Package: ccfindR

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ccfindR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ccfindR_1.0.0.tar.gz

StartedAt: 2018-10-16 20:18:20 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 20:22:26 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 245.8 seconds

RetCode: 0

Status:  OK

CheckDir: ccfindR.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ccfindR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ccfindR_1.0.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/ccfindR.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ccfindR/DESCRIPTION’ ... OK
* this is package ‘ccfindR’ version ‘1.0.0’
* 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 ‘ccfindR’ 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 ... 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
build_tree   15.010  0.155  15.291
cluster_id   12.328  0.182  12.595
vb_factorize 10.305  0.258  10.563
plot_tree    10.187  0.319  10.507
rename_tips  10.038  0.285  10.323
simulate_whx  9.864  0.266  10.129
* 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: OK

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ccfindR
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘ccfindR’ ...
** R
** 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
* DONE (ccfindR)

name	user	system	elapsed
basis-set-scNMFSet-method	0.511	0.021	0.533
basis-set	0.418	0.002	0.422
basis	0.553	0.003	0.564
build_tree	15.010	0.155	15.291
cell_map	2.120	0.033	2.167
cluster_id	12.328	0.182	12.595
coeff-set-scNMFSet-method	0.195	0.004	0.200
coeff-set	0.193	0.008	0.203
coeff	0.409	0.019	0.427
colData-scNMFSet-method	0.099	0.002	0.100
colData-set-scNMFSet-ANY-method	0.093	0.002	0.095
counts-scNMFSet-method	0.058	0.000	0.057
counts-set-scNMFSet-method	0.077	0.000	0.077
factorize	3.303	0.483	3.789
filter_cells	0.080	0.001	0.081
filter_genes	0.104	0.002	0.105
gene_map	1.337	0.030	1.370
measure-set-scNMFSet-method	0.185	0.002	0.187
measure-set	0.177	0.000	0.176
measure	0.380	0.001	0.381
meta_genes	1.303	0.014	1.319
normalize_count	0.087	0.001	0.089
plot_genes	0.059	0.001	0.060
plot_tree	10.187	0.319	10.507
ranks-set-scNMFSet-method	0.268	0.008	0.276
ranks-set	0.283	0.015	0.299
ranks	0.380	0.005	0.385
read_10x	0.176	0.003	0.179
remove_zeros	0.077	0.000	0.078
rename_tips	10.038	0.285	10.323
rowData-scNMFSet-method	0.052	0.001	0.052
scNMFSet-class	0.189	0.005	0.194
scNMFSet	0.056	0.003	0.058
show-scNMFSet-method	0.056	0.002	0.058
simulate_data	0.060	0.001	0.061
simulate_whx	9.864	0.266	10.129
vb_factorize	10.305	0.258	10.563
visualize_clusters	3.019	0.026	3.046
write_10x	0.058	0.001	0.059