrom1: no visible global function definition for ‘points’
chipAlongChrom1: no visible global function definition for ‘rug’
chipAlongChrom1: no visible global function definition for
  ‘sampleNames’
chipAlongChrom1: no visible global function definition for ‘legend’
compute.gc: no visible global function definition for ‘listLen’
computeRunningMedians: no visible global function definition for
  ‘varLabels’
computeRunningMedians: no visible global function definition for
  ‘pData’
computeRunningMedians: no visible global function definition for
  ‘sampleNames’
computeRunningMedians: no visible global function definition for
  ‘exprs’
computeRunningMedians: no visible global function definition for
  ‘featureNames’
computeRunningMedians: no visible global function definition for
  ‘phenoData’
computeRunningMedians: no visible global function definition for
  ‘featureNames<-’
computeRunningMedians: no visible global function definition for
  ‘featureData<-’
computeRunningMedians: no visible global function definition for
  ‘featureData’
computeRunningMedians: no visible global function definition for
  ‘sampleNames<-’
computeSlidingT: no visible global function definition for ‘exprs’
computeSlidingT: no visible global function definition for
  ‘featureNames’
computeSlidingT: no visible global function definition for
  ‘sampleNames’
computeSlidingT: no visible binding for global variable ‘median’
computeSlidingT: no visible global function definition for ‘median’
computeSlidingT: no visible global function definition for
  ‘featureNames<-’
computeSlidingT: no visible global function definition for
  ‘featureData<-’
computeSlidingT: no visible global function definition for
  ‘featureData’
computeSlidingT: no visible global function definition for
  ‘sampleNames<-’
corPlot: no visible global function definition for ‘exprs’
corPlot: no visible global function definition for ‘relevel’
corPlot: no visible global function definition for ‘pairs’
corPlot : <anonymous>: no visible global function definition for ‘par’
corPlot : <anonymous>: no visible global function definition for
  ‘abline’
exportCCData: no visible global function definition for ‘exprs’
exportCCData: no visible global function definition for ‘exprs<-’
exportCCData: no visible global function definition for
  ‘package.version’
exportCCData: no visible global function definition for ‘write.table’
exportCherList: no visible global function definition for ‘IRanges’
exportCherList: no visible global function definition for ‘GenomicData’
exportCherList: no visible global function definition for ‘export’
findChersOnSmoothed: no visible global function definition for ‘pData’
findChersOnSmoothed: no visible global function definition for
  ‘sampleNames’
findChersOnSmoothed: no visible global function definition for
  ‘featureNames’
findChersOnSmoothed : <anonymous>: no visible global function
  definition for ‘exprs’
ftr2xys: no visible global function definition for ‘read.delim’
ftr2xys: no visible global function definition for ‘write.table’
image.RGList: no visible global function definition for
  ‘colorRampPalette’
image.RGList: no visible global function definition for ‘brewer.pal’
image.RGList: no visible global function definition for ‘quantile’
image.RGList: no visible global function definition for ‘points’
merge.RGList: no visible global function definition for ‘makeUnique’
newVP: no visible global function definition for ‘pushViewport’
newVP: no visible global function definition for ‘viewport’
newVP: no visible global function definition for ‘grid.layout’
newVP: no visible global function definition for ‘grid.text’
newVP: no visible global function definition for ‘gpar’
newVP: no visible global function definition for ‘popViewport’
nimblegenScale : tukey.biweight: no visible global function definition
  for ‘median’
normalizeBetweenArraysVSN: no visible global function definition for
  ‘exprs’
oneChannelVSN: no visible global function definition for ‘predict’
pair2xys: no visible global function definition for ‘read.delim’
pair2xys: no visible global function definition for ‘write.table’
panel.cor: no visible global function definition for ‘par’
panel.cor: no visible global function definition for ‘cor’
panel.cor: no visible global function definition for ‘strwidth’
panel.cor: no visible global function definition for ‘text’
panel.scatter: no visible global function definition for ‘points’
panel.scatter: no visible global function definition for ‘abline’
plot.cher: no visible global function definition for ‘sampleNames’
plot.cher: no visible global function definition for ‘rug’
plot.cher: no visible global function definition for ‘legend’
plotAlongChromLegend : formatRow: no visible global function definition
  for ‘convertWidth’
plotAlongChromLegend : formatRow: no visible global function definition
  for ‘stringWidth’
plotAlongChromLegend : formatRow: no visible global function definition
  for ‘grid.rect’
plotAlongChromLegend : formatRow: no visible global function definition
  for ‘unit’
plotAlongChromLegend : formatRow: no visible binding for global
  variable ‘gpar’
plotAlongChromLegend : formatRow: no visible global function definition
  for ‘grid.text’
plotAlongChromLegend : formatRow: no visible global function definition
  for ‘gpar’
plotAlongChromLegend: no visible global function definition for
  ‘pushViewport’
plotAlongChromLegend: no visible global function definition for
  ‘viewport’
plotAlongChromLegend: no visible global function definition for
  ‘popViewport’
plotBM: no visible global function definition for ‘arrows’
plotBM: no visible global function definition for ‘axis’
plotFeatures: no visible global function definition for ‘pushViewport’
plotFeatures: no visible global function definition for ‘dataViewport’
plotFeatures: no visible global function definition for ‘grid.segments’
plotFeatures: no visible global function definition for ‘gpar’
plotFeatures: no visible global function definition for ‘listLen’
plotFeatures: no visible global function definition for ‘grid.rect’
plotFeatures: no visible global function definition for ‘convertWidth’
plotFeatures: no visible global function definition for ‘stringWidth’
plotFeatures: no visible global function definition for ‘grid.text’
plotFeatures: no visible global function definition for ‘popViewport’
plotOneChIPSample: no visible global function definition for ‘unit’
plotOneChIPSample: no visible global function definition for ‘quantile’
plotOneChIPSample: no visible global function definition for
  ‘pushViewport’
plotOneChIPSample: no visible global function definition for
  ‘dataViewport’
plotOneChIPSample: no visible global function definition for
  ‘grid.yaxis’
plotOneChIPSample: no visible global function definition for ‘gpar’
plotOneChIPSample: no visible global function definition for
  ‘grid.text’
plotOneChIPSample: no visible global function definition for
  ‘grid.lines’
plotOneChIPSample: no visible global function definition for
  ‘grid.polyline’
plotOneChIPSample: no visible global function definition for
  ‘grid.points’
plotOneChIPSample: no visible global function definition for
  ‘popViewport’
posToProbeAnno: no visible global function definition for ‘read.delim’
preprocess: no visible global function definition for
  ‘normalizeWithinArrays’
preprocess: no visible global function definition for
  ‘normalizeBetweenArrays’
quantilesOverPositions: no visible global function definition for
  ‘exprs’
quantilesOverPositions : <anonymous>: no visible global function
  definition for ‘approx’
quantilesOverPositions: no visible global function definition for
  ‘sampleNames’
quantilesOverPositions : <anonymous>: no visible binding for global
  variable ‘quantile’
quantilesOverPositions: no visible global function definition for
  ‘density’
quantilesOverPositions: no visible global function definition for
  ‘approx’
readNgIntensitiesTxt: no visible global function definition for
  ‘read.table’
readNgIntensitiesTxt: no visible global function definition for
  ‘removeExt’
readNimblegen: no visible global function definition for ‘readTargets’
readNimblegen: no visible global function definition for
  ‘readSpotTypes’
readNimblegen: no visible global function definition for
  ‘controlStatus’
sigGOTable: no visible global function definition for ‘mappedkeys’
sigGOTable: no visible binding for global variable ‘annFUN.gene2GO’
sigGOTable: no visible binding for global variable ‘annFUN.org’
sigGOTable: no visible global function definition for ‘runTest’
sigGOTable: no visible global function definition for ‘GenTable’
sigGOTable: no visible global function definition for ‘usedGO’
sigGOTable: no visible binding for global variable ‘p.value’
splitAndSimplify: no visible global function definition for ‘listLen’
takeMeanOverGroups: no visible global function definition for ‘pData’
takeMeanOverGroups: no visible global function definition for ‘exprs’
takeMeanOverGroups: no visible global function definition for
  ‘featureNames<-’
takeMeanOverGroups: no visible global function definition for
  ‘featureNames’
twoGaussiansNull: no visible binding for global variable
  ‘p.adjust.methods’
twoGaussiansNull: no visible global function definition for ‘Mclust’
twoGaussiansNull: no visible global function definition for ‘na.omit’
twoGaussiansNull: no visible global function definition for ‘pnorm’
upperBoundNull: no visible global function definition for ‘na.omit’
upperBoundNull: no visible global function definition for ‘quantile’
cbind2,ExpressionSet-ExpressionSet: no visible global function
  definition for ‘featureNames’
cbind2,ExpressionSet-ExpressionSet: no visible global function
  definition for ‘exprs’
cbind2,ExpressionSet-ExpressionSet: no visible global function
  definition for ‘sampleNames’
plot,cher-ExpressionSet: no visible global function definition for
  ‘sampleNames’
plot,qop-ANY: no visible global function definition for ‘axis’
plot,qop-ANY: no visible global function definition for ‘rainbow’
plot,qop-ANY: no visible global function definition for ‘lines’
plot,qop-ANY: no visible global function definition for ‘legend’
Undefined global functions or variables:
  GenTable GenomicData IRanges Mclust abline addVigs2WinMenu
  annFUN.gene2GO annFUN.org approx arrow arrows axis brewer.pal
  colorRampPalette colors controlStatus convertWidth cor dataViewport
  density draw.key export exprs exprs<- featureData featureData<-
  featureNames featureNames<- gpar grid.layout grid.lines grid.points
  grid.polyline grid.rect grid.segments grid.text grid.yaxis legend
  lines listLen makeUnique mappedkeys matchpt median mtext na.omit
  normalizeBetweenArrays normalizeWithinArrays p.adjust.methods p.value
  pData package.version pairs par phenoData pnorm points popViewport
  predict pushViewport quantile rainbow read.delim read.table
  readSpotTypes readTargets relevel removeExt rug runTest sampleNames
  sampleNames<- strheight stringWidth strwidth text unit usedGO
  varLabels viewport write.table
Consider adding
  importFrom("grDevices", "colorRampPalette", "colors", "rainbow")
  importFrom("graphics", "abline", "arrows", "axis", "legend", "lines",
             "mtext", "pairs", "par", "points", "rug", "strheight",
             "strwidth", "text")
  importFrom("stats", "approx", "cor", "density", "median", "na.omit",
             "p.adjust.methods", "pnorm", "predict", "quantile",
             "relevel")
  importFrom("utils", "read.delim", "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 for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... 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: 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/Ringo.Rcheck/00check.log’
for details.



Installation output

Ringo.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Ringo
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘Ringo’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c mmeansd.cpp -o mmeansd.o
mmeansd.cpp:29:24: warning: variable 'is' set but not used [-Wunused-but-set-variable]
    int * x, nval, hs, is, i;
                       ^
1 warning generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c mmedian.cpp -o mmedian.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c region_overlap.c -o region_overlap.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c ringo_init.c -o ringo_init.o
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o Ringo.so mmeansd.o mmedian.o region_overlap.o ringo_init.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/00LOCK-Ringo/00new/Ringo/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for ‘ls’ from package ‘base’ in package ‘Ringo’
** help
*** installing help indices
** building package indices
** installing vignettes
** 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 (Ringo)

Tests output


Example timings

Ringo.Rcheck/Ringo-Ex.timings

nameusersystemelapsed
arrayImage0.0890.0090.158
asExprSet0.1600.0080.296
autocorr0.1170.0080.201
cherByThreshold0.0080.0020.013
cherClass0.2050.0110.340
chipAlongChrom0.0870.0040.156
chipAlongChromOld0.0530.0050.097
computeRunningMedians0.1950.0130.370
compute_gc0.0010.0010.002
compute_sliding_t0.0500.0050.102
corrPlot0.0700.0040.134
exportCherList000
features2Probes0.1440.0090.274
findChersOnSmoothed0.0880.0030.152
ftr2xys000
newCER0.0010.0000.002
nonzero0.0120.0010.027
plotAutocorr0.0000.0000.001
plotBM0.0140.0030.026
posToProbeAnnoEnvironment0.0270.0030.047
preprocess0.1770.0060.287
probeAnnoClass0.0160.0020.031
qopS4000
quantilesOverPositions0.6580.0091.190
readNimblegen0.0710.0040.130
regionoverlap0.0040.0010.007
relateCERs0.0000.0000.003
sigGOTable0.0010.0010.000
sliding_meansd0.0020.0010.004
sliding_quantile0.0130.0030.023
twoGaussiansNull0.1420.0090.249
upperBoundNull0.0490.0020.081
validProbeAnno0.0170.0010.026