monocle 1.0.0
Cole Trapnell
| Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/monocle | | Last Changed Rev: 95439 / Revision: 102249 | | Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | OK | OK |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK |
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### Running command:
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### /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings monocle_1.0.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/monocle.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-linux-gnu (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 ‘1.0.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
‘HSMMSingleCell’ ‘Biobase’ ‘ggplot2’ ‘splines’ ‘VGAM’ ‘igraph’ ‘plyr’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ... [10s/13s] 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
Package in Depends field not imported from: ‘splines’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* 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’
count_leaf_descendents: no visible global function definition for ‘nei’
extract_fixed_ordering: no visible global function definition for ‘nei’
extract_good_branched_ordering: no visible binding for global variable
‘type’
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_branched_ordering: no visible binding for global variable
‘pseudo_time’
extract_good_ordering: no visible global function definition for ‘nei’
extract_ordering: no visible global function definition for ‘nei’
get_next_node_id: no visible binding for '<<-' assignment to
‘next_node’
get_next_node_id: no visible binding for global variable ‘next_node’
make_canonical: no visible binding for global variable ‘type’
make_canonical: no visible global function definition for ‘nei’
measure_diameter_path: no visible global function definition for ‘nei’
orderCells: no visible binding for '<<-' assignment to ‘next_node’
plot_genes_positive_cells: no visible binding for global variable
‘percent’
plot_genes_positive_cells: no visible global function definition for
‘geom_bar’
plot_spanning_tree: no visible binding for global variable
‘gene_short_name’
plot_spanning_tree: no visible global function definition for
‘geom_text’
plot_spanning_tree: no visible binding for global variable
‘sample_name’
pq_helper: no visible global function definition for
‘get.all.shortest.paths’
selectNegentropyGenes: no visible binding for global variable
‘log_expression’
selectNegentropyGenes: no visible global function definition for ‘vglm’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [50s/67s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
detectGenes 37.590 0.392 45.883
cellPairwiseDistances 1.636 0.092 5.512
* 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
NOTE: There were 3 notes.
See
‘/home/biocbuild/bbs-3.0-bioc/meat/monocle.Rcheck/00check.log’
for details.