BioC 3.5: CHECK report for monocle on oaxaca

Package: monocle

Version: 2.3.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings monocle_2.3.1.tar.gz

StartedAt: 2017-03-04 06:02:05 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 06:03:51 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 106.4 seconds

RetCode: 0

Status:  OK

CheckDir: monocle.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 monocle_2.3.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/monocle.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘monocle/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘monocle’ version ‘2.3.1’
* 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 ‘monocle’ 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
assign_cell_lineage: no visible global function definition for ‘nei’
buildBranchCellDataSet: no visible global function definition for ‘nei’
count_leaf_descendents: no visible global function definition for ‘nei’
cth_classifier_cds: no visible global function definition for ‘nei’
cth_classifier_cell: no visible global function definition for ‘nei’
diff_test_helper: no visible binding for global variable ‘Size_Factor’
extract_good_branched_ordering: no visible global function definition
  for ‘nei’
extract_good_branched_ordering : extract_branched_ordering_helper: no
  visible global function definition for ‘nei’
extract_good_branched_ordering : assign_cell_state_helper: no visible
  global function definition for ‘nei’
extract_good_branched_ordering : assign_pseudotime_helper: no visible
  global function definition for ‘nei’
extract_good_ordering: no visible global function definition for ‘nei’
fit_model_helper: no visible binding for global variable ‘Size_Factor’
make_canonical: no visible global function definition for ‘nei’
measure_diameter_path: no visible global function definition for ‘nei’
project2MST: no visible global function definition for ‘nei’
relative2abs : <anonymous>: no visible binding for global variable
  ‘FPKM’
Undefined global functions or variables:
  FPKM Size_Factor nei
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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-3.5-bioc/meat/monocle.Rcheck/00check.log’
for details.

* installing *source* package ‘monocle’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (monocle)

name	user	system	elapsed
cellPairwiseDistances-set	0.001	0.000	0.001
cellPairwiseDistances	0.001	0.000	0.000
clusterGenes	0	0	0
detectGenes	0	0	0
estimate_t	0.001	0.000	0.000
minSpanningTree-set	0.001	0.000	0.001
minSpanningTree	0	0	0
newCellDataSet	0.000	0.000	0.001
newCellTypeHierarchy	0.001	0.000	0.001
package-deprecated	0	0	0
plot_cell_trajectory	0.001	0.000	0.000
plot_clusters	0	0	0
plot_genes_in_pseudotime	0.001	0.000	0.000
plot_genes_jitter	0.000	0.000	0.001
plot_genes_positive_cells	0.001	0.000	0.001
reducedDimA-set	0.000	0.000	0.001
reducedDimA	0.000	0.000	0.001
reducedDimK-set	0	0	0
reducedDimK	0.001	0.000	0.001
reducedDimS-set	0.001	0.000	0.000
reducedDimS	0	0	0
reducedDimW-set	0	0	0
reducedDimW	0.000	0.000	0.001
relative2abs	0	0	0
selectNegentropyGenes	0.001	0.000	0.001