Package: ccfindR

Version: 1.0.0

Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:ccfindR.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings ccfindR_1.0.0.tar.gz

StartedAt: 2018-10-15 23:01:26 -0400 (Mon, 15 Oct 2018)

EndedAt: 2018-10-15 23:04:16 -0400 (Mon, 15 Oct 2018)

EllapsedTime: 170.3 seconds

RetCode: 0

Status:  OK

CheckDir: ccfindR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:ccfindR.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings ccfindR_1.0.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/ccfindR.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-pc-linux-gnu (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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
vb_factorize 9.464  0.092   9.563
build_tree   9.352  0.056   9.418
simulate_whx 8.968  0.100   9.079
plot_tree    8.792  0.108   8.907
rename_tips  8.692  0.068   8.767
cluster_id   8.620  0.128   8.757
* 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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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL ccfindR
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/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	0.328	0.012	0.341
basis-set	0.240	0.004	0.243
basis	0.412	0.000	0.415
build_tree	9.352	0.056	9.418
cell_map	1.160	0.048	1.209
cluster_id	8.620	0.128	8.757
coeff-set-scNMFSet-method	0.164	0.000	0.163
coeff-set	0.164	0.000	0.161
coeff	0.364	0.004	0.367
colData-scNMFSet-method	0.096	0.000	0.098
colData-set-scNMFSet-ANY-method	0.1	0.0	0.1
counts-scNMFSet-method	0.064	0.000	0.066
counts-set-scNMFSet-method	0.080	0.000	0.078
factorize	2.968	0.020	2.992
filter_cells	0.08	0.00	0.08
filter_genes	0.100	0.000	0.098
gene_map	1.100	0.028	1.131
measure-set-scNMFSet-method	0.164	0.000	0.164
measure-set	0.168	0.000	0.167
measure	0.364	0.000	0.363
meta_genes	1.116	0.020	1.137
normalize_count	0.076	0.000	0.078
plot_genes	0.060	0.000	0.059
plot_tree	8.792	0.108	8.907
ranks-set-scNMFSet-method	0.240	0.000	0.238
ranks-set	0.244	0.000	0.245
ranks	0.336	0.004	0.343
read_10x	0.184	0.000	0.182
remove_zeros	0.084	0.000	0.081
rename_tips	8.692	0.068	8.767
rowData-scNMFSet-method	0.056	0.000	0.053
scNMFSet-class	0.188	0.004	0.195
scNMFSet	0.052	0.000	0.055
show-scNMFSet-method	0.052	0.000	0.052
simulate_data	0.060	0.000	0.061
simulate_whx	8.968	0.100	9.079
vb_factorize	9.464	0.092	9.563
visualize_clusters	2.460	0.008	2.469
write_10x	0.056	0.000	0.054