BioC 3.6: CHECK report for cydar on veracruz1

Package: cydar

Version: 1.1.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings cydar_1.1.1.tar.gz

StartedAt: 2017-08-16 01:53:38 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 01:58:48 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 309.7 seconds

RetCode: 0

Status:  OK

CheckDir: cydar.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings cydar_1.1.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/cydar.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 ‘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   11.114  0.269  11.539
normalizeBatch  5.730  0.206   6.002
* 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/cydar.Rcheck/00check.log’
for details.

* installing *source* package ‘cydar’ ...
** libs
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2 -c compute_density.cpp -o compute_density.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2 -c compute_hyperstats.cpp -o compute_hyperstats.o
compute_hyperstats.cpp:84:26: warning: unused variable 'midweight' [-Wunused-variable]
            const double midweight=total_weight/2;
                         ^
1 warning generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2 -c compute_median_int.cpp -o compute_median_int.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2 -c count_cells.cpp -o count_cells.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2 -c drop_redundant.cpp -o drop_redundant.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2 -c find_knn.cpp -o find_knn.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2 -c get_nndist.cpp -o get_nndist.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2 -c init.cpp -o init.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2 -c matrix_info.cpp -o matrix_info.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2 -c objects.cpp -o objects.o
objects.cpp:202:23: warning: unused variable 'centerx' [-Wunused-variable]
        const double* centerx=centers.dptr+nmarkers*center;
                      ^
1 warning generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2 -c pack_indices.cpp -o pack_indices.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2 -c recount.cpp -o recount.o
clang++ -std=gnu++11 -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 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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/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)

name	user	system	elapsed
countCells	2.096	0.013	2.148
cyData-class	0.163	0.001	0.172
cyData-getset	0.082	0.011	0.093
cyData-subset	0.432	0.043	0.478
diffIntDistr	11.114	0.269	11.539
dnaGate	0.368	0.028	0.399
expandRadius	1.216	0.019	1.271
findFirstSphere	0.108	0.004	0.117
intensityRanges	1.190	0.016	1.223
interpretSpheres	2.273	0.026	2.347
labelSpheres	0.028	0.001	0.028
medIntensities	1.187	0.011	1.208
multiIntHist	0.005	0.001	0.006
neighborDistances	1.088	0.016	1.120
normalizeBatch	5.730	0.206	6.002
outlierGate	0.866	0.026	0.904
packIndices	0.000	0.000	0.001
pickBestMarkers	0.995	0.006	1.014
plotCells	0.243	0.002	0.248
poolCells	0.830	0.010	0.866
prepareCellData	1.108	0.015	1.139
recountCells	1.438	0.009	1.471
spatialFDR	0.078	0.001	0.078