cnvGSA 1.1.93
Robert Ziman
| Snapshot Date: 2012-06-20 15:22:40 -0700 (Wed, 20 Jun 2012) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/cnvGSA | | Last Changed Rev: 66155 / Revision: 66885 | | Last Changed Date: 2012-05-24 06:30:07 -0700 (Thu, 24 May 2012) |
| lamb1 | Linux (openSUSE 12.1) / x86_64 | OK | WARNINGS | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | WARNINGS | OK |
| pitt | Mac OS X Leopard (10.5.8) / i386 | OK | [ WARNINGS ] | OK |
| perceval | Mac OS X Leopard (10.5.8) / i386 | OK | WARNINGS | OK |
* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/cnvGSA.Rcheck'
* using R version 2.15.0 Patched (2012-04-26 r59216)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'cnvGSA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'cnvGSA' version '1.1.93'
* 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 whether package 'cnvGSA' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... WARNING
sort:
function(x, decreasing, ...)
sort.chromosomeLabels:
function(chrs)
See section 'Generic functions and methods' of the 'Writing R
Extensions' manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
f.add_binned_bhfdr: no visible binding for global variable 'GsSize'
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
'F.AddEnr' 'F.AssociationTest' 'F.BurdenSample' 'F.GsCounts'
'F.Pipeline' 'F.PreProcess' 'F.ProcessGenes' 'f.add_ann'
'f.add_attrib' 'f.add_binned_bhfdr' 'f.add_gstables' 'f.add_lrm'
'f.add_support' 'f.add_universes' 'f.burden_gs_coverage_bygset_unit'
'f.burden_gs_coverage_bysample_unit' 'f.burden_gs_pairs_unit'
'f.burden_gs_summaries' 'f.burden_sample_prop_cnv'
'f.burden_sample_prop_geniccnv' 'f.burden_sample_stats'
'f.burden_sample_summaries' 'f.burden_sample_test'
'f.check_cnv_gs_preTest' 'f.check_cnv_postproc' 'f.check_cnv_s2class'
'f.check_filters' 'f.check_genedata' 'f.check_genes' 'f.check_gs'
'f.check_testpar' 'f.complete_enrpar' 'f.fdr' 'f.fdr_unit' 'f.fet'
'f.fet_gene_unit' 'f.fet_unit' 'f.filter' 'f.gene_coverage_stats'
'f.init_filters' 'f.lengths_cnv.df' 'f.lrm_unit'
'f.lrm_unit_getSmInfo' 'f.make_gene_totals' 'f.make_table_bin'
'f.make_table_chr' 'f.make_table_cnv' 'f.make_table_gen'
'f.make_test_input_all' 'f.make_test_input_cnv'
'f.make_test_input_cnvGen' 'f.rem_genes' 'f.rem_top'
'f.rem_top_FET_unit' 'f.rem_top_fdr_unit' 'f.rem_top_topgene_unit'
'f.test_genes' 'sort.chromosomeLabels' 'writeSampleGmt'
'writeSampleGmt.SingleRow' 'writeSampleGvf'
'writeSampleGvf.SingleRecord'
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 ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK
WARNING: There were 2 warnings.
NOTE: There was 1 note.
See
'/Users/biocbuild/bbs-2.11-bioc/meat/cnvGSA.Rcheck/00check.log'
for details.
* installing *source* package 'cnvGSA' ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for 'summary' from package 'base' in package 'cnvGSA'
** help
*** installing help indices
** building package indices
** installing vignettes
'cnvGSA-vignette.Rnw'
** testing if installed package can be loaded
* DONE (cnvGSA)