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### Running command:
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### /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings spade_1.12.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/spade.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘spade/DESCRIPTION’ ... OK
* this is package ‘spade’ version ‘1.12.2’
* 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 ‘spade’ can be installed ... [13s/14s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
LICENSE
is not mentioned in the DESCRIPTION file.
* 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 ... WARNING
'library' or 'require' calls not declared from:
‘hash’ ‘rjson’
Packages in Depends field not imported from:
‘Rclusterpp’ ‘igraph’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
SPADE.createPopulationMapping: no visible global function definition
for ‘hash’
SPADE.driver: no visible global function definition for ‘fromJSON’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
‘SPADE.density’ ‘SPADE.removeExistingDensityAndClusterColumns’
‘SPADE.transform.FCS’
All user-level objects in a package should have documentation entries.
See the chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'SPADE.downsampleFCS':
SPADE.downsampleFCS
Code: function(infilename, outfilename, exclude_pctile = 0.01,
target_pctile = NULL, target_number = NULL,
target_percent = 0.1)
Docs: function(infilename, outfilename, exclude_pctile = 0.01,
target_pctile = 0.05, desired_samples = NULL)
Argument names in code not in docs:
target_number target_percent
Argument names in docs not in code:
desired_samples
Mismatches in argument names:
Position: 5 Code: target_number Docs: desired_samples
Mismatches in argument default values:
Name: 'target_pctile' Code: NULL Docs: 0.05
Codoc mismatches from documentation object 'SPADE.driver':
SPADE.driver
Code: function(files, file_pattern = "*.fcs", out_dir = ".",
cluster_cols = NULL, panels = NULL, comp = TRUE,
arcsinh_cofactor = NULL, transforms =
flowCore::arcsinhTransform(a = 0, b = 0.2),
downsampling_target_number = NULL,
downsampling_target_pctile = NULL,
downsampling_target_percent = 0.1,
downsampling_exclude_pctile = 0.01, k = 200,
clustering_samples = 50000, layout =
igraph:::layout.kamada.kawai, pctile_color = c(0.02,
0.98), fcs_channel_mappings_json = NULL)
Docs: function(files, file_pattern = "*.fcs", out_dir = ".",
cluster_cols = NULL, panels = NULL, comp = TRUE,
arcsinh_cofactor = NULL, transforms =
flowCore::arcsinhTransform(a = 0, b = 0.2),
downsampling_samples = 20000,
downsampling_exclude_pctile = 0.01,
downsampling_target_pctile = 0.05, k = 200,
clustering_samples = 50000, layout =
igraph:::layout.kamada.kawai, pctile_color = c(0.02,
0.98))
Argument names in code not in docs:
downsampling_target_number downsampling_target_percent
fcs_channel_mappings_json
Argument names in docs not in code:
downsampling_samples
Mismatches in argument names (first 3):
Position: 9 Code: downsampling_target_number Docs: downsampling_samples
Position: 10 Code: downsampling_target_pctile Docs: downsampling_exclude_pctile
Position: 11 Code: downsampling_target_percent Docs: downsampling_target_pctile
Mismatches in argument default values:
Name: 'downsampling_target_pctile' Code: NULL Docs: 0.05
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... NOTE
Package has both ‘src/Makevars.in’ and ‘src/Makevars’.
Installation with --no-configure' is unlikely to work. If you intended
‘src/Makevars’ to be used on Windows, rename it to ‘src/Makevars.win’
otherwise remove it. If ‘configure’ created ‘src/Makevars’, you need a
‘cleanup’ script.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [204s/95s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
SPADE.driver 198.812 0.776 90.465
* 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
WARNING: There were 3 warnings.
NOTE: There were 3 notes.
See
‘/home/biocbuild/bbs-2.14-bioc/meat/spade.Rcheck/00check.log’
for details.