revdep/README-r-1.1.md

In real-didi/RSQLiteFixed: 'SQLite' Interface for R

Setup

Platform

|setting |value | |:--------|:----------------------------| |version |R version 3.3.2 (2016-10-31) | |system |x86_64, linux-gnu | |ui |X11 | |language |(EN) | |collate |en_US.UTF-8 | |tz |Universal | |date |2016-11-25 |

Packages

|package |* |version |date |source | |:---------|:--|:----------|:----------|:----------------------------------| |BH | |1.62.0-1 |2016-11-19 |cran (@1.62.0-) | |DBI | |0.5-12 |2016-10-06 |Github (rstats-db/DBI@4f00863) | |DBItest | |1.3-10 |2016-10-06 |Github (rstats-db/DBItest@9e87611) | |knitr | |1.15.1 |2016-11-22 |cran (@1.15.1) | |memoise | |1.0.0 |2016-01-29 |CRAN (R 3.3.1) | |plogr | |0.1-1 |2016-09-24 |cran (@0.1-1) | |Rcpp | |0.12.8 |2016-11-17 |cran (@0.12.8) | |rmarkdown | |1.2 |2016-11-21 |cran (@1.2) | |RSQLite | |1.0.0 |2014-10-25 |CRAN (R 3.3.1) | |testthat | |1.0.2.9000 |2016-08-25 |Github (hadley/testthat@46d15da) |

Check results

117 packages

|package |version | errors| warnings| notes| |:------------------|:---------|------:|--------:|-----:| |affycoretools |1.46.1 | 0| 0| 0| |AnnotationDbi |1.36.0 | 0| 1| 5| |AnnotationForge |1.16.0 | 0| 0| 2| |AnnotationHubData |1.4.0 | 1| 0| 3| |AnnotationHub |2.6.4 | 0| 0| 1| |APSIM |0.9.1 | 0| 0| 0| |archivist |2.1.1 | 0| 0| 2| |BatchExperiments |1.4.1 | 0| 0| 2| |BatchJobs |1.6 | 0| 0| 0| |bibliospec |0.0.4 | 0| 0| 0| |biglm |0.9-1 | 0| 0| 5| |bioassayR |1.12.1 | 0| 0| 1| |BoSSA |2.0 | 0| 0| 0| |caroline |0.7.6 | 0| 0| 2| |Category |2.40.0 | 0| 0| 1| |ChemmineR |2.26.0 | 1| 0| 0| |chunked |0.3 | 0| 0| 0| |CITAN |2015.12-2 | 0| 0| 0| |clstutils |1.22.0 | 0| 2| 5| |CNEr |1.10.1 | 0| 2| 2| |CollapsABEL |0.10.8 | 0| 0| 0| |cummeRbund |2.16.0 | 0| 0| 6| |customProDB |1.14.0 | 0| 0| 3| |DBI |0.5-1 | 0| 0| 1| |DECIPHER |2.2.0 | 0| 0| 3| |diffrprojects |0.1.14 | 0| 0| 0| |dplyr |0.5.0 | 0| 0| 1| |ecd |0.8.2 | 1| 0| 0| |emuR |0.2.0 | 0| 0| 0| |ensembldb |1.6.2 | 0| 0| 2| |etl |0.3.4 | 0| 0| 0| |ETLUtils |1.3 | 0| 0| 0| |filehashSQLite |0.2-4 | 0| 0| 3| |filematrix |1.1.0 | 0| 1| 0| |freqweights |1.0.2 | 0| 0| 1| |gcbd |0.2.6 | 0| 1| 0| |GeneAnswers |2.16.0 | 1| 3| 6| |GenomicFeatures |1.26.0 | 0| 0| 2| |Genominator |1.28.0 | 0| 0| 4| |GEOmetadb |1.34.0 | 0| 0| 3| |GWASTools |1.20.0 | 0| 0| 1| |imputeMulti |0.6.3 | 0| 0| 1| |iontree |1.20.0 | 0| 0| 5| |KoNLP |0.80.0 | 0| 0| 1| |lumi |2.26.3 | 0| 1| 3| |macleish |0.3.0 | 0| 0| 0| |maGUI |1.0 | 1| 0| 0| |manta |1.20.0 | 0| 0| 7| |marmap |0.9.5 | 0| 0| 0| |MeSHDbi |1.10.0 | 0| 0| 2| |metagenomeFeatures |1.4.0 | 0| 2| 2| |MetaIntegrator |1.0.3 | 0| 0| 0| |metaseqR |1.14.0 | 1| 1| 4| |mgsa |1.22.0 | 0| 1| 4| |miRNAtap |1.8.0 | 0| 0| 2| |MmPalateMiRNA |1.24.0 | 0| 0| 4| |MonetDBLite |0.3.1 | 0| 0| 1| |MUCflights |0.0-3 | 0| 0| 3| |nutshell.bbdb |1.0 | 0| 0| 2| |nutshell |2.0 | 0| 0| 3| |oai |0.2.2 | 0| 0| 0| |oce |0.9-20 | 1| 0| 1| |oligoClasses |1.36.0 | 0| 1| 4| |oligo |1.38.0 | 1| 0| 9| |OrganismDbi |1.16.0 | 0| 0| 2| |PAnnBuilder |1.38.0 | 0| 3| 1| |pdInfoBuilder |1.38.0 | 0| 0| 1| |PGA |1.4.0 | 0| 0| 3| |pitchRx |1.8.2 | 0| 0| 1| |plethy |1.12.0 | 2| 1| 3| |poplite |0.99.16 | 1| 0| 1| |ProjectTemplate |0.7 | 0| 0| 0| |quantmod |0.4-7 | 0| 0| 1| |rangeMapper |0.3-0 | 0| 0| 0| |RecordLinkage |0.4-10 | 0| 0| 0| |recoup |1.2.0 | 2| 0| 1| |refGenome |1.7.0 | 0| 0| 0| |rgrass7 |0.1-9 | 0| 0| 0| |RImmPort |1.2.0 | 0| 1| 1| |RObsDat |16.03 | 0| 0| 0| |rplexos |1.1.8 | 0| 0| 0| |RQDA |0.2-7 | 1| 0| 1| |rtext |0.1.20 | 0| 0| 0| |rTRM |1.12.0 | 0| 0| 1| |rvertnet |0.5.0 | 0| 0| 0| |scrime |1.3.3 | 0| 0| 2| |SEERaBomb |2016.2 | 0| 0| 0| |seqplots |1.12.0 | 0| 0| 3| |SGP |1.5-0.0 | 0| 0| 0| |smnet |2.1 | 0| 0| 0| |snplist |0.16 | 0| 0| 0| |specL |1.8.0 | 0| 1| 3| |sqldf |0.4-10 | 0| 1| 2| |sqliter |0.1.0 | 0| 0| 0| |SRAdb |1.32.0 | 0| 0| 6| |srvyr |0.2.0 | 0| 0| 0| |SSN |1.1.8 | 0| 0| 0| |storr |1.0.1 | 0| 0| 0| |stream |1.2-3 | 0| 0| 1| |survey |3.31-2 | 0| 0| 0| |taRifx |1.0.6 | 0| 0| 4| |tcpl |1.2.2 | 0| 0| 1| |TFBSTools |1.12.1 | 0| 1| 2| |tigreBrowserWriter |0.1.2 | 1| 0| 0| |tigre |1.28.0 | 0| 0| 2| |trackeR |0.0.4 | 0| 1| 0| |TSdata |2016.8-1 | 0| 1| 0| |TSSQLite |2015.4-1 | 0| 0| 0| |TSsql |2015.1-2 | 0| 0| 1| |tweet2r |1.0 | 0| 0| 0| |twitteR |1.1.9 | 0| 0| 0| |UniProt.ws |2.14.0 | 0| 0| 1| |Uniquorn |1.2.0 | 0| 0| 2| |UPMASK |1.0 | 0| 0| 1| |VariantFiltering |1.10.1 | 0| 1| 4| |vegdata |0.9 | 0| 0| 0| |vmsbase |2.1.3 | 1| 0| 0|

affycoretools (1.46.1)

Maintainer: James W. MacDonald [e-mail]

0 errors | 0 warnings | 0 notes

AnnotationDbi (1.36.0)

Maintainer: Bioconductor Package Maintainer [e-mail]

0 errors | 1 warning | 5 notes

checking for unstated dependencies in ‘tests’ ... WARNING
'library' or 'require' call not declared from: ‘org.testing.db’

checking installed package size ... NOTE
  installed size is  8.6Mb
  sub-directories of 1Mb or more:
    extdata   6.0Mb

checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’ ‘utils’ ‘stats4’ ‘BiocGenerics’ ‘Biobase’ ‘IRanges’ ‘DBI’ ‘RSQLite’
A package should be listed in only one of these fields.

checking dependencies in R code ... NOTE
'library' or 'require' calls in package code:
  ‘GO.db’ ‘KEGG.db’ ‘RSQLite’ ‘graph’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported object imported by a ':::' call: ‘BiocGenerics:::testPackage’
  See the note in ?`:::` about the use of this operator.

checking R code for possible problems ... NOTE
.selectInp8: no visible global function definition for ‘.resort’
annotMessage: no visible binding for global variable ‘pkgName’
createORGANISMSeeds: no visible global function definition for
  ‘makeAnnDbMapSeeds’
makeGOGraph: no visible binding for global variable ‘GOBPPARENTS’
makeGOGraph: no visible binding for global variable ‘GOMFPARENTS’
makeGOGraph: no visible binding for global variable ‘GOCCPARENTS’
makeGOGraph: no visible global function definition for ‘ftM2graphNEL’
Undefined global functions or variables:
  .resort GOBPPARENTS GOCCPARENTS GOMFPARENTS ftM2graphNEL
  makeAnnDbMapSeeds pkgName

checking Rd line widths ... NOTE
Rd file 'inpIDMapper.Rd':
  \examples lines wider than 100 characters:
       YeastUPSingles = inpIDMapper(ids, "HOMSA", "SACCE", destIDType="UNIPROT", keepMultDestIDMatches = FALSE)

These lines will be truncated in the PDF manual.

AnnotationForge (1.16.0)

Maintainer: Bioconductor Package Maintainer [e-mail]

0 errors | 0 warnings | 2 notes

checking installed package size ... NOTE
  installed size is  6.0Mb
  sub-directories of 1Mb or more:
    AnnDbPkg-templates   1.7Mb
    extdata              3.3Mb

checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: ‘AnnotationDbi:::NCBIORG_DB_SeedGenerator’
  See the note in ?`:::` about the use of this operator.

AnnotationHubData (1.4.0)

Maintainer: Bioconductor Package Maintainer [e-mail]

1 error | 0 warnings | 3 notes

checking tests ... ERROR
Running the tests in ‘tests/AnnotationHubData_unit_tests.R’ failed.
Last 13 lines of output:
  ERROR in test_UCSCChainPreparer_recipe: Error : 1: Unknown IO error2: failed to load external entity "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=&retmax=0"


  Test files with failing tests

     test_recipe.R 
       test_UCSC2BitPreparer_recipe 
       test_UCSCChainPreparer_recipe 


  Error in BiocGenerics:::testPackage("AnnotationHubData") : 
    unit tests failed for package AnnotationHubData
  Execution halted

checking top-level files ... NOTE
Non-standard file/directory found at top level:
  ‘appveyor.yml’

checking dependencies in R code ... NOTE
Missing object imported by a ':::' call: ‘AnnotationHub:::.db_connection’
Unexported object imported by a ':::' call: ‘OrganismDbi:::.packageTaxIds’
  See the note in ?`:::` about the use of this operator.

checking R code for possible problems ... NOTE
.NCBIMetadataFromUrl: no visible binding for global variable ‘results’
.NCBIMetadataFromUrl: no visible binding for global variable ‘specData’
.makeComplexGR: no visible binding for global variable ‘seqname’
jsonPath: no visible binding for global variable ‘SourceFile’
jsonPath: no visible binding for global variable ‘HubRoot’
makeAnnotationHubMetadata : <anonymous>: no visible binding for global
  variable ‘Title’
makeAnnotationHubMetadata : <anonymous>: no visible binding for global
  variable ‘Description’
... 52 lines ...
  SourceFile SourceType SourceUrl SourceVersion Species TaxonomyId
  Title ahroot bucket checkTrue read.csv results seqname specData
  suppresWarnings
Consider adding
  importFrom("utils", "read.csv")
to your NAMESPACE file.

Found the following calls to data() loading into the global environment:
File ‘AnnotationHubData/R/makeNCBIToOrgDbs.R’:
  data(specData, package = "GenomeInfoDb")
See section ‘Good practice’ in ‘?data’.

AnnotationHub (2.6.4)

Maintainer: Bioconductor Package Maintainer [e-mail]

0 errors | 0 warnings | 1 note

checking Rd files ... NOTE
prepare_Rd: listResources.Rd:44-45: Dropping empty section \seealso

APSIM (0.9.1)

Maintainer: Justin Fainges [e-mail]

0 errors | 0 warnings | 0 notes

archivist (2.1.1)

Maintainer: Przemyslaw Biecek [e-mail] Bug reports: https://github.com/pbiecek/archivist/issues

0 errors | 0 warnings | 2 notes

checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘archivist.github’

checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘archivist.github’

BatchExperiments (1.4.1)

Maintainer: Michel Lang [e-mail] Bug reports: https://github.com/tudo-r/BatchExperiments/issues

0 errors | 0 warnings | 2 notes

checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  ‘BatchJobs:::addIntModulo’ ‘BatchJobs:::buffer’
  ‘BatchJobs:::checkDir’ ‘BatchJobs:::checkId’ ‘BatchJobs:::checkIds’
  ‘BatchJobs:::checkPart’ ‘BatchJobs:::createShardedDirs’
  ‘BatchJobs:::dbConnectToJobsDB’ ‘BatchJobs:::dbCreateJobStatusTable’
  ‘BatchJobs:::dbDoQuery’ ‘BatchJobs:::dbFindDone’
  ‘BatchJobs:::dbFindRunning’ ‘BatchJobs:::dbRemoveJobs’
  ‘BatchJobs:::dbSelectWithIds’ ‘BatchJobs:::getJobDirs’
  ‘BatchJobs:::getJobInfoInternal’ ‘BatchJobs:::getKillJob’
  ‘BatchJobs:::getListJobs’ ‘BatchJobs:::getRandomSeed’
  ‘BatchJobs:::getResult’ ‘BatchJobs:::isRegistryDir’
  ‘BatchJobs:::makeRegistryInternal’ ‘BatchJobs:::saveRegistry’
  ‘BatchJobs:::seeder’ ‘BatchJobs:::syncRegistry’
  See the note in ?`:::` about the use of this operator.

checking R code for possible problems ... NOTE
addExperiments.ExperimentRegistry: no visible global function
  definition for ‘is’
applyJobFunction.ExperimentRegistry: no visible global function
  definition for ‘setNames’
calcDynamic: no visible global function definition for ‘setNames’
checkExperimentRegistry: no visible global function definition for
  ‘head’
dbSummarizeExperiments: no visible global function definition for
  ‘setNames’
designIterator: no visible global function definition for ‘setNames’
getIndex : exprToIndex: no visible global function definition for
  ‘capture.output’
getProblemFilePaths: no visible global function definition for
  ‘setNames’
updateRegistry.ExperimentRegistry: no visible global function
  definition for ‘packageVersion’
Undefined global functions or variables:
  capture.output head is packageVersion setNames
Consider adding
  importFrom("methods", "is")
  importFrom("stats", "setNames")
  importFrom("utils", "capture.output", "head", "packageVersion")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').

BatchJobs (1.6)

Maintainer: Bernd Bischl [e-mail] Bug reports: https://github.com/tudo-r/BatchJobs/issues

0 errors | 0 warnings | 0 notes

bibliospec (0.0.4)

Maintainer: Witold E. Wolski [e-mail] Bug reports: https://github.com/protViz/bibliospec/issues

0 errors | 0 warnings | 0 notes

biglm (0.9-1)

Maintainer: Thomas Lumley [e-mail]

0 errors | 0 warnings | 5 notes

checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.

checking top-level files ... NOTE
Non-standard file/directory found at top level:
  ‘test’

checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘DBI’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.

checking foreign function calls ... NOTE
Call with DUP:
   .Fortran("regcf", as.integer(p), as.integer(p * p/2), bigQR$D, 
       bigQR$rbar, bigQR$thetab, bigQR$tol, beta = numeric(p), nreq = as.integer(nvar), 
       ier = integer(1), DUP = FALSE)
DUP is no longer supported and will be ignored.

checking R code for possible problems ... NOTE
bigglm.RODBC: no visible global function definition for ‘odbcQuery’
bigglm.RODBC : chunk: no visible global function definition for
  ‘odbcQuery’
bigglm.RODBC : chunk: no visible global function definition for
  ‘sqlGetResults’
bigglm,ANY-DBIConnection: no visible global function definition for
  ‘dbSendQuery’
bigglm,ANY-DBIConnection: no visible global function definition for
  ‘dbClearResult’
bigglm,ANY-DBIConnection : chunk: no visible global function definition
  for ‘dbClearResult’
bigglm,ANY-DBIConnection : chunk: no visible global function definition
  for ‘dbSendQuery’
bigglm,ANY-DBIConnection : chunk: no visible global function definition
  for ‘fetch’
Undefined global functions or variables:
  dbClearResult dbSendQuery fetch odbcQuery sqlGetResults

Found the following calls to data() loading into the global environment:
File ‘biglm/R/bigglm.R’:
  data(reset = TRUE)
  data(reset = FALSE)
See section ‘Good practice’ in ‘?data’.

bioassayR (1.12.1)

Maintainer: Tyler Backman [e-mail] Bug reports: https://github.com/TylerBackman/bioassayR/issues

0 errors | 0 warnings | 1 note

checking R code for possible problems ... NOTE
crossReactivityPrior: no visible global function definition for ‘sd’
crossReactivityProbability : <anonymous>: no visible global function
  definition for ‘pbeta’
Undefined global functions or variables:
  pbeta sd
Consider adding
  importFrom("stats", "pbeta", "sd")
to your NAMESPACE file.

BoSSA (2.0)

Maintainer: pierre lefeuvre [e-mail]

0 errors | 0 warnings | 0 notes

caroline (0.7.6)

Maintainer: David Schruth [e-mail]

0 errors | 0 warnings | 2 notes

checking dependencies in R code ... NOTE
'library' or 'require' calls in package code:
  ‘MASS’ ‘RSQLite’ ‘grid’ ‘sm’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.

checking R code for possible problems ... NOTE
.ci.median: no visible global function definition for ‘qbinom’
.ci.median: no visible global function definition for ‘median’
.ci.median: no visible global function definition for ‘pbinom’
.description: no visible global function definition for ‘var’
.description: no visible global function definition for ‘shapiro.test’
.description: no visible global function definition for ‘quantile’
.huber.NR: no visible global function definition for ‘median’
.kurtosis: no visible global function definition for ‘var’
.kurtosys: no visible global function definition for ‘var’
... 104 lines ...
  importFrom("graphics", "axis", "box", "identify", "image", "lines",
             "locator", "mtext", "par", "plot", "plot.new",
             "plot.window", "points", "polygon", "rect", "segments",
             "text", "title")
  importFrom("methods", "as")
  importFrom("stats", "median", "pbinom", "qbinom", "qnorm", "quantile",
             "runif", "sd", "shapiro.test", "var")
  importFrom("utils", "browseURL", "count.fields", "head", "read.delim",
             "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').

Category (2.40.0)

Maintainer: Bioconductor Package Maintainer [e-mail]

0 errors | 0 warnings | 1 note

checking R code for possible problems ... NOTE
.linearMTestInternal: no visible global function definition for
  ‘setNames’
Undefined global functions or variables:
  setNames
Consider adding
  importFrom("stats", "setNames")
to your NAMESPACE file.

ChemmineR (2.26.0)

Maintainer: Thomas Girke [e-mail]

1 error | 0 warnings | 0 notes

checking whether package ‘ChemmineR’ can be installed ... ERROR
Installation failed.
See ‘/home/muelleki/git/R/RSQLite/revdep/checks/ChemmineR.Rcheck/00install.out’ for details.

chunked (0.3)

Maintainer: Edwin de Jonge [e-mail] Bug reports: https://github.com/edwindj/chunked/issues

0 errors | 0 warnings | 0 notes

CITAN (2015.12-2)

Maintainer: Marek Gagolewski [e-mail] Bug reports: https://github.com/Rexamine/CITAN/issues

0 errors | 0 warnings | 0 notes

clstutils (1.22.0)

Maintainer: Noah Hoffman [e-mail]

0 errors | 2 warnings | 5 notes

checking for GNU extensions in Makefiles ... WARNING
Found the following file(s) containing GNU extensions:
  tests/unit/Makefile
Portable Makefiles do not use GNU extensions such as +=, :=, $(shell),
$(wildcard), ifeq ... endif. See section ‘Writing portable packages’ in
the ‘Writing R Extensions’ manual.

checking re-building of vignette outputs ... WARNING
Error in re-building vignettes:
  ...
Loading required package: clst
Loading required package: rjson
Loading required package: ape
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'pplacerDemo.tex' failed.
LaTeX errors:
! Package auto-pst-pdf Error: 
    "shell escape" (or "write18") is not enabled:
    auto-pst-pdf will not work!
.
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted


checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.

checking top-level files ... NOTE
Non-standard file/directory found at top level:
  ‘devmakefile’

checking dependencies in R code ... NOTE
'library' or 'require' call to ‘rjson’ which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' call to ‘RSVGTipsDevice’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘ape’ ‘rjson’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.

checking foreign function calls ... NOTE
Foreign function call to a different package:
  .Call("seq_root2tip", ..., PACKAGE = "ape")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.

checking R code for possible problems ... NOTE
edgeMap: no visible global function definition for ‘fromJSON’
findOutliers: no visible global function definition for ‘quantile’
findOutliers: no visible binding for global variable ‘median’
maxDists: no visible binding for global variable ‘median’
placeData: no visible global function definition for ‘read.table’
prettyTree: no visible binding for global variable ‘par’
prettyTree: no visible global function definition for ‘plot’
prettyTree: no visible binding for global variable ‘.PlotPhyloEnv’
prettyTree: no visible binding for global variable ‘points’
... 19 lines ...
taxonomyFromRefpkg: no visible global function definition for
  ‘read.csv’
Undefined global functions or variables:
  .PlotPhyloEnv dev.off devSVGTips fromJSON legend median par plot
  points quantile read.csv read.table setSVGShapeToolTip text
Consider adding
  importFrom("grDevices", "dev.off")
  importFrom("graphics", "legend", "par", "plot", "points", "text")
  importFrom("stats", "median", "quantile")
  importFrom("utils", "read.csv", "read.table")
to your NAMESPACE file.

CNEr (1.10.1)

Maintainer: Ge Tan [e-mail] Bug reports: https://github.com/ge11232002/CNEr/issues

0 errors | 2 warnings | 2 notes

checking compiled code ... WARNING
File ‘CNEr/libs/CNEr.so’:
  Found ‘abort’, possibly from ‘abort’ (C)
    Object: ‘ucsc/errabort.o’
  Found ‘exit’, possibly from ‘exit’ (C)
    Objects: ‘ucsc/errabort.o’, ‘ucsc/pipeline.o’
  Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)
    Object: ‘ucsc/pipeline.o’
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘ucsc/obscure.o’
  Found ‘stderr’, possibly from ‘stderr’ (C)
    Objects: ‘ucsc/axt.o’, ‘ucsc/errabort.o’, ‘ucsc/obscure.o’,
      ‘ucsc/verbose.o’, ‘ucsc/os.o’
  Found ‘stdout’, possibly from ‘stdout’ (C)
    Objects: ‘ucsc/common.o’, ‘ucsc/errabort.o’, ‘ucsc/verbose.o’,
      ‘ucsc/os.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.

checking re-building of vignette outputs ... WARNING
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 2-15 (CNEr.Rmd) 
Error: processing vignette 'CNEr.Rmd' failed with diagnostics:
could not find function "doc_date"
Execution halted


checking installed package size ... NOTE
  installed size is 28.9Mb
  sub-directories of 1Mb or more:
    R        11.0Mb
    extdata  15.9Mb
    libs      1.1Mb

checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  ‘BiocGenerics:::replaceSlots’ ‘S4Vectors:::make_zero_col_DataFrame’
  See the note in ?`:::` about the use of this operator.

CollapsABEL (0.10.8)

Maintainer: Kaiyin Zhong [e-mail] Bug reports: https://bitbucket.org/kindlychung/collapsabel2/issues

0 errors | 0 warnings | 0 notes

cummeRbund (2.16.0)

Maintainer: Loyal A. Goff [e-mail]

0 errors | 0 warnings | 6 notes

checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘BiocGenerics’ ‘RSQLite’ ‘ggplot2’ ‘reshape2’ ‘fastcluster’
  ‘rtracklayer’ ‘Gviz’
Adding so many packages to the search path is excessive and importing
selectively is preferable.

checking installed package size ... NOTE
  installed size is 11.5Mb
  sub-directories of 1Mb or more:
    R         4.1Mb
    doc       1.6Mb
    extdata   5.6Mb

checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘BiocGenerics’ ‘plyr’
A package should be listed in only one of these fields.

checking dependencies in R code ... NOTE
'library' or 'require' calls in package code:
  'NMFN' 'cluster' 'rjson' 'stringr'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'Gviz' 'RSQLite' 'fastcluster' 'ggplot2' 'reshape2' 'rtracklayer'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.

checking R code for possible problems ... NOTE
.CVdensity: no visible global function definition for 'ggplot'
.CVdensity: no visible global function definition for 'geom_density'
.CVdensity: no visible global function definition for 'aes'
.CVdensity: no visible binding for global variable 'CV'
.CVdensity: no visible binding for global variable 'sample_name'
.CVdensity: no visible global function definition for 'scale_x_log10'
.MAplot: no visible global function definition for 'ggplot'
.MAplot: no visible global function definition for 'geom_point'
.MAplot: no visible global function definition for 'aes'
... 1188 lines ...
  scale_y_log10 seqnames significant stat_density stat_smooth stat_sum
  stat_summary stdev str_split_fixed strand theme theme_bw toJSON
  tracking_id tracks unit v1 v2 value variable varnames write.table x
  xlab xlim y ylab
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "as.dendrogram", "as.dist", "as.formula",
             "cmdscale", "dist", "hclust", "order.dendrogram",
             "p.adjust", "prcomp")
  importFrom("utils", "read.delim", "read.table", "write.table")
to your NAMESPACE file.

checking Rd line widths ... NOTE
Rd file 'MAplot.Rd':
  \examples lines wider than 100 characters:
             a<-readCufflinks(system.file("extdata", package="cummeRbund")) #Create CuffSet object from sample data

Rd file 'QCplots.Rd':
  \examples lines wider than 100 characters:
             a<-readCufflinks(system.file("extdata", package="cummeRbund")) #Read cufflinks data and create CuffSet object

Rd file 'csBoxplot.Rd':
... 96 lines ...
                                     isoformFPKM = "isoforms.fpkm_tracking", isoformDiff = "isoform_exp.diff", isoformCount="isoforms.count_ ... [TRUNCATED]
                                     TSSFPKM = "tss_groups.fpkm_tracking", TSSDiff = "tss_group_exp.diff", TSSCount="tss_groups.count_tracki ... [TRUNCATED]
                                     CDSFPKM = "cds.fpkm_tracking", CDSExpDiff = "cds_exp.diff", CDSCount="cds.count_tracking", CDSRep="cds. ... [TRUNCATED]
  \examples lines wider than 100 characters:
             a<-readCufflinks(system.file("extdata", package="cummeRbund")) #Read cufflinks data in sample directory and creates CuffSet obj ... [TRUNCATED]

Rd file 'sigMatrix.Rd':
  \examples lines wider than 100 characters:
             a<-readCufflinks(system.file("extdata", package="cummeRbund")) #Create CuffSet object from sample data

These lines will be truncated in the PDF manual.

customProDB (1.14.0)

Maintainer: xiaojing wang [e-mail]

0 errors | 0 warnings | 3 notes

checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘IRanges’ ‘biomaRt’ ‘AnnotationDbi’
A package should be listed in only one of these fields.

checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  ‘biomaRt:::martBM’ ‘biomaRt:::martDataset’ ‘biomaRt:::martHost’
  See the note in ?`:::` about the use of this operator.

checking R code for possible problems ... NOTE
.Ensembl.getTable: no visible global function definition for
  ‘download.file’
.Ensembl.getTable: no visible global function definition for
  ‘read.table’
.getDatasetAttrGroups: no visible global function definition for ‘is’
.makeBiomartChrominfo: no visible global function definition for ‘is’
.parseBMMartParams: no visible global function definition for ‘is’
Bed2Range: no visible global function definition for ‘read.table’
Bed2Range: no visible binding for global variable ‘V5’
... 54 lines ...
  definition for ‘as’
Undefined global functions or variables:
  V5 aapos aaref aavar alleleCount alleles allsample as cds_end
  cds_start chrom download.file ensembl_gene_id genename is jun_type
  mrnaAcc name pro_name proname protAcc read.table rsid saveDb
  transcript txname write.table
Consider adding
  importFrom("methods", "as", "is")
  importFrom("utils", "download.file", "read.table", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').

DBI (0.5-1)

Maintainer: Kirill Müller [e-mail] Bug reports: https://github.com/rstats-db/DBI/issues

0 errors | 0 warnings | 1 note

checking S3 generic/method consistency ... NOTE
Found the following apparent S3 methods exported but not registered:
  print.list.pairs
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.

DECIPHER (2.2.0)

Maintainer: Erik Wright [e-mail]

0 errors | 0 warnings | 3 notes

checking installed package size ... NOTE
  installed size is  9.1Mb
  sub-directories of 1Mb or more:
    data      2.5Mb
    doc       3.8Mb
    extdata   1.4Mb

checking foreign function calls ... NOTE
Registration problems:
  symbol ‘functionCall’ in the local frame:
   .Call(functionCall, myXStringSet, as.numeric(subMatrix), gapOpening, 
       gapExtension, gapLetter, shiftPenalty, threshold, weight, 
       PACKAGE = "DECIPHER")
  symbol ‘consensusProfile’ in the local frame:
   .Call(consensusProfile, pattern, p.weight, NULL, PACKAGE = "DECIPHER")
  symbol ‘consensusProfile’ in the local frame:
   .Call(consensusProfile, subject, s.weight, NULL, PACKAGE = "DECIPHER")
... 11 lines ...
       structureMatrix)
  Evaluating ‘compression[1]’ during check gives error
‘object 'compression' not found’:
   .Call(compression[1], x, 2L - length(compression), compressRepeats, 
       processors, PACKAGE = "DECIPHER")
  Evaluating ‘compression[1]’ during check gives error
‘object 'compression' not found’:
   .Call(compression[1], x, 2L - length(compression), processors, 
       PACKAGE = "DECIPHER")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.

checking R code for possible problems ... NOTE
DesignSignatures: no visible binding for global variable ‘deltaHrules’
Undefined global functions or variables:
  deltaHrules

diffrprojects (0.1.14)

Maintainer: Peter Meissner [e-mail] Bug reports: https://github.com/petermeissner/diffrprojects/issues

0 errors | 0 warnings | 0 notes

dplyr (0.5.0)

Maintainer: Hadley Wickham [e-mail] Bug reports: https://github.com/hadley/dplyr/issues

0 errors | 0 warnings | 1 note

checking installed package size ... NOTE
  installed size is 23.4Mb
  sub-directories of 1Mb or more:
    libs  21.3Mb

ecd (0.8.2)

Maintainer: Stephen H-T. Lihn [e-mail]

1 error | 0 warnings | 0 notes

checking package dependencies ... ERROR
Package required and available but unsuitable version: ‘RSQLite’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.

emuR (0.2.0)

Maintainer: Raphael Winkelmann [e-mail] Bug reports: https://github.com/IPS-LMU/emuR/issues

0 errors | 0 warnings | 0 notes

ensembldb (1.6.2)

Maintainer: Johannes Rainer [e-mail] Bug reports: https://github.com/jotsetung/ensembldb/issues

0 errors | 0 warnings | 2 notes

checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  'GenomicFeatures:::fetchChromLengthsFromEnsembl'
  'GenomicFeatures:::fetchChromLengthsFromEnsemblPlants'
  See the note in ?`:::` about the use of this operator.

checking Rd line widths ... NOTE
Rd file 'EnsDb.Rd':
  \examples lines wider than 100 characters:
     dbcon <- dbConnect(MySQL(), user = my_user, pass = my_pass, host = my_host, dbname = "ensdb_hsapiens_v75")

These lines will be truncated in the PDF manual.

etl (0.3.4)

Maintainer: Ben Baumer [e-mail] Bug reports: https://github.com/beanumber/etl/issues

0 errors | 0 warnings | 0 notes

ETLUtils (1.3)

Maintainer: Jan Wijffels [e-mail]

0 errors | 0 warnings | 0 notes

filehashSQLite (0.2-4)

Maintainer: Roger D. Peng [e-mail]

0 errors | 0 warnings | 3 notes

checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘filehash’ ‘DBI’
A package should be listed in only one of these fields.

checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘RSQLite’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.

checking R code for possible problems ... NOTE
createSQLite: no visible global function definition for ‘dbDriver’
createSQLite: no visible global function definition for ‘dbConnect’
createSQLite: no visible global function definition for
  ‘dbUnloadDriver’
createSQLite: no visible global function definition for ‘dbGetQuery’
initializeSQLite: no visible global function definition for ‘dbDriver’
initializeSQLite: no visible global function definition for ‘dbConnect’
initializeSQLite: no visible global function definition for ‘new’
dbDelete,filehashSQLite-character: no visible global function
... 7 lines ...
  definition for ‘dbGetQuery’
dbList,filehashSQLite: no visible global function definition for
  ‘dbGetQuery’
dbMultiFetch,filehashSQLite-character: no visible global function
  definition for ‘dbGetQuery’
Undefined global functions or variables:
  dbConnect dbDriver dbGetQuery dbUnloadDriver new
Consider adding
  importFrom("methods", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').

filematrix (1.1.0)

Maintainer: Andrey A Shabalin [e-mail] Bug reports: https://github.com/andreyshabalin/filematrix/issues

0 errors | 1 warning | 0 notes

checking re-building of vignette outputs ... WARNING
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 2-23 (Best_Prectices.Rmd) 
Error: processing vignette 'Best_Prectices.Rmd' failed with diagnostics:
could not find function "doc_date"
Execution halted

freqweights (1.0.2)

Maintainer: Emilio Torres-Manzanera [e-mail]

0 errors | 0 warnings | 1 note

checking R code for possible problems ... NOTE
.corfreq: no visible global function definition for ‘complete.cases’
.covfreq: no visible global function definition for ‘complete.cases’
.hclustvfreq: no visible global function definition for
  ‘complete.cases’
.quantilefreq : <anonymous>: no visible global function definition for
  ‘approx’
coef.biglmfreq: no visible global function definition for ‘coef’
predict.biglmfreq: no visible global function definition for ‘predict’
predict.lmfreq: no visible global function definition for ‘predict’
summary.lmfreq: no visible global function definition for ‘coef’
summary.lmfreq: no visible global function definition for ‘pt’
summary.lmfreq: no visible global function definition for ‘AIC’
update.biglmfreq: no visible global function definition for ‘update’
Undefined global functions or variables:
  AIC approx coef complete.cases predict pt update
Consider adding
  importFrom("stats", "AIC", "approx", "coef", "complete.cases",
             "predict", "pt", "update")
to your NAMESPACE file.

gcbd (0.2.6)

Maintainer: Dirk Eddelbuettel [e-mail]

0 errors | 1 warning | 0 notes

checking re-building of vignette outputs ... WARNING
Error in re-building vignettes:
  ...
Warning in packageDescription("getopt") : no package 'getopt' was found
Error: processing vignette 'gcbd.Rnw' failed with diagnostics:
at gcbd.Rnw:863, subscript out of bounds
Execution halted

GeneAnswers (2.16.0)

Maintainer: Lei Huang [e-mail] and Gang Feng [e-mail]

1 error | 3 warnings | 6 notes

checking examples ... ERROR
Running examples in ‘GeneAnswers-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: chartPlots
> ### Title: Pie Chart and Bar Plots
> ### Aliases: chartPlots
> ### Keywords: methods
> 
> ### ** Examples
> 
> x <- matrix(c(6,9,3,30,13,2,15,20), nrow = 4, ncol=2, byrow=FALSE,
+                dimnames = list(c("group1", "group2", "group3", "group4"),
+                                c("value1", "value2")))
> chartPlots(x, chartType='all', specifiedCol = "value2", top = 3)
Error in x11() : screen devices should not be used in examples etc
Calls: chartPlots -> x11
Execution halted

checking whether package ‘GeneAnswers’ can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘stats::decompose’ by ‘igraph::decompose’ when loading ‘GeneAnswers’
  Warning: replacing previous import ‘stats::spectrum’ by ‘igraph::spectrum’ when loading ‘GeneAnswers’
See ‘/home/muelleki/git/R/RSQLite/revdep/checks/GeneAnswers.Rcheck/00install.out’ for details.

checking sizes of PDF files under ‘inst/doc’ ... WARNING
  ‘gs+qpdf’ made some significant size reductions:
     compacted ‘geneAnswers.pdf’ from 1373Kb to 600Kb
  consider running tools::compactPDF(gs_quality = "ebook") on these files

checking re-building of vignette outputs ... WARNING
Error in re-building vignettes:
  ...
Warning: replacing previous import ‘stats::spectrum’ by ‘igraph::spectrum’ when loading ‘GeneAnswers’
Loading required package: org.Hs.eg.db

Loading required package: GO.db

Loading required package: KEGG.db

... 8 lines ...
Loading required package: org.Mm.eg.db

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'geneAnswers.tex' failed.
LaTeX errors:
! Package auto-pst-pdf Error: 
    "shell escape" (or "write18") is not enabled:
    auto-pst-pdf will not work!
.
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted

checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘igraph’ ‘RCurl’ ‘annotate’ ‘Biobase’ ‘XML’ ‘RSQLite’ ‘MASS’
  ‘Heatplus’ ‘RColorBrewer’
Adding so many packages to the search path is excessive and importing
selectively is preferable.

checking installed package size ... NOTE
  installed size is 36.1Mb
  sub-directories of 1Mb or more:
    External  32.4Mb
    data       1.1Mb
    doc        1.6Mb

checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘annotate’
A package should be listed in only one of these fields.

checking dependencies in R code ... NOTE
'library' or 'require' calls to packages already attached by Depends:
  ‘Biobase’ ‘Heatplus’ ‘MASS’ ‘RColorBrewer’ ‘XML’ ‘igraph’
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  ‘GO.db’ ‘KEGG.db’ ‘biomaRt’ ‘reactome.db’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.

checking R code for possible problems ... NOTE
Found an obsolete/platform-specific call in the following functions:
  ‘chartPlots’ ‘drawTable’
Found the platform-specific device:
  ‘x11’
dev.new() is the preferred way to open a new device, in the unlikely
event one is needed.
File ‘GeneAnswers/R/zzz.R’:
  .onLoad calls:
    require(Biobase)
... 78 lines ...
  data("DmIALite", package = "GeneAnswers")
File ‘GeneAnswers/R/getDOLiteTerms.R’:
  data("DOLiteTerm", package = "GeneAnswers")
File ‘GeneAnswers/R/zzz.R’:
  data("DOLite", package = "GeneAnswers")
  data("DOLiteTerm", package = "GeneAnswers")
  data("HsIALite", package = "GeneAnswers")
  data("MmIALite", package = "GeneAnswers")
  data("RnIALite", package = "GeneAnswers")
  data("DmIALite", package = "GeneAnswers")
See section ‘Good practice’ in ‘?data’.

checking Rd line widths ... NOTE
Rd file 'GeneAnswers-class.Rd':
  \examples lines wider than 100 characters:
     x <- geneAnswersBuilder(humanGeneInput, 'org.Hs.eg.db', categoryType='GO.BP', testType='hyperG', pvalueT=0.01, FDR.correct=TRUE, geneEx ... [TRUNCATED]

Rd file 'GeneAnswers-package.Rd':
  \examples lines wider than 100 characters:
     x <- geneAnswersBuilder(humanGeneInput, 'org.Hs.eg.db', categoryType='GO.BP', testType='hyperG', pvalueT=0.01, FDR.correct=TRUE, geneEx ... [TRUNCATED]

Rd file 'buildNet.Rd':
... 144 lines ...
     ## Not run: topDOLITEGenes(x, geneSymbol=TRUE, orderby='pvalue', top=10, topGenes='ALL', genesOrderBy='pValue', file=TRUE)

Rd file 'topPATHGenes.Rd':
  \examples lines wider than 100 characters:
     ## Not run: topPATHGenes(x, geneSymbol=TRUE, orderby='genenum', top=6, topGenes=8, genesOrderBy='foldChange')

Rd file 'topREACTOME.PATHGenes.Rd':
  \examples lines wider than 100 characters:
     ## Not run: topREACTOME.PATHGenes(x, geneSymbol=TRUE, orderby='pvalue', top=10, topGenes='ALL', genesOrderBy='pValue', file=TRUE)

These lines will be truncated in the PDF manual.

GenomicFeatures (1.26.0)

Maintainer: Bioconductor Package Maintainer [e-mail]

0 errors | 0 warnings | 2 notes

checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘BiocGenerics’ ‘S4Vectors’ ‘IRanges’ ‘GenomeInfoDb’ ‘GenomicRanges’
  ‘AnnotationDbi’
Adding so many packages to the search path is excessive and importing
selectively is preferable.

checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  ‘AnnotationDbi:::.getMetaValue’ ‘AnnotationDbi:::.valid.colnames’
  ‘AnnotationDbi:::.valid.metadata.table’
  ‘AnnotationDbi:::.valid.table.colnames’ ‘AnnotationDbi:::dbEasyQuery’
  ‘AnnotationDbi:::dbQuery’ ‘AnnotationDbi:::smartKeys’
  ‘biomaRt:::martBM’ ‘biomaRt:::martDataset’ ‘biomaRt:::martHost’
  ‘rtracklayer:::resourceDescription’ ‘rtracklayer:::ucscTableOutputs’
  See the note in ?`:::` about the use of this operator.

Genominator (1.28.0)

Maintainer: James Bullard [e-mail]

0 errors | 0 warnings | 4 notes

checking dependencies in R code ... NOTE
'library' or 'require' calls to packages already attached by Depends:
  ‘GenomeGraphs’ ‘IRanges’
  Please remove these calls from your code.
'library' or 'require' call to ‘ShortRead’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘GenomeGraphs’ ‘RSQLite’
  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 ... NOTE
Found the following apparent S3 methods exported but not registered:
  plot.genominator.coverage plot.genominator.goodness.of.fit
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.

checking R code for possible problems ... NOTE
addPrimingWeights: no visible global function definition for
  ‘varLabels’
addPrimingWeights: no visible global function definition for
  ‘alignData’
addPrimingWeights: no visible global function definition for ‘subseq’
addPrimingWeights: no visible global function definition for ‘sread’
addPrimingWeights: no visible global function definition for
  ‘AlignedDataFrame’
addPrimingWeights: no visible global function definition for ‘pData’
... 46 lines ...
  function definition for ‘qunif’
plot.genominator.goodness.of.fit : <anonymous>: no visible global
  function definition for ‘qqplot’
Undefined global functions or variables:
  AlignedDataFrame DisplayPars alignData chromosome gdPlot
  geneRegionBiomart makeAnnotationTrack makeBaseTrack makeGenericArray
  makeGenomeAxis mkAllStrings pData position ppoints qchisq qqplot
  qunif readAligned sread subseq tables varLabels varMetadata
Consider adding
  importFrom("stats", "ppoints", "qchisq", "qqplot", "qunif")
to your NAMESPACE file.

checking Rd line widths ... NOTE
Rd file 'makeGeneRepresentation.Rd':
  \usage lines wider than 90 characters:
     "background"), gene.id = "ensembl_gene_id", transcript.id = "ensembl_transcript_id", bind.columns, ignoreStrand = TRUE, verbose = getOp ... [TRUNCATED]

These lines will be truncated in the PDF manual.

GEOmetadb (1.34.0)

Maintainer: Jack Zhu [e-mail]

0 errors | 0 warnings | 3 notes

checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.

checking R code for possible problems ... NOTE
getSQLiteFile: no visible global function definition for
  ‘download.file’
Undefined global functions or variables:
  download.file
Consider adding
  importFrom("utils", "download.file")
to your NAMESPACE file.

checking Rd line widths ... NOTE
Rd file 'geoConvert.Rd':
  \usage lines wider than 90 characters:
     geoConvert(in_list, out_type = c("gse", "gpl", "gsm", "gds", "smatrix"), sqlite_db_name = "GEOmetadb.sqlite")

These lines will be truncated in the PDF manual.

GWASTools (1.20.0)

Maintainer: Stephanie M. Gogarten [e-mail], Adrienne Stilp [e-mail]

0 errors | 0 warnings | 1 note

checking Rd line widths ... NOTE
Rd file 'assocRegression.Rd':
  \examples lines wider than 100 characters:
     scanAnnot$blood.pressure[scanAnnot$case.cntl.status==1] <- rnorm(sum(scanAnnot$case.cntl.status==1), mean=100, sd=10)
     scanAnnot$blood.pressure[scanAnnot$case.cntl.status==0] <- rnorm(sum(scanAnnot$case.cntl.status==0), mean=90, sd=5)

Rd file 'createDataFile.Rd':
  \usage lines wider than 90 characters:
                    precision="single", compress="ZIP_RA:8M", compress.geno="ZIP_RA", compress.annot="ZIP_RA",

These lines will be truncated in the PDF manual.

imputeMulti (0.6.3)

Maintainer: Alex Whitworth [e-mail]

0 errors | 0 warnings | 1 note

checking dependencies in R code ... NOTE
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘count_compare’

iontree (1.20.0)

Maintainer: Mingshu Cao [e-mail]

0 errors | 0 warnings | 5 notes

checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.

checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.

checking R code for possible problems ... NOTE
buildIonTree: no visible binding for global variable ‘median’
metaDataImport: no visible global function definition for
  ‘flush.console’
metaDataImport: no visible global function definition for ‘fix’
plotSpectrum: no visible global function definition for ‘text’
plotSpectrum: no visible global function definition for ‘identify’
saveMSnRaw: no visible global function definition for ‘flush.console’
searchMS2: no visible global function definition for ‘par’
plot,iontree: no visible global function definition for ‘par’
plot,iontree: no visible global function definition for ‘layout’
Undefined global functions or variables:
  fix flush.console identify layout median par text
Consider adding
  importFrom("graphics", "identify", "layout", "par", "text")
  importFrom("stats", "median")
  importFrom("utils", "fix", "flush.console")
to your NAMESPACE file.

checking Rd files ... NOTE
prepare_Rd: buildIonTree.Rd:18-19: Dropping empty section \details
prepare_Rd: buildIonTree.Rd:20-26: Dropping empty section \value
prepare_Rd: buildIonTree.Rd:27-29: Dropping empty section \references
prepare_Rd: buildIonTree.Rd:37-39: Dropping empty section \seealso
prepare_Rd: createDB.Rd:19-20: Dropping empty section \details
prepare_Rd: createDB.Rd:30-32: Dropping empty section \note
prepare_Rd: createDB.Rd:24-26: Dropping empty section \references
prepare_Rd: createDB.Rd:34-36: Dropping empty section \seealso
prepare_Rd: distMS2.Rd:18-19: Dropping empty section \details
... 50 lines ...
prepare_Rd: saveMSnRaw.Rd:33-35: Dropping empty section \note
prepare_Rd: saveMSnRaw.Rd:27-29: Dropping empty section \references
prepare_Rd: saveMSnRaw.Rd:36-38: Dropping empty section \seealso
prepare_Rd: searchMS2.Rd:23-25: Dropping empty section \details
prepare_Rd: searchMS2.Rd:35-36: Dropping empty section \note
prepare_Rd: searchMS2.Rd:29-31: Dropping empty section \references
prepare_Rd: searchMS2.Rd:38-40: Dropping empty section \seealso
prepare_Rd: searchMS2.Rd:41-42: Dropping empty section \examples
prepare_Rd: topIons.Rd:17-19: Dropping empty section \details
prepare_Rd: topIons.Rd:29-31: Dropping empty section \note
prepare_Rd: topIons.Rd:23-25: Dropping empty section \references

checking Rd line widths ... NOTE
Rd file 'searchMS2.Rd':
  \usage lines wider than 90 characters:
     searchMS2(querySpec, premz, dbname = "mzDB.db", scoreFun = "distMS2", output.record = 5, plot.top = TRUE)

These lines will be truncated in the PDF manual.

KoNLP (0.80.0)

Maintainer: Heewon Jeon [e-mail] Bug reports: https://github.com/haven-jeon/KoNLP/issues

0 errors | 0 warnings | 1 note

checking installed package size ... NOTE
  installed size is  6.4Mb
  sub-directories of 1Mb or more:
    java   5.9Mb

lumi (2.26.3)

Maintainer: Pan Du [e-mail]

0 errors | 1 warning | 3 notes

checking dependencies in R code ... WARNING
'::' or ':::' import not declared from: ‘bigmemoryExtras’

checking installed package size ... NOTE
  installed size is  6.8Mb
  sub-directories of 1Mb or more:
    R      2.8Mb
    data   3.6Mb

checking Rd line widths ... NOTE
Rd file 'IlluminaID2nuID.Rd':
  \usage lines wider than 90 characters:
     IlluminaID2nuID(IlluminaID, lib.mapping=NULL, species = c("Human", "Mouse", "Rat", "Unknown"), chipVersion = NULL, ...)

Rd file 'addAnnotationInfo.Rd':
  \usage lines wider than 90 characters:
     addAnnotationInfo(methyLumiM, lib = 'FDb.InfiniumMethylation.hg19', annotationColumn=c('COLOR_CHANNEL', 'CHROMOSOME', 'POSITION'))

Rd file 'addNuID2lumi.Rd':
... 177 lines ...
     smoothQuantileNormalization(dataMatrix, ref = NULL, adjData=NULL, logMode = TRUE, bandwidth = NULL, degree = 1, verbose = FALSE, ...)

Rd file 'ssn.Rd':
  \usage lines wider than 90 characters:
     ssn(x.lumi, targetArray = NULL, scaling = TRUE, bgMethod=c('density', 'mean', 'median', 'none'), fgMethod=c('mean', 'density', 'median' ... [TRUNCATED]

Rd file 'vst.Rd':
  \usage lines wider than 90 characters:
     vst(u, std, nSupport = min(length(u), 500), backgroundStd=NULL, fitMethod = c('linear', 'quadratic'), lowCutoff = 1/3, ifPlot = FALSE)

These lines will be truncated in the PDF manual.

checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘bigmemoryExtras’

macleish (0.3.0)

Maintainer: Ben Baumer [e-mail]

0 errors | 0 warnings | 0 notes

maGUI (1.0)

Maintainer: Dhammapal Bharne [e-mail]

1 error | 0 warnings | 0 notes

checking whether package ‘maGUI’ can be installed ... ERROR
Installation failed.
See ‘/home/muelleki/git/R/RSQLite/revdep/checks/maGUI.Rcheck/00install.out’ for details.

manta (1.20.0)

Maintainer: Chris Berthiaume [e-mail], Adrian Marchetti [e-mail]

0 errors | 0 warnings | 7 notes

checking installed package size ... NOTE
  installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc       1.4Mb
    extdata   4.0Mb

checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.

checking dependencies in R code ... NOTE
'library' or 'require' calls in package code:
  ‘RSQLite’ ‘plotrix’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.meta2metasum’

checking S3 generic/method consistency ... NOTE
Found the following apparent S3 methods exported but not registered:
  plot.manta summary.manta
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.

checking R code for possible problems ... NOTE
.MTDheatplot: no visible global function definition for ‘gray’
.MTDheatplot: no visible global function definition for
  ‘colorRampPalette’
.MTDheatplot: no visible global function definition for ‘abline’
.MTDheatplot: no visible global function definition for ‘segments’
.MTDheatplot: no visible global function definition for ‘par’
.MTDheatplot: no visible global function definition for ‘plot’
.aggBinCounts: no visible global function definition for ‘hist’
.aggDESigCumDist: no visible global function definition for ‘hist’
... 51 lines ...
  importFrom("graphics", "abline", "boxplot", "hist", "legend", "par",
             "plot", "segments")
  importFrom("methods", "new")
  importFrom("stats", "aggregate", "anova", "lm", "p.adjust", "var")
  importFrom("utils", "read.delim")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').

Found the following assignments to the global environment:
File ‘manta/R/Util.R’:
  assign(keys[i], value, envir = .GlobalEnv)

checking Rd line widths ... NOTE
Rd file 'compbiasPlot.Rd':
  \usage lines wider than 90 characters:
     compbiasPlot(x, pair=nv(levels(x$samples$group)[1:2] , c('ref','obs')), meta.lev='phylum',  meta.lev.lim=nrow(x$meta.sum[[meta.lev]]),  ... [TRUNCATED]

Rd file 'compbiasTest.Rd':
  \usage lines wider than 90 characters:
     compbiasTest(x, pair=nv(levels(x$samples$group)[1:2] , c('ref','obs')), meta.lev='phylum',  meta.lev.lim=min(10,nrow(x$meta.sum[[meta.l ... [TRUNCATED]

Rd file 'in2manta.Rd':
... 9 lines ...

Rd file 'plot.manta.Rd':
  \usage lines wider than 90 characters:
                            meta.level=names(x$meta.sum)[1], meta.lgnd.lim=6, lgd.pos='topright', lgd.cex=.75, lgd.trunk=FALSE, pie.lwd=1,

Rd file 'readSeastar.Rd':
  \usage lines wider than 90 characters:
     clmn.names=c('seq_id','bit_score','read_count','raw_abundance','fractional_abundance','mean_coverage','mean_read_length','seq_len','gc_ ... [TRUNCATED]
     name.clmn='seq_id', ret.df=FALSE, ret.clmn='read_count', ct.calc=expression(raw_abundance*seq_len), header = FALSE, ...)

These lines will be truncated in the PDF manual.

checking Rd \usage sections ... NOTE
S3 methods shown with full name in documentation object 'summary.manta':
  ‘summary.manta’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.

marmap (0.9.5)

Maintainer: Eric Pante [e-mail]

0 errors | 0 warnings | 0 notes

MeSHDbi (1.10.0)

Maintainer: Koki Tsuyuzaki [e-mail]

0 errors | 0 warnings | 2 notes

checking R code for possible problems ... NOTE
.div: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  na.omit
Consider adding
  importFrom("stats", "na.omit")
to your NAMESPACE file.

checking Rd line widths ... NOTE
Rd file 'makeMeSHPackage.Rd':
  \examples lines wider than 100 characters:
                                             maintainer = "Koki Tsuyuzaki <[e-mail]>",

These lines will be truncated in the PDF manual.

metagenomeFeatures (1.4.0)

Maintainer: Nathan D. Olson [e-mail] Bug reports: https://github.com/HCBravoLab/metagenomeFeatures/issues

0 errors | 2 warnings | 2 notes

checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic 'taxa_columns' and siglist 'MgDb'
  generic 'taxa_keys' and siglist 'MgDb'
  generic 'taxa_keytypes' and siglist 'MgDb'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.

checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'annotateFeatures'
  ‘query_key’
Documented arguments not in \usage in documentation object 'annotateFeatures':
  ‘db_keys’ ‘query_df’

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 installed package size ... NOTE
  installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R         1.1Mb
    extdata   3.4Mb

checking R code for possible problems ... NOTE
.mgDb_annotateFeatures: no visible binding for global variable
  ‘db_keys’
.select.taxa: no visible binding for global variable ‘Keys’
.select.taxa: no visible binding for global variable ‘.’
aggregate_taxa: no visible binding for global variable ‘.’
aggregate_taxa: no visible binding for global variable ‘index’
aggregate_taxa: no visible global function definition for
  ‘newMRexperiment’
vignette_pheno_data: no visible global function definition for
  ‘read.csv’
Undefined global functions or variables:
  . Keys db_keys index newMRexperiment read.csv
Consider adding
  importFrom("utils", "read.csv")
to your NAMESPACE file.

MetaIntegrator (1.0.3)

Maintainer: Winston A. Haynes [e-mail]

0 errors | 0 warnings | 0 notes

metaseqR (1.14.0)

Maintainer: Panagiotis Moulos [e-mail]

1 error | 1 warning | 4 notes

checking tests ... ERROR
Running the tests in ‘tests/runTests.R’ failed.
Last 13 lines of output:

  Test files with failing tests

     test_estimate_aufc_weights.R 
       test_estimate_aufc_weights 

     test_metaseqr.R 
       test_metaseqr 


  Error in BiocGenerics:::testPackage("metaseqR") : 
    unit tests failed for package metaseqR
  Execution halted

checking re-building of vignette outputs ... WARNING
Error in re-building vignettes:
  ...

The following objects are masked from 'package:ShortRead':

    left, right

Loading required package: lattice
    Welcome to 'DESeq'. For improved performance, usability and
... 8 lines ...
    plotMA

The following object is masked from 'package:BiocGenerics':

    plotMA

Loading required package: qvalue
Quitting from lines 119-159 (metaseqr-pdf.Rnw) 
Error: processing vignette 'metaseqr-pdf.Rnw' failed with diagnostics:
13 simultaneous processes spawned
Execution halted

checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘TCC’

checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.

checking dependencies in R code ... NOTE
'library' or 'require' calls in package code:
  ‘BSgenome’ ‘BiocInstaller’ ‘GenomicRanges’ ‘RMySQL’ ‘RSQLite’
  ‘Rsamtools’ ‘TCC’ ‘VennDiagram’ ‘parallel’ ‘rtracklayer’ ‘survcomp’
  ‘zoo’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.

checking R code for possible problems ... NOTE
biasPlotToJSON: no visible binding for global variable ‘nams’
cddat: no visible global function definition for ‘assayData’
cddat: no visible global function definition for ‘ks.test’
cddat: no visible global function definition for ‘p.adjust’
cdplot: no visible global function definition for ‘plot’
cdplot: no visible global function definition for ‘lines’
countsBioToJSON: no visible binding for global variable ‘nams’
diagplot.avg.ftd : <anonymous>: no visible binding for global variable
  ‘sd’
... 246 lines ...
             "dev.off", "jpeg", "pdf", "png", "postscript", "tiff")
  importFrom("graphics", "abline", "arrows", "axis", "grid", "lines",
             "mtext", "par", "plot", "plot.new", "plot.window", "points",
             "text", "title")
  importFrom("methods", "as", "new")
  importFrom("stats", "as.dist", "cmdscale", "cor", "end", "ks.test",
             "mad", "median", "model.matrix", "na.exclude", "optimize",
             "p.adjust", "p.adjust.methods", "pchisq", "quantile",
             "rexp", "rnbinom", "runif", "sd", "start", "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').

mgsa (1.22.0)

Maintainer: Sebastian Bauer [e-mail]

0 errors | 1 warning | 4 notes

checking for GNU extensions in Makefiles ... WARNING
Found the following file(s) containing GNU extensions:
  src/Makevars
  src/Makevars.in
Portable Makefiles do not use GNU extensions such as +=, :=, $(shell),
$(wildcard), ifeq ... endif. See section ‘Writing portable packages’ in
the ‘Writing R Extensions’ manual.

checking top-level files ... NOTE
Non-standard files/directories found at top level:
  ‘acinclude.m4’ ‘aclocal.m4’ ‘script’

checking whether the namespace can be loaded with stated dependencies ... NOTE
Warning: no function found corresponding to methods exports from ‘mgsa’ for: ‘show’

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.

checking dependencies in R code ... NOTE
'library' or 'require' call to ‘gplots’ which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  ‘DBI’ ‘GO.db’ ‘RSQLite’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘gplots’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.

checking R code for possible problems ... NOTE
createMgsaGoSets: no visible global function definition for ‘new’
mcmcSummary: no visible binding for global variable ‘sd’
mgsa.wrapper: no visible global function definition for ‘str’
mgsa.wrapper: no visible global function definition for ‘new’
readGAF: no visible global function definition for ‘read.delim’
readGAF: no visible global function definition for ‘na.omit’
readGAF: no visible global function definition for ‘new’
initialize,MgsaSets: no visible global function definition for
  ‘callNextMethod’
... 10 lines ...
  ‘close.screen’
Undefined global functions or variables:
  barplot2 callNextMethod close.screen na.omit new par read.delim
  relist screen sd split.screen str
Consider adding
  importFrom("graphics", "close.screen", "par", "screen", "split.screen")
  importFrom("methods", "callNextMethod", "new")
  importFrom("stats", "na.omit", "sd")
  importFrom("utils", "read.delim", "relist", "str")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').

miRNAtap (1.8.0)

Maintainer: Maciej Pajak [e-mail]

0 errors | 0 warnings | 2 notes

checking dependencies in R code ... NOTE
'library' or 'require' call to ‘miRNAtap.db’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.

checking R code for possible problems ... NOTE
getTargetsFromSource: no visible binding for global variable
  ‘miRNAtap.db’
getTargetsFromSource : <anonymous>: no visible binding for global
  variable ‘miRNAtap.db’
translate: no visible binding for global variable ‘miRNAtap.db’
Undefined global functions or variables:
  miRNAtap.db

MmPalateMiRNA (1.24.0)

Maintainer: Guy Brock [e-mail]

0 errors | 0 warnings | 4 notes

checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘Biobase’ ‘xtable’ ‘limma’ ‘statmod’ ‘lattice’ ‘vsn’
Adding so many packages to the search path is excessive and importing
selectively is preferable.

checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘limma’ ‘lattice’ ‘Biobase’
A package should be listed in only one of these fields.

checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘methods’ ‘statmod’ ‘vsn’ ‘xtable’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.

checking R code for possible problems ... NOTE
clustPlot: no visible global function definition for ‘par’
clustPlot: no visible global function definition for ‘plot’
clustPlot: no visible global function definition for ‘axis’
clustPlot: no visible global function definition for ‘lines’
clustPlot: no visible global function definition for ‘legend’
fixOutliers : <anonymous>: no visible global function definition for
  ‘sd’
imputeKNN: no visible global function definition for ‘sd’
imputeKNN: no visible global function definition for ‘cor’
... 36 lines ...
  definition for ‘assayData’
levelplot,list-missing: no visible global function definition for
  ‘median’
Undefined global functions or variables:
  RG.MA as.formula assayData axis cor featureData legend lines mad
  median pData par plot sd stack
Consider adding
  importFrom("graphics", "axis", "legend", "lines", "par", "plot")
  importFrom("stats", "as.formula", "cor", "mad", "median", "sd")
  importFrom("utils", "stack")
to your NAMESPACE file.

MonetDBLite (0.3.1)

Maintainer: Hannes Muehleisen [e-mail] Bug reports: https://github.com/hannesmuehleisen/MonetDBLite/issues

0 errors | 0 warnings | 1 note

checking installed package size ... NOTE
  installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb

MUCflights (0.0-3)

Maintainer: Manuel Eugster [e-mail]

0 errors | 0 warnings | 3 notes

checking dependencies in R code ... NOTE
'library' or 'require' call to ‘XML’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘NightDay’ ‘RSQLite’ ‘XML’ ‘geosphere’ ‘sp’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.

checking R code for possible problems ... NOTE
drawMap: no visible global function definition for ‘plot’
drawMap: no visible global function definition for ‘box’
drawMap: no visible global function definition for ‘points’
getFlights: no visible binding for global variable ‘htmlTreeParse’
getFlights: no visible binding for global variable ‘xpathSApply’
getFlights: no visible binding for global variable ‘xmlAttrs’
getFlights: no visible binding for global variable ‘free’
movie.routes: no visible global function definition for
  ‘txtProgressBar’
... 16 lines ...
routes: no visible global function definition for ‘gcIntermediate’
Undefined global functions or variables:
  box data dev.off distHaversine free gcIntermediate htmlTreeParse jpeg
  lines mtext plot points setTxtProgressBar text txtProgressBar
  xmlAttrs xpathSApply
Consider adding
  importFrom("grDevices", "dev.off", "jpeg")
  importFrom("graphics", "box", "lines", "mtext", "plot", "points",
             "text")
  importFrom("utils", "data", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.

checking Rd line widths ... NOTE
Rd file 'flights.Rd':
  \usage lines wider than 90 characters:
     flights(from = NULL, to = NULL, path = system.file("MUCflights.RData", package = "MUCflights"))

These lines will be truncated in the PDF manual.

nutshell.bbdb (1.0)

Maintainer: Joseph Adler [e-mail]

0 errors | 0 warnings | 2 notes

checking installed package size ... NOTE
  installed size is 39.0Mb
  sub-directories of 1Mb or more:
    extdata  38.9Mb

checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
Deprecated license: CC BY-NC-ND 3.0 US

nutshell (2.0)

Maintainer: Joseph Adler [e-mail]

0 errors | 0 warnings | 3 notes

checking installed package size ... NOTE
  installed size is  8.8Mb
  sub-directories of 1Mb or more:
    data   8.7Mb

checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
Deprecated license: CC BY-NC-ND 3.0 US

checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘nutshell.audioscrobbler’ ‘nutshell.bbdb’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.

oai (0.2.2)

Maintainer: Scott Chamberlain [e-mail] Bug reports: https://github.com/ropensci/oai/issues

0 errors | 0 warnings | 0 notes

oce (0.9-20)

Maintainer: Dan Kelley [e-mail] Bug reports: https://github.com/dankelley/oce/issues

1 error | 0 warnings | 1 note

checking examples ... ERROR
Running examples in ‘oce-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: read.oce
> ### Title: Read an Oceanographic Data File
> ### Aliases: read.oce
> 
> ### ** Examples
> 
> 
> library(oce)
> x <- read.oce(system.file("extdata", "ctd.cnv", package="oce"))
> plot(x) # summary with TS and profiles
Error in if (!is.null(x@metadata$startTime) && 4 < nchar(x@metadata$startTime,  : 
  missing value where TRUE/FALSE needed
Calls: plot -> plot -> .local
Execution halted

checking installed package size ... NOTE
  installed size is  5.4Mb
  sub-directories of 1Mb or more:
    help   2.1Mb

oligoClasses (1.36.0)

Maintainer: Benilton Carvalho [e-mail] and Robert Scharpf [e-mail]

0 errors | 1 warning | 4 notes

checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic '[' and siglist 'CNSet,ANY,ANY,ANY'
  generic '[' and siglist 'gSetList,ANY,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.

checking package dependencies ... NOTE
Packages which this enhances but not available for checking:
  ‘doMC’ ‘doMPI’ ‘doSNOW’ ‘doRedis’

checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: ‘Biobase:::assayDataEnvLock’
  See the note in ?`:::` about the use of this operator.

checking R code for possible problems ... NOTE
getSequenceLengths: no visible binding for global variable ‘seqlengths’
pdPkgFromBioC: no visible binding for global variable ‘contrib.url’
pdPkgFromBioC: no visible global function definition for
  ‘available.packages’
pdPkgFromBioC: no visible global function definition for
  ‘install.packages’
chromosome,gSetList: no visible global function definition for
  ‘chromosomeList’
coerce,CNSet-CopyNumberSet: no visible global function definition for
  ‘totalCopynumber’
geometry,FeatureSet: no visible global function definition for ‘getPD’
Undefined global functions or variables:
  available.packages chromosomeList contrib.url getPD install.packages
  seqlengths totalCopynumber
Consider adding
  importFrom("utils", "available.packages", "contrib.url",
             "install.packages")
to your NAMESPACE file.

checking Rd line widths ... NOTE
Rd file 'AssayDataList.Rd':
  \examples lines wider than 100 characters:
     r <- lapply(r, function(x,dns) {dimnames(x) <- dns; return(x)}, dns=list(letters[1:5], LETTERS[1:5]))

Rd file 'GenomeAnnotatedDataFrameFrom-methods.Rd':
  \examples lines wider than 100 characters:
                                 dimnames=list(c("rs10000092","rs1000055", "rs100016", "rs10003241", "rs10004197"), NULL))

Rd file 'largeObjects.Rd':
  \usage lines wider than 90 characters:
     initializeBigMatrix(name=basename(tempfile()), nr=0L, nc=0L, vmode = "integer", initdata = NA)

Rd file 'oligoSetExample.Rd':
  \examples lines wider than 100 characters:
                                     copyNumber=integerMatrix(log2(locusLevelData[["copynumber"]]/100), 100),

These lines will be truncated in the PDF manual.

oligo (1.38.0)

Maintainer: Benilton Carvalho [e-mail]

1 error | 0 warnings | 9 notes

checking examples ... ERROR
Running examples in ‘oligo-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: MAplot
> ### Title: MA plots
> ### Aliases: MAplot MAplot-methods MAplot,FeatureSet-method
> ###   MAplot,TilingFeatureSet-method MAplot,PLMset-method
> ###   MAplot,ExpressionSet-method MAplot,matrix-method
... 8 lines ...
+   groups <- factor(rep(c('brain', 'UnivRef'), each=3))
+   data.frame(sampleNames(nimbleExpressionFS), groups)
+   MAplot(nimbleExpressionFS, pairs=TRUE, ylim=c(-.5, .5), groups=groups)
+ }
Loading required package: oligoData
Loading required package: pd.hg18.60mer.expr
Loading required package: RSQLite
Loading required package: DBI
Error in loadNamespace(name) : there is no package called ‘KernSmooth’
Calls: MAplot ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted

checking package dependencies ... NOTE
Packages which this enhances but not available for checking: ‘doMC’ ‘doMPI’

checking installed package size ... NOTE
  installed size is 30.3Mb
  sub-directories of 1Mb or more:
    R         1.2Mb
    doc      12.9Mb
    scripts  15.7Mb

checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘biomaRt’ ‘AnnotationDbi’ ‘GenomeGraphs’ ‘RCurl’ ‘ff’
A package should be listed in only one of these fields.

checking top-level files ... NOTE
Non-standard file/directory found at top level:
  ‘TODO.org’

checking whether the namespace can be loaded with stated dependencies ... NOTE
Warning: no function found corresponding to methods exports from ‘oligo’ for: ‘show’

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.

checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: ‘Biobase:::annotatedDataFrameFromMatrix’
  See the note in ?`:::` about the use of this operator.

checking foreign function calls ... NOTE
Foreign function calls to a different package:
  .Call("ReadHeader", ..., PACKAGE = "affyio")
  .Call("read_abatch", ..., PACKAGE = "affyio")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.

checking R code for possible problems ... NOTE
image,FeatureSet: warning in matrix(NA, nr = geom[1], nc = geom[2]):
  partial argument match of 'nr' to 'nrow'
image,FeatureSet: warning in matrix(NA, nr = geom[1], nc = geom[2]):
  partial argument match of 'nc' to 'ncol'
NUSE: no visible global function definition for ‘abline’
RLE: no visible global function definition for ‘abline’
basicMvApairsPlot: no visible binding for global variable
  ‘smoothScatter’
basicMvApairsPlot: no visible global function definition for ‘frame’
... 36 lines ...
Undefined global functions or variables:
  IQR abline aggregate approx complete.cases data frame intensities
  loess man_fsetid mtext predict rnorm smooth.spline smoothScatter
  splinefun text
Consider adding
  importFrom("graphics", "abline", "frame", "mtext", "smoothScatter",
             "text")
  importFrom("stats", "IQR", "aggregate", "approx", "complete.cases",
             "loess", "predict", "rnorm", "smooth.spline", "splinefun")
  importFrom("utils", "data")
to your NAMESPACE file.

checking Rd line widths ... NOTE
Rd file 'basicRMA.Rd':
  \usage lines wider than 90 characters:
     basicRMA(pmMat, pnVec, normalize = TRUE, background = TRUE, bgversion = 2, destructive = FALSE, verbose = TRUE, ...)

Rd file 'fitProbeLevelModel.Rd':
  \usage lines wider than 90 characters:
     fitProbeLevelModel(object, background=TRUE, normalize=TRUE, target="core", method="plm", verbose=TRUE, S4=TRUE, ...)

Rd file 'getProbeInfo.Rd':
  \usage lines wider than 90 characters:
     getProbeInfo(object, field, probeType = "pm", target = "core", sortBy = c("fid", "man_fsetid", "none"), ...)
  \examples lines wider than 100 characters:
        agenGene <- getProbeInfo(affyGeneFS, field=c('fid', 'fsetid', 'type'), target='probeset', subset= type == 'control->bgp->antigenomic ... [TRUNCATED]

Rd file 'preprocessTools.Rd':
  \usage lines wider than 90 characters:
     backgroundCorrect(object, method=backgroundCorrectionMethods(), copy=TRUE, extra, subset=NULL, target='core', verbose=TRUE)
     normalize(object, method=normalizationMethods(), copy=TRUE, subset=NULL,target='core', verbose=TRUE, ...)

These lines will be truncated in the PDF manual.

OrganismDbi (1.16.0)

Maintainer: Biocore Data Team [e-mail]

0 errors | 0 warnings | 2 notes

checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: ‘BiocGenerics:::testPackage’
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.biocAnnPackages’ ‘.extractPkgsAndCols’ ‘.gentlyExtractDbFiles’
  ‘.lookupDbNameFromKeytype’ ‘.mungeGraphData’ ‘.taxIdToOrgDb’
  ‘.taxIdToOrgDbName’ ‘.testGraphData’ ‘.testKeys’ ‘OrganismDb’

checking R code for possible problems ... NOTE
Found the following assignments to the global environment:
File ‘OrganismDbi/R/createOrganismPackage.R’:
  assign(txdbName, txdb, .GlobalEnv)
  assign(orgdbName, orgdb, .GlobalEnv)
  assign(orgdbName, orgdb, .GlobalEnv)

PAnnBuilder (1.38.0)

Maintainer: Li Hong [e-mail]

0 errors | 3 warnings | 1 note

checking dependencies in R code ... WARNING
'library' or 'require' call to ‘Biobase’ which was already attached by Depends.
  Please remove these calls from your code.
':::' calls which should be '::':
  ‘AnnotationDbi:::as.list’ ‘base:::get’ ‘tools:::list_files_with_type’
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
  ‘AnnotationDbi:::createAnnDbBimaps’
  ‘AnnotationDbi:::prefixAnnObjNames’ ‘tools:::makeLazyLoadDB’
  See the note in ?`:::` about the use of this operator.
  Including base/recommended package(s):
  ‘tools’
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘getShortSciName’ ‘twoStepSplit’

checking R code for possible problems ... WARNING
Found an obsolete/platform-specific call in the following function:
  ‘makeLLDB’
Found the defunct/removed function:
  ‘.saveRDS’

In addition to the above warning(s), found the following notes:

File ‘PAnnBuilder/R/zzz.R’:
  .onLoad calls:
    require(Biobase)

Package startup functions should not change the search path.
See section ‘Good practice’ in '?.onAttach'.

Found the following calls to data() loading into the global environment:
File ‘PAnnBuilder/R/writeManPage.R’:
  data("descriptionInfo")
  data("descriptionInfo")
See section ‘Good practice’ in ‘?data’.

checking re-building of vignette outputs ... WARNING
Error in re-building vignettes:
  ...
             }


trying URL 'http://gpcr2.biocomp.unibo.it/bacello/dataset.htm'
Content type 'text/html; charset=iso-8859-1' length 5062 bytes
==================================================
downloaded 5062 bytes
... 8 lines ...
Warning in rsqlite_disconnect(conn@ptr) :
  There are 1 result in use. The connection will be released when they are closed
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'PAnnBuilder.tex' failed.
LaTeX errors:
! Package auto-pst-pdf Error: 
    "shell escape" (or "write18") is not enabled:
    auto-pst-pdf will not work!
.
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted

checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’ ‘utils’ ‘Biobase’ ‘RSQLite’ ‘AnnotationDbi’
A package should be listed in only one of these fields.

pdInfoBuilder (1.38.0)

Maintainer: Benilton Carvalho [e-mail]

0 errors | 0 warnings | 1 note

checking R code for possible problems ... NOTE
cdf2table: no visible global function definition for ‘getDoParWorkers’
cdf2table: no visible global function definition for ‘%dopar%’
cdf2table: no visible global function definition for ‘foreach’
cdf2table: no visible binding for global variable ‘unitLst’
cdfUnits2table: no visible global function definition for ‘%do%’
cdfUnits2table: no visible global function definition for ‘foreach’
cdfUnits2table: no visible binding for global variable ‘i’
createChrDict: no visible global function definition for ‘na.omit’
getAllFSetMpsTables: no visible global function definition for
  ‘%dopar%’
getAllFSetMpsTables: no visible global function definition for
  ‘foreach’
getAllFSetMpsTables: no visible binding for global variable ‘i’
parseBpmapCel: no visible global function definition for ‘aggregate’
parseCdfSeqAnnotSnp: no visible global function definition for
  ‘aggregate’
parseNgsTrio: no visible global function definition for ‘aggregate’
Undefined global functions or variables:
  %do% %dopar% aggregate foreach getDoParWorkers i na.omit unitLst
Consider adding
  importFrom("stats", "aggregate", "na.omit")
to your NAMESPACE file.

PGA (1.4.0)

Maintainer: Bo Wen [e-mail], Shaohang Xu [e-mail]

0 errors | 0 warnings | 3 notes

checking installed package size ... NOTE
  installed size is  5.6Mb
  sub-directories of 1Mb or more:
    extdata   1.8Mb

checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  ‘biomaRt:::martBM’ ‘biomaRt:::martDataset’ ‘biomaRt:::martHost’
  ‘customProDB:::makeTranscriptDbFromBiomart_archive’
  See the note in ?`:::` about the use of this operator.

checking R code for possible problems ... NOTE
.base_transfer: no visible binding for global variable ‘peptide’
.base_transfer: no visible binding for global variable ‘refbase’
.base_transfer: no visible binding for global variable ‘varbase’
.base_transfer: no visible binding for global variable ‘aaref’
.base_transfer: no visible binding for global variable ‘aavar’
.base_transfer: no visible binding for global variable ‘Type’
.base_transfer: no visible binding for global variable ‘Freq’
.get_30aa_splited_seq: no visible global function definition for ‘.’
.get_30aa_splited_seq: no visible binding for global variable ‘id’
... 216 lines ...
reportSNV: no visible binding for global variable ‘abc’
reportSNV: no visible binding for global variable ‘xyz’
Undefined global functions or variables:
  . .I .N .SD CUFF_ID Change Class Evalue Frame Freq ID Index Mass
  MutNum Query Qvalue Strand Substring Type aapos aaref aavar abc
  alleleCount alleles charge chr chrom cumlen delta_da delta_ppm evalue
  gene_name genename genome<- id isSAP isUnique junType jun_type label
  miss mods mrnaAcc mz name output pep peptide pincoding position
  pro_name proname prot protAcc protein rbindlist readAAStringSet
  readDNAStringSet refbase rsid seqlengths seqlevels seqlevels<- subseq
  transcript tx_name txid txname varbase writeXStringSet x xyz y

pitchRx (1.8.2)

Maintainer: Carson Sievert [e-mail] Bug reports: http://github.com/cpsievert/pitchRx/issues

0 errors | 0 warnings | 1 note

checking package dependencies ... NOTE
Package suggested but not available for checking: ‘ggsubplot’

plethy (1.12.0)

Maintainer: Daniel Bottomly [e-mail]

2 errors | 1 warning | 3 notes

checking examples ... ERROR
Running examples in ‘plethy-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: BuxcoDB-class
> ### Title: Class '"BuxcoDB"'
> ### Aliases: BuxcoDB-class BuxcoDB addAnnotation,BuxcoDB-method
> ###   addAnnotation annoTable,BuxcoDB-method annoTable
> ###   annoCols,BuxcoDB-method annoCols annoLevels,BuxcoDB-method annoLevels
... 53 lines ...
> 
> tables(bux.db)
[1] "WBPth"
> 
> variables(bux.db)
 [1] "f"     "TVb"   "MVb"   "Penh"  "PAU"   "Rpef"  "Comp"  "PIFb"  "PEFb" 
[10] "Ti"    "Te"    "EF50"  "Tr"    "Tbody" "Tc"    "RH"    "Rinx" 
> 
> addAnnotation(bux.db, query=day.infer.query, index=FALSE)
Error: is.null(dbGetQuery(db.con, i)) is not TRUE
Execution halted

checking tests ... ERROR
Running the tests in ‘tests/runTests.R’ failed.
Last 13 lines of output:
       test.db.insert.autoincrement 
       test.dbImport 
       test.examine.table.lines 
       test.get.err.breaks 
       test.parse.buxco 
       test.retrieveData 
       test.summaryMeasures 
       test.write.sample.db 


  Error in BiocGenerics:::testPackage("plethy") : 
    unit tests failed for package plethy
  Execution halted

checking re-building of vignette outputs ... WARNING
Error in re-building vignettes:
  ...

    IQR, mad, xtabs

The following objects are masked from ‘package:base’:

    Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame,
    cbind, colnames, do.call, duplicated, eval, evalq, get, grep, grepl,
... 8 lines ...
Attaching package: ‘S4Vectors’

The following objects are masked from ‘package:base’:

    colMeans, colSums, expand.grid, rowMeans, rowSums


Error: processing vignette 'plethy.Rnw' failed with diagnostics:
 chunk 3 
Error : is.null(dbGetQuery(db.con, query.list[[i]])) is not TRUE
Execution halted

checking dependencies in R code ... NOTE
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘csv.to.table’ ‘find.break.ranges.integer’ ‘fix.time’ ‘multi.grep’

checking R code for possible problems ... NOTE
generate.sample.buxco : <anonymous> : <anonymous> : <anonymous> :
  <anonymous>: no visible global function definition for ‘rnorm’
make.db.package: no visible global function definition for
  ‘packageDescription’
mvtsplot.data.frame: no visible global function definition for ‘colors’
mvtsplot.data.frame: no visible global function definition for ‘par’
mvtsplot.data.frame: no visible global function definition for ‘layout’
mvtsplot.data.frame: no visible global function definition for
  ‘strwidth’
... 14 lines ...
tsplot,BuxcoDB: no visible binding for global variable ‘Sample_Name’
Undefined global functions or variables:
  Axis Days Sample_Name Value abline bxp colors layout legend lines
  median mtext packageDescription par plot rnorm strwidth terms
Consider adding
  importFrom("grDevices", "colors")
  importFrom("graphics", "Axis", "abline", "bxp", "layout", "legend",
             "lines", "mtext", "par", "plot", "strwidth")
  importFrom("stats", "median", "rnorm", "terms")
  importFrom("utils", "packageDescription")
to your NAMESPACE file.

checking Rd line widths ... NOTE
Rd file 'parsing.Rd':
  \usage lines wider than 90 characters:
     parse.buxco(file.name = NULL, table.delim = "Table", burn.in.lines = c("Measurement", "Create measurement", "Waiting for", "Site Acknow ... [TRUNCATED]
       chunk.size = 500, db.name = "bux_test.db", max.run.time.minutes = 60, overwrite = TRUE, verbose=TRUE, make.package = F, author = NULL ... [TRUNCATED]
     parse.buxco.basic(file.name=NULL, table.delim="Table", burn.in.lines=c("Measurement", "Create measurement", "Waiting for", "Site Acknow ... [TRUNCATED]

Rd file 'utilities.Rd':
  \usage lines wider than 90 characters:
     get.err.breaks(bux.db, max.exp.count=150, max.acc.count=900, vary.perc=.1, label.val="ERR")
     proc.sanity(bux.db, max.exp.time=300, max.acc.time=1800, max.exp.count=150, max.acc.count=900)
  \examples lines wider than 100 characters:
     err.dta <- data.frame(samples=samples, count=count, measure_break=measure_break, table_break=table_break, phase=phase, stringsAsFactors ... [TRUNCATED]
     sample.labels <- data.frame(samples=c("sample_1","sample_3"), response_type=c("high", "low"),stringsAsFactors=FALSE)

These lines will be truncated in the PDF manual.

poplite (0.99.16)

Maintainer: Daniel Bottomly [e-mail]

1 error | 0 warnings | 1 note

checking tests ... ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  1. Failure: createTable (@test-poplite.R#252) 
  2. Failure: createTable (@test-poplite.R#252) 
  3. Failure: createTable (@test-poplite.R#252) 
  4. Failure: createTable (@test-poplite.R#252) 
  5. Failure: insertStatement (@test-poplite.R#330) 
  6. Failure: insertStatement (@test-poplite.R#350) 
  7. Failure: insertStatement (@test-poplite.R#330) 
  8. Failure: insertStatement (@test-poplite.R#350) 
  9. Failure: insertStatement (@test-poplite.R#330) 
  1. ...

  Error: testthat unit tests failed
  Execution halted

checking R code for possible problems ... NOTE
filter_.Database: no visible global function definition for ‘stack’
get.starting.point : <anonymous>: no visible global function definition
  for ‘na.omit’
select_.Database: no visible global function definition for ‘stack’
tsl.to.graph: no visible global function definition for ‘stack’
join,Database: no visible global function definition for ‘stack’
join,Database : .get.select.cols: no visible global function definition
  for ‘setNames’
join,Database: no visible binding for global variable ‘new.ancil’
join,Database: no visible global function definition for ‘setNames’
Undefined global functions or variables:
  na.omit new.ancil setNames stack
Consider adding
  importFrom("stats", "na.omit", "setNames")
  importFrom("utils", "stack")
to your NAMESPACE file.

ProjectTemplate (0.7)

Maintainer: Kenton White [e-mail] Bug reports: https://github.com/johnmyleswhite/ProjectTemplate/issues

0 errors | 0 warnings | 0 notes

quantmod (0.4-7)

Maintainer: Joshua M. Ulrich [e-mail] Bug reports: https://github.com/joshuaulrich/quantmod/issues

0 errors | 0 warnings | 1 note

checking R code for possible problems ... NOTE
Found the following calls to attach():
File ‘quantmod/R/attachSymbols.R’:
  attach(NULL, pos = pos, name = DB$name)
  attach(NULL, pos = pos, name = DB$name)
See section ‘Good practice’ in ‘?attach’.

rangeMapper (0.3-0)

Maintainer: Mihai Valcu [e-mail]

0 errors | 0 warnings | 0 notes

RecordLinkage (0.4-10)

Maintainer: Andreas Borg [e-mail]

0 errors | 0 warnings | 0 notes

recoup (1.2.0)

Maintainer: Panagiotis Moulos [e-mail]

2 errors | 0 warnings | 1 note

checking examples ... ERROR
Running examples in ‘recoup-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: calcCoverage
> ### Title: Calculate coverages over a genomic region
> ### Aliases: calcCoverage
> 
> ### ** Examples
> 
> # Load some data
> data("recoup_test_data",package="recoup")
> 
> # Calculate coverage Rle
> mask <- makeGRangesFromDataFrame(df=test.genome,
+     keep.extra.columns=TRUE)
> small.cov <- calcCoverage(test.input[[1]]$ranges,mask)
Error in .check_ncores(cores) : 16 simultaneous processes spawned
Calls: calcCoverage ... splitBySeqname -> cmclapply -> mclapply -> .check_ncores
Execution halted
** found \donttest examples: check also with --run-donttest

checking tests ... ERROR
Running the tests in ‘tests/runTests.R’ failed.
Last 13 lines of output:
  1 Test Suite : 
  recoup RUnit Tests - 1 test function, 1 error, 0 failures
  ERROR in test_recoup: Error in .check_ncores(cores) : 16 simultaneous processes spawned

  Test files with failing tests

     test_recoup.R 
       test_recoup 


  Error in BiocGenerics:::testPackage("recoup") : 
    unit tests failed for package recoup
  Execution halted

checking R code for possible problems ... NOTE
areColors : <anonymous>: no visible global function definition for
  ‘col2rgb’
buildAnnotationStore: no visible global function definition for
  ‘Seqinfo’
calcCoverage: no visible global function definition for ‘is’
calcDesignPlotProfiles : <anonymous>: no visible global function
  definition for ‘smooth.spline’
calcPlotProfiles : <anonymous>: no visible global function definition
  for ‘smooth.spline’
... 94 lines ...
Consider adding
  importFrom("grDevices", "bmp", "col2rgb", "dev.new", "dev.off", "jpeg",
             "pdf", "png", "postscript", "tiff")
  importFrom("graphics", "plot")
  importFrom("methods", "as", "is")
  importFrom("stats", "approx", "kmeans", "lowess", "quantile",
             "smooth.spline", "spline", "var")
  importFrom("utils", "download.file", "packageVersion", "read.delim",
             "unzip")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').

refGenome (1.7.0)

Maintainer: Wolfgang Kaisers [e-mail]

0 errors | 0 warnings | 0 notes

rgrass7 (0.1-9)

Maintainer: Roger Bivand [e-mail]

0 errors | 0 warnings | 0 notes

RImmPort (1.2.0)

Maintainer: Ravi Shankar [e-mail]

0 errors | 1 warning | 1 note

checking sizes of PDF files under ‘inst/doc’ ... WARNING
  ‘gs+qpdf’ made some significant size reductions:
     compacted ‘RImmPort_Article.pdf’ from 731Kb to 336Kb
  consider running tools::compactPDF(gs_quality = "ebook") on these files

checking R code for possible problems ... NOTE
getCellularQuantification: no visible binding for global variable
  ‘experiment_sample_accession’
getCellularQuantification: no visible binding for global variable
  ‘control_files_names’
getCellularQuantification: no visible binding for global variable
  ‘ZBREFIDP’
getGeneticsFindings: no visible binding for global variable
  ‘experiment_sample_accession’
getNucleicAcidQuantification: no visible binding for global variable
  ‘experiment_sample_accession’
getProteinQuantification: no visible binding for global variable
  ‘experiment_sample_accession’
getTiterAssayResults: no visible binding for global variable
  ‘experiment_sample_accession’
Undefined global functions or variables:
  ZBREFIDP control_files_names experiment_sample_accession

RObsDat (16.03)

Maintainer: Dominik Reusser [e-mail]

0 errors | 0 warnings | 0 notes

rplexos (1.1.8)

Maintainer: Clayton Barrows [e-mail] Bug reports: https://github.com/NREL/rplexos/issues

0 errors | 0 warnings | 0 notes

RQDA (0.2-7)

Maintainer: HUANG Ronggui [e-mail]

1 error | 0 warnings | 1 note

checking whether package ‘RQDA’ can be installed ... ERROR
Installation failed.
See ‘/home/muelleki/git/R/RSQLite/revdep/checks/RQDA.Rcheck/00install.out’ for details.

checking package dependencies ... NOTE
Packages which this enhances but not available for checking:
  ‘rjpod’ ‘d3Network’

rtext (0.1.20)

Maintainer: Peter Meissner [e-mail] Bug reports: https://github.com/petermeissner/rtext/issues

0 errors | 0 warnings | 0 notes

rTRM (1.12.0)

Maintainer: Diego Diez [e-mail] Bug reports: https://github.com/ddiez/rTRM/issues

0 errors | 0 warnings | 1 note

checking Rd line widths ... NOTE
Rd file 'findTRM.Rd':
  \usage lines wider than 90 characters:
     findTRM(g, target, query, method = "nsa", max.bridge = 1, extended = FALSE, strict = FALSE, type = "igraph")

Rd file 'plotGraph.Rd':
  \usage lines wider than 90 characters:
     plotGraph(g, layout = layout.fruchterman.reingold, mar = .5, vertex.pch = 21, vertex.cex, vertex.col, vertex.bg, vertex.lwd, edge.col,  ... [TRUNCATED]

Rd file 'plotTRM.Rd':
  \usage lines wider than 90 characters:
     plotTRM(g, layout = layout.fruchterman.reingold, mar = .5, vertex.col, vertex.cex, vertex.lwd, edge.col, edge.lwd, edge.lty, label = TR ... [TRUNCATED]

Rd file 'processBiogrid.Rd':
  \usage lines wider than 90 characters:
     processBiogrid(dblist, org = "human", simplify = TRUE, type = "physical", mimic.old = FALSE)

These lines will be truncated in the PDF manual.

rvertnet (0.5.0)

Maintainer: Scott Chamberlain [e-mail] Bug reports: https://github.com/ropensci/rvertnet/issues

0 errors | 0 warnings | 0 notes

scrime (1.3.3)

Maintainer: Holger Schwender [e-mail]

0 errors | 0 warnings | 2 notes

checking dependencies in R code ... NOTE
'library' or 'require' calls in package code:
  ‘MASS’ ‘oligoClasses’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.

checking R code for possible problems ... NOTE
abf: no visible global function definition for ‘qnorm’
abf: no visible global function definition for ‘dnorm’
analyse.models: no visible global function definition for ‘read.table’
buildSNPannotation: no visible global function definition for ‘db’
buildSNPannotation: no visible global function definition for
  ‘dbListFields’
buildSNPannotation: no visible global function definition for
  ‘dbGetQuery’
chisqClass2: no visible global function definition for ‘pchisq’
... 48 lines ...
Undefined global functions or variables:
  as.dist db dbGetQuery dbListFields dist dnorm glm is mvrnorm pchisq
  pnorm predict qnorm rbinom read.table rgamma runif sd write.table
Consider adding
  importFrom("methods", "is")
  importFrom("stats", "as.dist", "dist", "dnorm", "glm", "pchisq",
             "pnorm", "predict", "qnorm", "rbinom", "rgamma", "runif",
             "sd")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').

SEERaBomb (2016.2)

Maintainer: Tomas Radivoyevitch [e-mail]

0 errors | 0 warnings | 0 notes

seqplots (1.12.0)

Maintainer: Przemyslaw Stempor [e-mail] Bug reports: http://github.com/przemol/seqplots/issues

0 errors | 0 warnings | 3 notes

checking installed package size ... NOTE
  installed size is  9.1Mb
  sub-directories of 1Mb or more:
    R          1.2Mb
    doc        2.4Mb
    seqplots   4.9Mb

checking foreign function calls ... NOTE
Foreign function call to a different package:
  .Call("BWGFile_summary", ..., PACKAGE = "rtracklayer")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.

checking R code for possible problems ... NOTE
getPlotSetArray : <anonymous>: no visible global function definition
  for ‘qt’
getSF : <anonymous>: no visible global function definition for ‘approx’
ggHeatmapPlotWrapper: no visible global function definition for
  ‘colorRampPalette’
ggHeatmapPlotWrapper: no visible binding for global variable ‘Var2’
ggHeatmapPlotWrapper: no visible binding for global variable ‘Var1’
ggHeatmapPlotWrapper: no visible binding for global variable ‘value’
heatmapPlotWrapper: no visible global function definition for
... 39 lines ...
  capture.output colorRampPalette cutree dist hclust image kmeans
  layout lines mtext par plot.new qt rainbow rect rgb title value
Consider adding
  importFrom("grDevices", "adjustcolor", "colorRampPalette", "rainbow",
             "rgb")
  importFrom("graphics", "abline", "axis", "box", "image", "layout",
             "lines", "mtext", "par", "plot.new", "rect", "title")
  importFrom("stats", "approx", "as.dendrogram", "cutree", "dist",
             "hclust", "kmeans", "qt")
  importFrom("utils", "capture.output")
to your NAMESPACE file.

SGP (1.5-0.0)

Maintainer: Damian W. Betebenner [e-mail] Bug reports: https://github.com/CenterForAssessment/SGP/issues

0 errors | 0 warnings | 0 notes

smnet (2.1)

Maintainer: Alastair Rushworth [e-mail]

0 errors | 0 warnings | 0 notes

snplist (0.16)

Maintainer: Alexander Sibley [e-mail]

0 errors | 0 warnings | 0 notes

specL (1.8.0)

Maintainer: Christian Panse [e-mail], Witold E. Wolski [e-mail] Bug reports: https://github.com/fgcz/specL/issues

0 errors | 1 warning | 3 notes

checking re-building of vignette outputs ... WARNING
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 2-25 (cdsw.Rmd) 
Error: processing vignette 'cdsw.Rmd' failed with diagnostics:
could not find function "doc_date"
Execution halted


checking S3 generic/method consistency ... NOTE
Found the following apparent S3 methods exported but not registered:
  merge.specLSet plot.psm plot.psmSet summary.psmSet
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.

checking R code for possible problems ... NOTE
.onAttach: no visible global function definition for ‘packageVersion’
plot,specLSet: no visible global function definition for ‘draw.circle’
summary,specLSet : <anonymous>: no visible binding for global variable
  ‘iRTpeptides’
Undefined global functions or variables:
  draw.circle iRTpeptides packageVersion
Consider adding
  importFrom("utils", "packageVersion")
to your NAMESPACE file.

checking Rd files ... NOTE
prepare_Rd: ms1.p2069.Rd:28-32: Dropping empty section \references
prepare_Rd: ms1.p2069.Rd:23-26: Dropping empty section \examples

sqldf (0.4-10)

Maintainer: G. Grothendieck [e-mail] Bug reports: http://groups.google.com/group/sqldf

0 errors | 1 warning | 2 notes

checking whether package ‘sqldf’ can be installed ... WARNING
Found the following significant warnings:
  Warning: no DISPLAY variable so Tk is not available
See ‘/home/muelleki/git/R/RSQLite/revdep/checks/sqldf.Rcheck/00install.out’ for details.

checking dependencies in R code ... NOTE
'library' or 'require' call to ‘tcltk’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.

checking R code for possible problems ... NOTE
read.csv.sql: no visible global function definition for ‘download.file’
sqldf: no visible global function definition for ‘modifyList’
sqldf: no visible global function definition for ‘head’
Undefined global functions or variables:
  download.file head modifyList
Consider adding
  importFrom("utils", "download.file", "head", "modifyList")
to your NAMESPACE file.

sqliter (0.1.0)

Maintainer: Wilson Freitas [e-mail]

0 errors | 0 warnings | 0 notes

SRAdb (1.32.0)

Maintainer: Jack Zhu [e-mail] Bug reports: https://github.com/seandavi/SRAdb/issues/new

0 errors | 0 warnings | 6 notes

checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.

checking top-level files ... NOTE
Non-standard file/directory found at top level:
  ‘SRAdb-package.Rd’

checking for left-over files ... NOTE
The following files look like leftovers:
  ‘SRAdb/SRAdb-package.Rd’
Please remove them from your package.

checking dependencies in R code ... NOTE
'library' or 'require' call to ‘RCurl’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘RSQLite’ ‘graph’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.

checking R code for possible problems ... NOTE
.socketWrite: no visible global function definition for ‘write.socket’
.socketWrite: no visible global function definition for ‘read.socket’
IGVsocket: no visible global function definition for ‘make.socket’
colDescriptions: no visible global function definition for ‘dbGetQuery’
entityGraph: no visible global function definition for ‘na.omit’
entityGraph: no visible global function definition for ‘new’
entityGraph : <anonymous>: no visible global function definition for
  ‘addEdge’
getFASTQfile: no visible global function definition for ‘download.file’
... 11 lines ...
startIGV: no visible global function definition for ‘browseURL’
Undefined global functions or variables:
  SQLite addEdge browseURL dbConnect dbDisconnect dbGetQuery
  download.file make.socket na.omit new read.socket write.socket
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "na.omit")
  importFrom("utils", "browseURL", "download.file", "make.socket",
             "read.socket", "write.socket")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').

checking Rd line widths ... NOTE
Rd file 'IGVsession.Rd':
  \examples lines wider than 100 characters:
             ## Wait until IGV fully launched and make sure the listen port for IGV is open (If not configured in IGV, follow these steops:  ... [TRUNCATED]

Rd file 'IGVsnapshot.Rd':
  \examples lines wider than 100 characters:
       ## Create a snapshot of the current IGV window, which is usually the first launched IGV with listen port 60151 open

Rd file 'SRAdb-package.Rd':
... 68 lines ...
Rd file 'sraConvert.Rd':
  \usage lines wider than 90 characters:
     sraConvert(in_acc, out_type = c("sra", "submission", "study", "sample", "experiment", "run"), sra_con)
  \examples lines wider than 100 characters:
             a <- sraConvert( in_acc=c(" SRR000137", "SRR000138 "), out_type=c('sample'), sra_con=sra_con )

Rd file 'sraGraph.Rd':
  \examples lines wider than 100 characters:
             ## create a graphNEL object from SRA accessions, which are full text search results of terms 'primary thyroid cell line'

These lines will be truncated in the PDF manual.

srvyr (0.2.0)

Maintainer: Greg Freedman Ellis [e-mail] Bug reports: https://github.com/gergness/srvyr/issues

0 errors | 0 warnings | 0 notes

SSN (1.1.8)

Maintainer: Jay Ver Hoef [e-mail]

0 errors | 0 warnings | 0 notes

storr (1.0.1)

Maintainer: Rich FitzJohn [e-mail]

0 errors | 0 warnings | 0 notes

stream (1.2-3)

Maintainer: Michael Hahsler [e-mail] Bug reports: https://github.com/mhahsler/stream/issues

0 errors | 0 warnings | 1 note

checking installed package size ... NOTE
  installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   3.6Mb

survey (3.31-2)

Maintainer: "Thomas Lumley" [e-mail]

0 errors | 0 warnings | 0 notes

taRifx (1.0.6)

Maintainer: Ari B. Friedman [e-mail]

0 errors | 0 warnings | 4 notes

checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.

checking dependencies in R code ... NOTE
'library' or 'require' calls in package code:
  ‘gdata’ ‘ggplot2’ ‘grid’ ‘lattice’ ‘xtable’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.

checking S3 generic/method consistency ... NOTE
Found the following apparent S3 methods exported but not registered:
  as.matrix.by stack.list
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.

checking R code for possible problems ... NOTE
as.data.frame.by: no visible global function definition for ‘na.omit’
autoplot.microbenchmark : uq: no visible global function definition for
  ‘quantile’
autoplot.microbenchmark : lq: no visible global function definition for
  ‘quantile’
autoplot.microbenchmark: no visible global function definition for
  ‘ggplot’
autoplot.microbenchmark: no visible global function definition for
  ‘aes’
... 90 lines ...
  grid.points grid.polyline grid.rect grid.segments grid.text
  interleave label<- latticeParseFormula median na.omit opts
  panel.densityplot panel.lines panel.xyplot par pf plot.new
  popViewport pushViewport quantile sd seekViewport stat_summary terms
  text theme_text time unit upViewport viewport write.csv xtable
Consider adding
  importFrom("graphics", "barplot", "par", "plot.new", "text")
  importFrom("stats", "ecdf", "median", "na.omit", "pf", "quantile",
             "sd", "terms", "time")
  importFrom("utils", "write.csv")
to your NAMESPACE file.

tcpl (1.2.2)

Maintainer: Dayne L Filer [e-mail]

0 errors | 0 warnings | 1 note

checking installed package size ... NOTE
  installed size is  9.9Mb
  sub-directories of 1Mb or more:
    sql   8.7Mb

TFBSTools (1.12.1)

Maintainer: Ge Tan [e-mail] Bug reports: https://github.com/ge11232002/TFBSTools/issues

0 errors | 1 warning | 2 notes

checking re-building of vignette outputs ... WARNING
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 2-16 (TFBSTools.Rmd) 
Error: processing vignette 'TFBSTools.Rmd' failed with diagnostics:
could not find function "doc_date"
Execution halted


checking installed package size ... NOTE
  installed size is 12.1Mb
  sub-directories of 1Mb or more:
    R  11.3Mb

checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  ‘S4Vectors:::new_SimpleList_from_list’ ‘seqLogo:::pwm2ic’
  See the note in ?`:::` about the use of this operator.

tigreBrowserWriter (0.1.2)

Maintainer: Antti Honkela [e-mail] Bug reports: https://github.com/PROBIC/tigreBrowserWriter/issues

1 error | 0 warnings | 0 notes

checking examples ... ERROR
Running examples in ‘tigreBrowserWriter-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: closeDb
> ### Title: Finalise and close the database
> ### Aliases: closeDb
> 
> ### ** Examples
> 
>   db <- initializeDb("", "My Dataset")
Warning: RSQLite::dbGetPreparedQuery() is deprecated, please switch to DBI::dbGetQuery(params = bind.data).
Warning: Named parameters not used in query: name, species, source, platform, desc, save_location, figure_filename
Warning: Named parameters not used in query: dname
>   # ...
>   closeDb(db)
Warning: Named parameters not used in query: parent_id, name
Warning: Named parameters not used in query: name, parent_id
Error in rsqlite_bind_rows(res@ptr, params) : 
  Query requires 1 params; 2 supplied.
Calls: closeDb ... <Anonymous> -> db_bind -> rsqlite_bind_rows -> .Call
Execution halted

tigre (1.28.0)

Maintainer: Antti Honkela [e-mail] Bug reports: https://github.com/ahonkela/tigre/issues

0 errors | 0 warnings | 2 notes

checking top-level files ... NOTE
Non-standard file/directory found at top level:
  ‘demos’

checking R code for possible problems ... NOTE
GPPlot: no visible global function definition for ‘polygon’
export.scores: no visible global function definition for ‘png’
export.scores: no visible global function definition for ‘dev.off’
gpdisimLogLikeGradients: no visible global function definition for
  ‘tail’
[,scoreList: no visible global function definition for ‘slotNames’
c,scoreList: no visible global function definition for ‘slotNames’
Undefined global functions or variables:
  dev.off png polygon slotNames tail
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "polygon")
  importFrom("methods", "slotNames")
  importFrom("utils", "tail")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').

trackeR (0.0.4)

Maintainer: Hannah Frick [e-mail] Bug reports: https://github.com/hfrick/trackeR/issues

0 errors | 1 warning | 0 notes

checking re-building of vignette outputs ... WARNING
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: zoo

Attaching package: 'zoo'

The following objects are masked from 'package:base':
... 7 lines ...

The following object is masked from 'package:base':

    append

Map from URL : http://maps.googleapis.com/maps/api/staticmap?center=57.157231,-2.104296&zoom=13&size=640x640&scale=2&maptype=terrain&sensor=false
Quitting from lines 90-91 (TourDetrackeR.Rmd) 
Error: processing vignette 'TourDetrackeR.Rmd' failed with diagnostics:
GeomRasterAnn was built with an incompatible version of ggproto.
Please reinstall the package that provides this extension.
Execution halted

TSdata (2016.8-1)

Maintainer: Paul Gilbert [e-mail]

0 errors | 1 warning | 0 notes

checking re-building of vignette outputs ... WARNING
Error in re-building vignettes:
  ...
INFO: Configuration file: /home/muelleki/R/x86_64-pc-linux-gnu-library/3.3/RJSDMX/configuration.properties
Nov 25, 2016 12:03:42 AM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery
INFO: Contacting web service with query: http://stats.oecd.org/restsdmx/sdmx.ashx//GetDataStructure/QNA
Nov 25, 2016 12:03:43 AM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery
INFO: Contacting web service with query: http://stats.oecd.org/restsdmx/sdmx.ashx//GetDataStructure/QNA
Nov 25, 2016 12:03:43 AM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery
INFO: Contacting web service with query: http://stats.oecd.org/restsdmx/sdmx.ashx//GetData/QNA/CAN.B1_GE.CARSA.Q?format=compact_v2
... 8 lines ...
SEVERE: Connection failed. HTTP error code : 500, message: Internal Server Error
SDMX meaning: Error on the provider side.
Nov 25, 2016 12:03:44 AM it.bancaditalia.oss.sdmx.client.RestSdmxClient getDataFlowStructure
SEVERE: Exception caught parsing results from call to provider Eurostat

Error: processing vignette 'Guide.Stex' failed with diagnostics:
 chunk 5 
Error in .local(serIDs, con, ...) : 
  ei_nama_q.Q.MIO-EUR.NSA.CP.NA-P72.IT error: it.bancaditalia.oss.sdmx.util.SdmxException: Exception. Class: it.bancaditalia.oss.sdmx.util.SdmxException .Message: Connection failed. HTTP error code : 500, message: Internal Server Error
SDMX meaning: Error on the provider side.
Execution halted

TSSQLite (2015.4-1)

Maintainer: Paul Gilbert [e-mail]

0 errors | 0 warnings | 0 notes

TSsql (2015.1-2)

Maintainer: Paul Gilbert [e-mail]

0 errors | 0 warnings | 1 note

checking R code for possible problems ... NOTE
TSgetSQL: no visible global function definition for ‘ts’
TSputSQL: no visible global function definition for ‘is.ts’
TSputSQL: no visible global function definition for ‘frequency’
TSputSQL: no visible global function definition for ‘time’
TSquery: no visible global function definition for ‘ts’
Undefined global functions or variables:
  frequency is.ts time ts
Consider adding
  importFrom("stats", "frequency", "is.ts", "time", "ts")
to your NAMESPACE file.

tweet2r (1.0)

Maintainer: Pau Aragó [e-mail]

0 errors | 0 warnings | 0 notes

twitteR (1.1.9)

Maintainer: Jeff Gentry [e-mail]

0 errors | 0 warnings | 0 notes

UniProt.ws (2.14.0)

Maintainer: Bioconductor Package Maintainer [e-mail]

0 errors | 0 warnings | 1 note

checking R code for possible problems ... NOTE
.getSomeUniprotGoodies: no visible global function definition for
  ‘head’
.tryReadResult: no visible global function definition for ‘read.delim’
.tryReadResult: no visible global function definition for ‘URLencode’
availableUniprotSpecies: no visible global function definition for
  ‘read.delim’
availableUniprotSpecies: no visible global function definition for
  ‘head’
lookupUniprotSpeciesFromTaxId: no visible global function definition
  for ‘read.delim’
Undefined global functions or variables:
  URLencode head read.delim
Consider adding
  importFrom("utils", "URLencode", "head", "read.delim")
to your NAMESPACE file.

Uniquorn (1.2.0)

Maintainer: 'Raik Otto' [e-mail]

0 errors | 0 warnings | 2 notes

checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.

checking top-level files ... NOTE
Non-standard file/directory found at top level:
  ‘unitTests’

UPMASK (1.0)

Maintainer: Alberto Krone-Martins [e-mail]

0 errors | 0 warnings | 1 note

checking R code for possible problems ... NOTE
UPMASKfile: no visible global function definition for ‘read.table’
UPMASKfile: no visible global function definition for ‘write.table’
analyse_randomKde2d: no visible global function definition for ‘hist’
analyse_randomKde2d: no visible global function definition for ‘lines’
analyse_randomKde2d_AutoCalibrated: no visible global function
  definition for ‘hist’
analyse_randomKde2d_AutoCalibrated: no visible global function
  definition for ‘lines’
create_randomKde2d: no visible global function definition for ‘image’
... 18 lines ...
kde2dForSubset: no visible global function definition for ‘image’
kde2dForSubset: no visible global function definition for ‘points’
Undefined global functions or variables:
  contour dev.new hist image lines pairs par plot points rainbow
  read.table rgb write.table
Consider adding
  importFrom("grDevices", "dev.new", "rainbow", "rgb")
  importFrom("graphics", "contour", "hist", "image", "lines", "pairs",
             "par", "plot", "points")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.

VariantFiltering (1.10.1)

Maintainer: Robert Castelo [e-mail] Bug reports: https://github.com/rcastelo/VariantFiltering/issues

0 errors | 1 warning | 4 notes

checking sizes of PDF files under ‘inst/doc’ ... WARNING
  ‘gs+qpdf’ made some significant size reductions:
     compacted ‘usingVariantFiltering.pdf’ from 415Kb to 153Kb
  consider running tools::compactPDF(gs_quality = "ebook") on these files

checking installed package size ... NOTE
  installed size is  7.8Mb
  sub-directories of 1Mb or more:
    R         3.6Mb
    extdata   3.5Mb

checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  'S4Vectors:::labeledLine' 'VariantAnnotation:::.checkArgs'
  'VariantAnnotation:::.consolidateHits'
  'VariantAnnotation:::.returnEmpty'
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  '.adjustForStrandSense'

checking Rd line widths ... NOTE
Rd file 'MafDb-class.Rd':
  \examples lines wider than 100 characters:
       ## founder mutation in a regulatory element located within the HERC2 gene inhibiting OCA2 expression.

Rd file 'MafDb2-class.Rd':
  \examples lines wider than 100 characters:
       ## founder mutation in a regulatory element located within the HERC2 gene inhibiting OCA2 expression.

Rd file 'VariantFilteringParam-class.Rd':
... 19 lines ...

Rd file 'autosomalRecessiveHeterozygous.Rd':
  \usage lines wider than 90 characters:
                                                                      BPPARAM=bpparam("SerialParam"))

Rd file 'autosomalRecessiveHomozygous.Rd':
  \usage lines wider than 90 characters:
                                                                    use=c("everything", "complete.obs", "all.obs"),
                                                                    BPPARAM=bpparam("SerialParam"))

These lines will be truncated in the PDF manual.

checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘phastCons100way.UCSC.hg38’

vegdata (0.9)

Maintainer: Florian Jansen [e-mail]

0 errors | 0 warnings | 0 notes

vmsbase (2.1.3)

Maintainer: Lorenzo D'Andrea [e-mail]

1 error | 0 warnings | 0 notes

checking whether package ‘vmsbase’ can be installed ... ERROR
Installation failed.
See ‘/home/muelleki/git/R/RSQLite/revdep/checks/vmsbase.Rcheck/00install.out’ for details.

real-didi/RSQLiteFixed documentation built on May 21, 2019, 1:45 p.m.