spade 1.10.2
Michael Linderman
| Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/spade | | Last Changed Rev: 82054 / Revision: 88450 | | Last Changed Date: 2013-10-23 11:37:00 -0700 (Wed, 23 Oct 2013) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | WARNINGS | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | [ WARNINGS ] | OK |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | WARNINGS | OK |
* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/spade.Rcheck'
* using R version 3.0.3 (2014-03-06)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'spade/DESCRIPTION' ... OK
* this is package 'spade' version '1.10.2'
* 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 whether package 'spade' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
'igraph' 'Rclusterpp'
A package should be listed in only one of these fields.
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... WARNING
'library' or 'require' calls not declared from:
'hash' 'rjson'
Namespaces in Imports field not imported from:
'Rclusterpp' 'igraph'
All declared Imports should be used.
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 ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'D:/biocbld/bbs-2.13-bioc/meat/spade.buildbin-libdir/spade/libs/i386/spade.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'D:/biocbld/bbs-2.13-bioc/meat/spade.buildbin-libdir/spade/libs/x64/spade.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console. The detected symbols
are linked into the code but might come from libraries and not actually
be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in 'inst/doc':
'SPADE.Rnw'
A 'vignettes' directory will be required as from R 3.1.0
* checking examples ...
** running examples for arch 'i386' ... [32s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
SPADE.driver 26.41 4.61 23.85
** running examples for arch 'x64' ... [37s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
SPADE.driver 29.4 4.62 28.81
* 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 6 notes.
See
'D:/biocbld/bbs-2.13-bioc/meat/spade.Rcheck/00check.log'
for details.