AneuFinder 1.5.0
Aaron Taudt
| Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/AneuFinder | | Last Changed Rev: 129129 / Revision: 131943 | | Last Changed Date: 2017-04-24 15:50:57 -0400 (Mon, 24 Apr 2017) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | ERROR | skipped | | |
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK |  |
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | [ OK ] | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings AneuFinder_1.5.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/AneuFinder.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AneuFinder/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AneuFinder’ version ‘1.5.0’
* 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 ‘AneuFinder’ 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 loading without being on the library search path ... 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
Aneufinder: multiple local function definitions for ‘parallel.helper’
with different formal arguments
* 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 compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* 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
simulateReads 69.889 5.664 77.840
correctGC 47.317 2.978 53.142
heatmapAneuploidies 40.037 0.095 41.191
plotHeterogeneity 28.451 0.156 29.454
getSCEcoordinates 21.775 0.616 23.839
karyotypeMeasures 20.466 0.132 21.182
heatmapGenomewide 15.927 0.183 16.561
findCNVs.strandseq 14.173 0.483 15.868
heatmapGenomewideClusters 11.560 0.042 11.862
findCNVs 7.489 0.506 9.157
consensusSegments 7.029 0.031 7.242
subsetByCNVprofile 6.441 0.042 6.679
variableWidthBins 5.799 0.476 7.539
binReads 5.365 0.227 6.746
collapseBins 4.668 0.229 5.954
bed2GRanges 3.796 0.073 6.051
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.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: 1 NOTE
See
‘/Users/biocbuild/bbs-3.6-bioc/meat/AneuFinder.Rcheck/00check.log’
for details.
* installing *source* package ‘AneuFinder’ ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c R_interface.cpp -o R_interface.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c densities.cpp -o densities.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c init.cpp -o init.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c loghmm.cpp -o loghmm.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c scalehmm.cpp -o scalehmm.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c utility.cpp -o utility.o
clang++ -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 AneuFinder.so R_interface.o densities.o init.o loghmm.o scalehmm.o utility.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.6-bioc/meat/AneuFinder.Rcheck/AneuFinder/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (AneuFinder)