Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-24 11:44 -0500 (Tue, 24 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
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 380/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
CNAnorm 1.53.0 (landing page) Stefano Berri
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the CNAnorm package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CNAnorm.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. |
Package: CNAnorm |
Version: 1.53.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CNAnorm.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CNAnorm_1.53.0.tar.gz |
StartedAt: 2024-12-23 18:39:55 -0500 (Mon, 23 Dec 2024) |
EndedAt: 2024-12-23 18:40:19 -0500 (Mon, 23 Dec 2024) |
EllapsedTime: 23.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: CNAnorm.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CNAnorm.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CNAnorm_1.53.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/CNAnorm.Rcheck’ * using R Under development (unstable) (2024-11-20 r87352) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘CNAnorm/DESCRIPTION’ ... OK * this is package ‘CNAnorm’ version ‘1.53.0’ * 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 ‘CNAnorm’ can be installed ... OK * used Fortran compiler: ‘GNU Fortran (GCC) 12.2.0’ * used SDK: ‘MacOSX11.3.sdk’ * 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 code 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 .OTquantileWeights: no visible global function definition for ‘median’ .OTquantileWeights: no visible global function definition for ‘quantile’ .TTquantileWeights: no visible global function definition for ‘median’ .TTquantileWeights: no visible global function definition for ‘quantile’ .exportTable: no visible global function definition for ‘write.table’ .gaussianWeights: no visible global function definition for ‘median’ .gaussianWeights: no visible global function definition for ‘sd’ .guessPeaksAndPloidy: no visible global function definition for ‘density’ .guessPeaksAndPloidy: no visible global function definition for ‘median’ .peakPloidy: no visible global function definition for ‘median’ .plotGenome: no visible global function definition for ‘text’ .plotGenome: no visible global function definition for ‘par’ .plotGenome: no visible global function definition for ‘points’ .plotGenome: no visible global function definition for ‘axis’ .plotGenome: no visible global function definition for ‘axTicks’ .plotGenome: no visible global function definition for ‘title’ .plotGenome: no visible global function definition for ‘mtext’ .plotGenome: no visible global function definition for ‘abline’ .plotGenome: no visible global function definition for ‘data’ .plotGenome: no visible global function definition for ‘lines’ .plotPeaks: no visible global function definition for ‘density’ .plotPeaks: no visible global function definition for ‘median’ .plotPeaks: no visible global function definition for ‘lines’ .plotPeaks: no visible global function definition for ‘abline’ .plotPeaks: no visible global function definition for ‘text’ .plotPeaks: no visible global function definition for ‘legend’ .plotPeaks_old: no visible global function definition for ‘median’ .plotPeaks_old: no visible global function definition for ‘lines’ .plotPeaks_old: no visible global function definition for ‘abline’ .plotPeaks_old: no visible global function definition for ‘text’ .plotPeaks_old: no visible global function definition for ‘legend’ Rcheck: no visible global function definition for ‘lm’ bandseg: no visible global function definition for ‘filter’ brute.seg: no visible global function definition for ‘median’ findOutliers: no visible global function definition for ‘median’ findOutliers: no visible global function definition for ‘density’ gcNormalize: no visible global function definition for ‘loess’ gcNormalize: no visible global function definition for ‘predict’ gcNormalize: no visible global function definition for ‘median’ get.initial.values: no visible global function definition for ‘var’ get.initial.values: no visible global function definition for ‘quantile’ getMQR: no visible global function definition for ‘lm’ global.norm: no visible global function definition for ‘lm’ global.norm: no visible global function definition for ‘predict’ medianWinSize: no visible global function definition for ‘median’ myDensity: no visible global function definition for ‘median’ myDensity: no visible global function definition for ‘sd’ myDensity: no visible global function definition for ‘density’ myPeaks: no visible global function definition for ‘embed’ pdetect: no visible global function definition for ‘rnorm’ pdetect: no visible global function definition for ‘density’ pdetect: no visible global function definition for ‘var’ pdetect: no visible global function definition for ‘quantile’ pdetect: no visible global function definition for ‘dnorm’ pdetect: no visible global function definition for ‘median’ pdetect.iter: no visible global function definition for ‘var’ pdetect.iter: no visible global function definition for ‘dnorm’ pdetect.iter: no visible global function definition for ‘median’ plotPeaksMixture: no visible global function definition for ‘median’ plotPeaksMixture: no visible global function definition for ‘hist’ plotPeaksMixture: no visible global function definition for ‘abline’ rseg: no visible global function definition for ‘median’ smoothseg: no visible global function definition for ‘lines’ exportTable,CNAnorm: no visible global function definition for ‘write.table’ peakPloidy,CNAnorm: no visible global function definition for ‘median’ plotGenome,CNAnorm: no visible global function definition for ‘text’ plotGenome,CNAnorm: no visible global function definition for ‘par’ plotGenome,CNAnorm: no visible global function definition for ‘points’ plotGenome,CNAnorm: no visible global function definition for ‘axis’ plotGenome,CNAnorm: no visible global function definition for ‘axTicks’ plotGenome,CNAnorm: no visible global function definition for ‘title’ plotGenome,CNAnorm: no visible global function definition for ‘mtext’ plotGenome,CNAnorm: no visible global function definition for ‘abline’ plotGenome,CNAnorm: no visible global function definition for ‘data’ plotGenome,CNAnorm: no visible global function definition for ‘lines’ plotPeaks,CNAnorm: no visible global function definition for ‘density’ plotPeaks,CNAnorm: no visible global function definition for ‘median’ plotPeaks,CNAnorm: no visible global function definition for ‘lines’ plotPeaks,CNAnorm: no visible global function definition for ‘abline’ plotPeaks,CNAnorm: no visible global function definition for ‘text’ plotPeaks,CNAnorm: no visible global function definition for ‘legend’ Undefined global functions or variables: abline axTicks axis data density dnorm embed filter hist legend lines lm loess median mtext par points predict quantile rnorm sd text title var write.table Consider adding importFrom("graphics", "abline", "axTicks", "axis", "hist", "legend", "lines", "mtext", "par", "points", "text", "title") importFrom("stats", "density", "dnorm", "embed", "filter", "lm", "loess", "median", "predict", "quantile", "rnorm", "sd", "var") importFrom("utils", "data", "write.table") to your NAMESPACE file. * checking Rd files ... NOTE checkRd: (-1) peakPloidy.Rd:67-68: Lost braces 67 | \bold{peakRatio}{Threshold used to call a peak. Peaks smaller than | ^ checkRd: (-1) peakPloidy.Rd:70-73: Lost braces 70 | \bold{spacingTolerance}{A parameter smaller than 1 which describes how | ^ checkRd: (-1) peakPloidy.Rd:75-76: Lost braces 75 | \bold{interceptRatio}{Minimum value for the intercept of the linear model. | ^ * 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 line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking usage of KIND in Fortran files ... OK * 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 ... 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 ‘/Users/biocbuild/bbs-3.21-bioc/meat/CNAnorm.Rcheck/00check.log’ for details.
CNAnorm.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CNAnorm ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘CNAnorm’ ... ** using staged installation ** libs using Fortran compiler: ‘GNU Fortran (GCC) 12.2.0’ using SDK: ‘MacOSX11.3.sdk’ /opt/gfortran/bin/gfortran -arch arm64 -fPIC -Wall -g -O2 -c daxpy.f -o daxpy.o /opt/gfortran/bin/gfortran -arch arm64 -fPIC -Wall -g -O2 -c ddot.f -o ddot.o /opt/gfortran/bin/gfortran -arch arm64 -fPIC -Wall -g -O2 -c dgbfa.f -o dgbfa.o /opt/gfortran/bin/gfortran -arch arm64 -fPIC -Wall -g -O2 -c dgbsl.f -o dgbsl.o /opt/gfortran/bin/gfortran -arch arm64 -fPIC -Wall -g -O2 -c dscal.f -o dscal.o /opt/gfortran/bin/gfortran -arch arm64 -fPIC -Wall -g -O2 -c dsmooth.f -o dsmooth.o f951: Warning: Nonconforming tab character in column 1 of line 14 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 15 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 16 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 17 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 18 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 19 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 20 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 21 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 22 [-Wtabs] f951: Warning: Nonconforming tab character in column 3 of line 23 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 24 [-Wtabs] f951: 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of line 94 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 95 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 96 [-Wtabs] dsmooth.f:62:21: 62 | do 10 i=1,n-1 | 1 Warning: Nonconforming tab character at (1) [-Wtabs] dsmooth.f:70:8: 70 | & diff(i-1)*diff(i+1) .lt. 0.) isplit(i)=1 | 1 Warning: Nonconforming tab character at (1) [-Wtabs] dsmooth.f:50:6: 50 | function amed3(a,b,c) | ^ Warning: ‘__result_amed3’ may be used uninitialized [-Wmaybe-uninitialized] /opt/gfortran/bin/gfortran -arch arm64 -fPIC -Wall -g -O2 -c idamax.f -o idamax.o clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o CNAnorm.so daxpy.o ddot.o dgbfa.o dgbsl.o dscal.o dsmooth.o idamax.o -L/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lemutls_w -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/00LOCK-CNAnorm/00new/CNAnorm/libs ** 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 ** 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 (CNAnorm)
CNAnorm.Rcheck/CNAnorm-Ex.timings
name | user | system | elapsed | |
CNAnorm-class | 0.006 | 0.002 | 0.012 | |
DerivData-class | 0.001 | 0.001 | 0.002 | |
InData-class | 0.001 | 0.001 | 0.001 | |
Params-class | 0.001 | 0.000 | 0.001 | |
addDNACopy-methods | 0.488 | 0.003 | 0.493 | |
addSmooth-methods | 0.331 | 0.005 | 0.341 | |
chrsAndpos-methods | 0.013 | 0.004 | 0.019 | |
dataFrame2object | 0.001 | 0.001 | 0.002 | |
discreteNorm-methods | 0.005 | 0.001 | 0.006 | |
exportTable-method | 0.036 | 0.003 | 0.041 | |
gcNorm-methods | 0.312 | 0.002 | 0.323 | |
peakPloidy | 3.758 | 0.393 | 4.395 | |
plotGenome-methods | 0.542 | 0.006 | 0.553 | |
plotPeaks-methods | 0.090 | 0.002 | 0.094 | |
ratio-methods | 0.267 | 0.001 | 0.286 | |
suggValid-methods | 0.005 | 0.001 | 0.006 | |
validation-methods | 0.003 | 0.001 | 0.003 | |
workflowWrapper | 0.499 | 0.006 | 0.514 | |