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BioC 3.6: CHECK report for cydar on malbec1

This page was generated on 2017-08-16 13:25:35 -0400 (Wed, 16 Aug 2017).

Package 311/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cydar 1.1.1
Aaron Lun
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/cydar
Last Changed Rev: 129832 / Revision: 131943
Last Changed Date: 2017-05-24 13:14:09 -0400 (Wed, 24 May 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: cydar
Version: 1.1.1
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings cydar_1.1.1.tar.gz
StartedAt: 2017-08-15 22:24:21 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 22:28:56 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 274.7 seconds
RetCode: 0
Status:  OK 
CheckDir: cydar.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings cydar_1.1.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/cydar.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cydar/DESCRIPTION’ ... OK
* this is package ‘cydar’ version ‘1.1.1’
* 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 ‘cydar’ 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 ... NOTE
Unexported objects imported by ':::' calls:
  ‘S4Vectors:::selectSome’
  ‘SummarizedExperiment:::.SummarizedExperiment.charbound’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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
diffIntDistr   10.684  0.156  10.847
normalizeBatch  5.344  0.024   5.370
* 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-3.6-bioc/meat/cydar.Rcheck/00check.log’
for details.


cydar.Rcheck/00install.out:

* installing *source* package ‘cydar’ ...
** libs
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -c compute_density.cpp -o compute_density.o
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -c compute_hyperstats.cpp -o compute_hyperstats.o
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -c compute_median_int.cpp -o compute_median_int.o
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -c count_cells.cpp -o count_cells.o
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -c drop_redundant.cpp -o drop_redundant.o
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -c find_knn.cpp -o find_knn.o
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -c get_nndist.cpp -o get_nndist.o
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -c init.cpp -o init.o
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -c matrix_info.cpp -o matrix_info.o
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -c objects.cpp -o objects.o
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -c pack_indices.cpp -o pack_indices.o
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -c recount.cpp -o recount.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.6-bioc/R/lib -L/usr/local/lib -o cydar.so compute_density.o compute_hyperstats.o compute_median_int.o count_cells.o drop_redundant.o find_knn.o get_nndist.o init.o matrix_info.o objects.o pack_indices.o recount.o -L/home/biocbuild/bbs-3.6-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.6-bioc/meat/cydar.Rcheck/cydar/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 (cydar)

cydar.Rcheck/cydar-Ex.timings:

nameusersystemelapsed
countCells2.4760.0082.488
cyData-class0.1240.0000.123
cyData-getset0.0920.0040.095
cyData-subset0.3760.0360.410
diffIntDistr10.684 0.15610.847
dnaGate1.0200.0001.044
expandRadius1.2000.0001.202
findFirstSphere0.0880.0040.094
intensityRanges1.2400.0001.342
interpretSpheres2.5040.0082.513
labelSpheres0.0240.0000.023
medIntensities1.3600.0001.358
multiIntHist0.0080.0000.007
neighborDistances1.2680.0001.268
normalizeBatch5.3440.0245.370
outlierGate0.8560.0000.856
packIndices0.0000.0000.001
pickBestMarkers1.1080.0001.141
plotCells0.1880.0040.194
poolCells0.8200.0000.821
prepareCellData1.1200.0001.117
recountCells1.5880.0041.592
spatialFDR0.0720.0000.070