Package: M3C

Version: 1.8.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:M3C.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings M3C_1.8.0.tar.gz

StartedAt: 2020-04-15 03:29:16 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 03:32:53 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 217.0 seconds

RetCode: 0

Status:  OK

CheckDir: M3C.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:M3C.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings M3C_1.8.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/M3C.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘M3C/DESCRIPTION’ ... OK
* this is package ‘M3C’ version ‘1.8.0’
* package encoding: UTF-8
* 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 ‘M3C’ 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 ... NOTE
CDF: no visible binding for global variable ‘consensusindex’
CDF: no visible binding for global variable ‘k’
CDF: no visible binding for global variable ‘K’
CDF: no visible binding for global variable ‘PAC_SCORE’
M3C: no visible binding for global variable ‘i’
M3C: no visible binding for global variable ‘K’
M3C: no visible binding for global variable ‘RCSI’
M3C: no visible binding for global variable ‘P_SCORE’
clustersim: no visible binding for global variable ‘X3’
clustersim: no visible binding for global variable ‘PC1’
clustersim: no visible binding for global variable ‘PC2’
pca: no visible binding for global variable ‘label’
tsne: no visible binding for global variable ‘X1’
tsne: no visible binding for global variable ‘X2’
tsne: no visible binding for global variable ‘label’
umap: no visible binding for global variable ‘X1’
umap: no visible binding for global variable ‘X2’
umap: no visible binding for global variable ‘label’
Undefined global functions or variables:
  K PAC_SCORE PC1 PC2 P_SCORE RCSI X1 X2 X3 consensusindex i k label
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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
clustersim 6.926  0.228    7.43
M3C        3.075  0.176  114.25
* 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-3.10-bioc/meat/M3C.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL M3C
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘M3C’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (M3C)

name	user	system	elapsed
M3C	3.075	0.176	114.250
clustersim	6.926	0.228	7.430
featurefilter	0.467	0.007	0.477
pca	0.056	0.003	0.058
tsne	0.127	0.005	0.132
umap	0.364	0.029	0.396