AneuFinder 1.4.0
Aaron Taudt
| Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017) | | URL: https://git.bioconductor.org/packages/AneuFinder | | Branch: RELEASE_3_5 | | Last Commit: e5bdf4d | | Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings AneuFinder_1.4.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/AneuFinder.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-pc-linux-gnu (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 ‘1.4.0’
* 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 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 41.576 7.536 49.167
heatmapAneuploidies 38.572 0.036 38.647
correctGC 24.620 7.596 41.399
plotHeterogeneity 25.296 0.048 25.373
getSCEcoordinates 22.244 0.040 23.453
karyotypeMeasures 17.780 0.020 17.812
heatmapGenomewide 15.848 0.040 15.953
findCNVs.strandseq 15.516 0.008 17.026
heatmapGenomewideClusters 10.280 0.012 10.296
findCNVs 8.448 0.264 9.883
consensusSegments 7.036 0.004 7.049
subsetByCNVprofile 5.544 0.000 5.547
binReads 5.332 0.040 6.487
variableWidthBins 5.320 0.016 6.627
collapseBins 4.572 0.008 5.789
bed2GRanges 4.060 0.020 5.875
* 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
‘/home/biocbuild/bbs-3.5-bioc/meat/AneuFinder.Rcheck/00check.log’
for details.
* installing *source* package ‘AneuFinder’ ...
** libs
g++ -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c R_interface.cpp -o R_interface.o
g++ -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c densities.cpp -o densities.o
g++ -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c init.cpp -o init.o
g++ -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c loghmm.cpp -o loghmm.o
loghmm.cpp:320:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for
^
loghmm.cpp:480:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for
^
loghmm.cpp:518:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for
^
loghmm.cpp:583:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for
^
g++ -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c scalehmm.cpp -o scalehmm.o
scalehmm.cpp:384:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for
^
scalehmm.cpp:400:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for
^
scalehmm.cpp:694:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for
^
scalehmm.cpp:732:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for
^
scalehmm.cpp:791:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for
^
g++ -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c utility.cpp -o utility.o
g++ -shared -L/home/biocbuild/bbs-3.5-bioc/R/lib -L/usr/local/lib -o AneuFinder.so R_interface.o densities.o init.o loghmm.o scalehmm.o utility.o -L/home/biocbuild/bbs-3.5-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.5-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)