Stefano Berri
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/CNAnorm |
| git_branch: RELEASE_3_13 |
| git_last_commit: fd0b875 |
| git_last_commit_date: 2021-05-19 11:50:07 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:32 -0400 (Fri, 15 Oct 2021).
|
To the developers/maintainers of the CNAnorm package: - Please 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 How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 341/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CNAnorm 1.38.0 (landing page) Stefano Berri
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: CNAnorm |
| Version: 1.38.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CNAnorm.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CNAnorm_1.38.0.tar.gz |
| StartedAt: 2021-10-14 17:34:07 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 17:35:23 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 75.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CNAnorm.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CNAnorm.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CNAnorm_1.38.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/CNAnorm.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CNAnorm/DESCRIPTION’ ... OK
* this is package ‘CNAnorm’ version ‘1.38.0’
* 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 ... NOTE
Found the following hidden files and directories:
.git_fetch_output.txt
.git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘CNAnorm’ 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
* 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 ... 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 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
peakPloidy 20.427 0.699 21.143
* 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
‘/Users/biocbuild/bbs-3.13-bioc/meat/CNAnorm.Rcheck/00check.log’
for details.
CNAnorm.Rcheck/00install.out
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL CNAnorm
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘CNAnorm’ ...
** using staged installation
** libs
gfortran -mmacosx-version-min=10.13 -fno-optimize-sibling-calls -fPIC -Wall -g -O2 -c daxpy.f -o daxpy.o
gfortran -mmacosx-version-min=10.13 -fno-optimize-sibling-calls -fPIC -Wall -g -O2 -c ddot.f -o ddot.o
gfortran -mmacosx-version-min=10.13 -fno-optimize-sibling-calls -fPIC -Wall -g -O2 -c dgbfa.f -o dgbfa.o
gfortran -mmacosx-version-min=10.13 -fno-optimize-sibling-calls -fPIC -Wall -g -O2 -c dgbsl.f -o dgbsl.o
gfortran -mmacosx-version-min=10.13 -fno-optimize-sibling-calls -fPIC -Wall -g -O2 -c dscal.f -o dscal.o
gfortran -mmacosx-version-min=10.13 -fno-optimize-sibling-calls -fPIC -Wall -g -O2 -c dsmooth.f -o dsmooth.o
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dsmooth.f:62:20:
do 10 i=1,n-1
1
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dsmooth.f:70:7:
& diff(i-1)*diff(i+1) .lt. 0.) isplit(i)=1
1
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dsmooth.f:50:0:
function amed3(a,b,c)
Warning: ‘__result_amed3’ may be used uninitialized in this function [-Wmaybe-uninitialized]
gfortran -mmacosx-version-min=10.13 -fno-optimize-sibling-calls -fPIC -Wall -g -O2 -c idamax.f -o idamax.o
clang -mmacosx-version-min=10.13 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o CNAnorm.so daxpy.o ddot.o dgbfa.o dgbsl.o dscal.o dsmooth.o idamax.o -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.1/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 | 0.022 | 0.004 | 0.026 | |
| DerivData-class | 0.004 | 0.002 | 0.007 | |
| InData-class | 0.004 | 0.002 | 0.006 | |
| Params-class | 0.004 | 0.002 | 0.005 | |
| addDNACopy-methods | 0.954 | 0.013 | 0.969 | |
| addSmooth-methods | 0.545 | 0.015 | 0.561 | |
| chrsAndpos-methods | 0.043 | 0.010 | 0.053 | |
| dataFrame2object | 0.005 | 0.002 | 0.006 | |
| discreteNorm-methods | 0.020 | 0.003 | 0.022 | |
| exportTable-method | 0.130 | 0.005 | 0.177 | |
| gcNorm-methods | 0.461 | 0.003 | 0.465 | |
| peakPloidy | 20.427 | 0.699 | 21.143 | |
| plotGenome-methods | 1.217 | 0.019 | 1.237 | |
| plotPeaks-methods | 0.236 | 0.005 | 0.241 | |
| ratio-methods | 0.488 | 0.005 | 0.494 | |
| suggValid-methods | 0.016 | 0.002 | 0.017 | |
| validation-methods | 0.011 | 0.001 | 0.012 | |
| workflowWrapper | 1.201 | 0.011 | 1.213 | |