GSReg 1.10.0
Bahman Afsari , Elana J. Fertig
| Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017) | | URL: https://git.bioconductor.org/packages/GSReg | | Branch: RELEASE_3_5 | | Last Commit: a334d7b | | Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | WARNINGS | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | WARNINGS | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | [ WARNINGS ] | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GSReg_1.10.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/GSReg.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GSReg/DESCRIPTION’ ... OK
* this is package ‘GSReg’ version ‘1.10.0’
* 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 ‘GSReg’ 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
‘AnnotationDbi’ ‘GenomicFeatures’ ‘Homo.sapiens’ ‘org.Hs.eg.db’
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
GSReg.DIRAC.Pathways: no visible global function definition for ‘pnorm’
GSReg.DIRAC.mu: no visible global function definition for ‘var’
GSReg.Variance: no visible global function definition for ‘var’
GSReg.Variance: no visible global function definition for ‘pnorm’
GSReg.kendall.tau.distance.Restricted.Sparse.internal: no visible
global function definition for ‘as’
GSReg.overlapJunction: no visible binding for global variable
‘TxDb.Hsapiens.UCSC.hg19.knownGene’
GSReg.overlapJunction: no visible binding for global variable
‘org.Hs.eg.db’
GSReg.overlapJunction: no visible global function definition for
‘genes’
GSReg.overlapJunction: no visible global function definition for
‘mapIds’
GSReg.overlapJunction: no visible global function definition for
‘GRanges’
GSReg.overlapJunction: no visible global function definition for ‘Rle’
GSReg.overlapJunction: no visible global function definition for
‘IRanges’
GSReg.overlapJunction: no visible global function definition for
‘findOverlaps’
GSReg.overlapJunction: no visible global function definition for
‘queryHits’
GSReg.overlapJunction: no visible global function definition for
‘subjectHits’
GSReg.overlapJunction : <anonymous>: no visible global function
definition for ‘findOverlaps’
GSReg.overlapJunction : <anonymous>: no visible global function
definition for ‘Matrix’
GSReg.overlapJunction : <anonymous>: no visible global function
definition for ‘queryHits’
GSReg.overlapJunction : <anonymous>: no visible global function
definition for ‘subjectHits’
Undefined global functions or variables:
GRanges IRanges Matrix Rle TxDb.Hsapiens.UCSC.hg19.knownGene as
findOverlaps genes mapIds org.Hs.eg.db pnorm queryHits subjectHits
var
Consider adding
importFrom("methods", "as")
importFrom("stats", "pnorm", "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
‘GSReg.kendall.tau.distance.template’
Undocumented data sets:
‘geneExrsGSReg’ ‘junc.RPM.Simulated’ ‘phenotypes’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'GSReg.GeneSets.DIRAC':
GSReg.GeneSets.DIRAC
Code: function(geneexpres, pathways, phenotypes, Nperm = 0, alpha =
0, minGeneNum = 5)
Docs: function(geneexpres, pathways, phenotypes, Nperm = 0, alpha =
0.05, minGeneNum = 5)
Mismatches in argument default values:
Name: 'alpha' Code: 0 Docs: 0.05
Codoc mismatches from documentation object 'GSReg.GeneSets.EVA':
GSReg.GeneSets.EVA
Code: function(geneexpres, pathways, phenotypes, verbose = T,
minGeneNum = 5, distFunc = GSReg.kendall.tau.distance,
distparamPathways, ...)
Docs: function(geneexpres, pathways, phenotypes, minGeneNum = 5)
Argument names in code not in docs:
verbose distFunc distparamPathways ...
Mismatches in argument names:
Position: 4 Code: verbose Docs: minGeneNum
* checking Rd \usage sections ... WARNING
Objects in \usage without \alias in documentation object 'GSReg.kendall.tau.distance':
‘GSReg.kendall.tau.distance.template’
Bad \usage lines found in documentation object 'GSReg.overlapJunction':
GSReg.overlapJunction <- function(juncExprs,
GenestoStudy=NULL,
geneexpr=NULL,
minmeanloggeneexp= 3,
alpha =0,
sparse = F,
genesCoordinatesTxDB = TxDb.Hsapiens.UCSC.hg19.knownGene,
geneIDInTxDB = 'ENTREZID',
geneIDOut = 'SYMBOL',
org=org.Hs.eg.db, ...)
Bad \usage lines found in documentation object 'GSReg.SEVA':
function(juncExprs,
phenoVect,
verbose=T,
sparse =F, ...)
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... NOTE
The following files look like leftovers/mistakes:
‘Rplots.pdf’
Please remove them from your package.
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 3 WARNINGs, 3 NOTEs
See
‘/Users/biocbuild/bbs-3.5-bioc/meat/GSReg.Rcheck/00check.log’
for details.
* installing *source* package ‘GSReg’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c init.c -o init.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c kendallTauDistance.cc -o kendallTauDistance.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c kendallTauDistanceFromTemp.cc -o kendallTauDistanceFromTemp.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c kendallTauDistanceRestricted.cc -o kendallTauDistanceRestricted.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c nij.cc -o nij.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c vect2compC.cc -o vect2compC.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o GSReg.so init.o kendallTauDistance.o kendallTauDistanceFromTemp.o kendallTauDistanceRestricted.o nij.o vect2compC.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.5-bioc/meat/GSReg.Rcheck/GSReg/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GSReg)