Last updated on 2020-08-07 01:50:17 CEST.
| Package | NOTE |
|---|---|
| mlgt | 12 |
| mlPhaser | 12 |
Current CRAN status:
Version: 0.16
Check: top-level files
Result: NOTE
Non-standard file/directory found at top level:
'CHANGELOG.txt'
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-linux-x86_64, r-release-linux-x86_64
Version: 0.16
Check: dependencies in R code
Result: NOTE
Packages in Depends field not imported from:
'methods' 'seqinr'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-macos-x86_64, r-release-windows-ix86+x86_64, r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64
Version: 0.16
Check: R code for possible problems
Result: NOTE
alignReport: no visible global function definition for 'pdf'
alignReport: no visible global function definition for 'as.alignment'
alignReport: no visible global function definition for 'consensus'
alignReport: no visible global function definition for 'con'
alignReport: no visible global function definition for 'par'
alignReport: no visible global function definition for 'plot.new'
alignReport: no visible global function definition for 'title'
alignReport: no visible global function definition for 'legend'
alignReport: no visible global function definition for 'barplot'
alignReport: no visible global function definition for 'hist'
alignReport: no visible global function definition for 'abline'
alignReport: no visible global function definition for 'dev.off'
callGenotypes: no visible global function definition for 'new'
createKnownAlleleList: no visible global function definition for
'read.alignment'
createKnownAlleleList: no visible global function definition for
'write.fasta'
createKnownAlleleList: no visible global function definition for
'read.fasta'
createKnownAlleleList: no visible global function definition for 's2c'
createKnownAlleleList: no visible binding for global variable 'name'
createKnownAlleleList: no visible global function definition for 'new'
createKnownAlleleList: no visible global function definition for
'as.SeqFastadna'
dumpVariantMap.mlgtResult: no visible global function definition for
'write.fasta'
dumpVariantMap.mlgtResult: no visible binding for global variable 's2c'
dumpVariants: no visible global function definition for 'as.alignment'
dumpVariants: no visible global function definition for 'write.fasta'
dumpVariants: no visible binding for global variable 's2c'
errorCorrect.alignment: no visible global function definition for
'consensus'
errorCorrect.alignment: no visible global function definition for 'con'
errorCorrect.alignment: no visible global function definition for
'as.matrix.alignment'
errorCorrect.alignment: no visible binding for global variable 'c2s'
errorCorrect.alignment: no visible global function definition for
'as.alignment'
errorCorrect.mlgtResult: no visible global function definition for
'getSequence'
errorCorrect.mlgtResult: no visible global function definition for
'as.alignment'
errorCorrect.mlgtResult: no visible global function definition for
'new'
errorCorrect.mlgtResult: no visible global function definition for
'as.SeqFastadna'
getSubSeqsTable: no visible global function definition for 'new'
getSubSeqsTable: no visible global function definition for 'read.fasta'
getSubSeqsTable: no visible global function definition for
'write.fasta'
getSubSeqsTable: no visible global function definition for
'as.alignment'
getSubSeqsTable: no visible global function definition for 's2c'
getTopBlastHits: no visible global function definition for 'read.delim'
inspectBlastResults: no visible global function definition for 'par'
inspectBlastResults: no visible global function definition for 'hist'
makeVarAlleleBlastMap: no visible global function definition for
'getName'
makeVarAlleleBlastMap: no visible global function definition for
'write.fasta'
mergeMlgtResults.complex: no visible global function definition for
'na.omit'
mlgt.mlgtDesign: no visible global function definition for 'read.delim'
mlgt.mlgtDesign: no visible global function definition for
'getSequence'
mlgt.mlgtDesign: no visible global function definition for 'new'
mlgt.mlgtDesign: no visible global function definition for
'as.SeqFastadna'
plotGenotypeEvidence.genotypeCall: no visible global function
definition for 'par'
plotGenotypeEvidence.genotypeCall: no visible global function
definition for 'hist'
plotGenotypeEvidence.genotypeCall: no visible global function
definition for 'abline'
plotGenotypeEvidence.genotypeCall: no visible global function
definition for 'legend'
plotGenotypeEvidence.genotypeCall.file: no visible global function
definition for 'pdf'
plotGenotypeEvidence.genotypeCall.file: no visible global function
definition for 'dev.off'
plotGenotypeEvidence.list: no visible global function definition for
'pdf'
plotGenotypeEvidence.list: no visible global function definition for
'dev.off'
prepareMlgtRun.listDesign: no visible global function definition for
'new'
prepareMlgtRun.mlgtDesign: no visible global function definition for
'write.fasta'
printBlastResultGraphs: no visible global function definition for 'pdf'
printBlastResultGraphs: no visible global function definition for
'dev.off'
stripGapColumns: no visible global function definition for 'con'
stripGapColumns: no visible binding for global variable 'c2s'
stripGapColumns: no visible global function definition for
'as.alignment'
writeGenotypeCallsToFile.genotypeCall: no visible global function
definition for 'packageVersion'
writeGenotypeCallsToFile.genotypeCall: no visible global function
definition for 'write.table'
writeGenotypeCallsToFile.list: no visible global function definition
for 'write.table'
errorCorrect,missing-list: no visible global function definition for
'consensus'
errorCorrect,missing-list: no visible global function definition for
'con'
errorCorrect,missing-list: no visible global function definition for
'as.matrix.alignment'
errorCorrect,missing-list: no visible binding for global variable 'c2s'
errorCorrect,missing-list: no visible global function definition for
'as.alignment'
errorCorrect,mlgtResult-missing: no visible global function definition
for 'getSequence'
errorCorrect,mlgtResult-missing: no visible global function definition
for 'as.alignment'
errorCorrect,mlgtResult-missing: no visible global function definition
for 'new'
errorCorrect,mlgtResult-missing: no visible global function definition
for 'as.SeqFastadna'
mlgt,mlgtDesign: no visible global function definition for 'read.delim'
mlgt,mlgtDesign: no visible global function definition for
'getSequence'
mlgt,mlgtDesign: no visible global function definition for 'new'
mlgt,mlgtDesign: no visible global function definition for
'as.SeqFastadna'
plotGenotypeEvidence,genotypeCall-missing-character: no visible global
function definition for 'pdf'
plotGenotypeEvidence,genotypeCall-missing-character: no visible global
function definition for 'dev.off'
plotGenotypeEvidence,genotypeCall-missing-missing: no visible global
function definition for 'par'
plotGenotypeEvidence,genotypeCall-missing-missing: no visible global
function definition for 'hist'
plotGenotypeEvidence,genotypeCall-missing-missing: no visible global
function definition for 'abline'
plotGenotypeEvidence,genotypeCall-missing-missing: no visible global
function definition for 'legend'
plotGenotypeEvidence,missing-list-character: no visible global function
definition for 'pdf'
plotGenotypeEvidence,missing-list-character: no visible global function
definition for 'dev.off'
prepareMlgtRun,missing-character-character-character-list-list-list-character-character:
no visible global function definition for 'new'
prepareMlgtRun,mlgtDesign-missing-missing-missing-missing-missing-missing-missing-character:
no visible global function definition for 'write.fasta'
writeGenotypeCallsToFile,list-missing: no visible global function
definition for 'write.table'
writeGenotypeCallsToFile,missing-genotypeCall: no visible global
function definition for 'packageVersion'
writeGenotypeCallsToFile,missing-genotypeCall: no visible global
function definition for 'write.table'
Undefined global functions or variables:
abline as.SeqFastadna as.alignment as.matrix.alignment barplot c2s
con consensus dev.off getName getSequence hist legend na.omit name
new packageVersion par pdf plot.new read.alignment read.delim
read.fasta s2c title write.fasta write.table
Consider adding
importFrom("grDevices", "dev.off", "pdf")
importFrom("graphics", "abline", "barplot", "hist", "legend", "par",
"plot.new", "title")
importFrom("methods", "new")
importFrom("stats", "na.omit")
importFrom("utils", "packageVersion", "read.delim", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-macos-x86_64, r-release-windows-ix86+x86_64
Version: 0.16
Check: R code for possible problems
Result: NOTE
alignReport: no visible global function definition for ‘pdf’
alignReport: no visible global function definition for ‘as.alignment’
alignReport: no visible global function definition for ‘consensus’
alignReport: no visible global function definition for ‘con’
alignReport: no visible global function definition for ‘par’
alignReport: no visible global function definition for ‘plot.new’
alignReport: no visible global function definition for ‘title’
alignReport: no visible global function definition for ‘legend’
alignReport: no visible global function definition for ‘barplot’
alignReport: no visible global function definition for ‘hist’
alignReport: no visible global function definition for ‘abline’
alignReport: no visible global function definition for ‘dev.off’
callGenotypes: no visible global function definition for ‘new’
createKnownAlleleList: no visible global function definition for
‘read.alignment’
createKnownAlleleList: no visible global function definition for
‘write.fasta’
createKnownAlleleList: no visible global function definition for
‘read.fasta’
createKnownAlleleList: no visible global function definition for ‘s2c’
createKnownAlleleList: no visible binding for global variable ‘name’
createKnownAlleleList: no visible global function definition for ‘new’
createKnownAlleleList: no visible global function definition for
‘as.SeqFastadna’
dumpVariantMap.mlgtResult: no visible global function definition for
‘write.fasta’
dumpVariantMap.mlgtResult: no visible binding for global variable ‘s2c’
dumpVariants: no visible global function definition for ‘as.alignment’
dumpVariants: no visible global function definition for ‘write.fasta’
dumpVariants: no visible binding for global variable ‘s2c’
errorCorrect.alignment: no visible global function definition for
‘consensus’
errorCorrect.alignment: no visible global function definition for ‘con’
errorCorrect.alignment: no visible global function definition for
‘as.matrix.alignment’
errorCorrect.alignment: no visible binding for global variable ‘c2s’
errorCorrect.alignment: no visible global function definition for
‘as.alignment’
errorCorrect.mlgtResult: no visible global function definition for
‘getSequence’
errorCorrect.mlgtResult: no visible global function definition for
‘as.alignment’
errorCorrect.mlgtResult: no visible global function definition for
‘new’
errorCorrect.mlgtResult: no visible global function definition for
‘as.SeqFastadna’
getSubSeqsTable: no visible global function definition for ‘new’
getSubSeqsTable: no visible global function definition for ‘read.fasta’
getSubSeqsTable: no visible global function definition for
‘write.fasta’
getSubSeqsTable: no visible global function definition for
‘as.alignment’
getSubSeqsTable: no visible global function definition for ‘s2c’
getTopBlastHits: no visible global function definition for ‘read.delim’
inspectBlastResults: no visible global function definition for ‘par’
inspectBlastResults: no visible global function definition for ‘hist’
makeVarAlleleBlastMap: no visible global function definition for
‘getName’
makeVarAlleleBlastMap: no visible global function definition for
‘write.fasta’
mergeMlgtResults.complex: no visible global function definition for
‘na.omit’
mlgt.mlgtDesign: no visible global function definition for ‘read.delim’
mlgt.mlgtDesign: no visible global function definition for
‘getSequence’
mlgt.mlgtDesign: no visible global function definition for ‘new’
mlgt.mlgtDesign: no visible global function definition for
‘as.SeqFastadna’
plotGenotypeEvidence.genotypeCall: no visible global function
definition for ‘par’
plotGenotypeEvidence.genotypeCall: no visible global function
definition for ‘hist’
plotGenotypeEvidence.genotypeCall: no visible global function
definition for ‘abline’
plotGenotypeEvidence.genotypeCall: no visible global function
definition for ‘plot’
plotGenotypeEvidence.genotypeCall: no visible global function
definition for ‘legend’
plotGenotypeEvidence.genotypeCall.file: no visible global function
definition for ‘pdf’
plotGenotypeEvidence.genotypeCall.file: no visible global function
definition for ‘dev.off’
plotGenotypeEvidence.list: no visible global function definition for
‘pdf’
plotGenotypeEvidence.list: no visible global function definition for
‘dev.off’
prepareMlgtRun.listDesign: no visible global function definition for
‘new’
prepareMlgtRun.mlgtDesign: no visible global function definition for
‘write.fasta’
printBlastResultGraphs: no visible global function definition for ‘pdf’
printBlastResultGraphs: no visible global function definition for
‘dev.off’
stripGapColumns: no visible global function definition for ‘con’
stripGapColumns: no visible binding for global variable ‘c2s’
stripGapColumns: no visible global function definition for
‘as.alignment’
writeGenotypeCallsToFile.genotypeCall: no visible global function
definition for ‘packageVersion’
writeGenotypeCallsToFile.genotypeCall: no visible global function
definition for ‘write.table’
writeGenotypeCallsToFile.list: no visible global function definition
for ‘write.table’
errorCorrect,missing-list: no visible global function definition for
‘consensus’
errorCorrect,missing-list: no visible global function definition for
‘con’
errorCorrect,missing-list: no visible global function definition for
‘as.matrix.alignment’
errorCorrect,missing-list: no visible binding for global variable ‘c2s’
errorCorrect,missing-list: no visible global function definition for
‘as.alignment’
errorCorrect,mlgtResult-missing: no visible global function definition
for ‘getSequence’
errorCorrect,mlgtResult-missing: no visible global function definition
for ‘as.alignment’
errorCorrect,mlgtResult-missing: no visible global function definition
for ‘new’
errorCorrect,mlgtResult-missing: no visible global function definition
for ‘as.SeqFastadna’
mlgt,mlgtDesign: no visible global function definition for ‘read.delim’
mlgt,mlgtDesign: no visible global function definition for
‘getSequence’
mlgt,mlgtDesign: no visible global function definition for ‘new’
mlgt,mlgtDesign: no visible global function definition for
‘as.SeqFastadna’
plotGenotypeEvidence,genotypeCall-missing-character: no visible global
function definition for ‘pdf’
plotGenotypeEvidence,genotypeCall-missing-character: no visible global
function definition for ‘dev.off’
plotGenotypeEvidence,genotypeCall-missing-missing: no visible global
function definition for ‘par’
plotGenotypeEvidence,genotypeCall-missing-missing: no visible global
function definition for ‘hist’
plotGenotypeEvidence,genotypeCall-missing-missing: no visible global
function definition for ‘abline’
plotGenotypeEvidence,genotypeCall-missing-missing: no visible global
function definition for ‘plot’
plotGenotypeEvidence,genotypeCall-missing-missing: no visible global
function definition for ‘legend’
plotGenotypeEvidence,missing-list-character: no visible global function
definition for ‘pdf’
plotGenotypeEvidence,missing-list-character: no visible global function
definition for ‘dev.off’
prepareMlgtRun,missing-character-character-character-list-list-list-character-character:
no visible global function definition for ‘new’
prepareMlgtRun,mlgtDesign-missing-missing-missing-missing-missing-missing-missing-character:
no visible global function definition for ‘write.fasta’
writeGenotypeCallsToFile,list-missing: no visible global function
definition for ‘write.table’
writeGenotypeCallsToFile,missing-genotypeCall: no visible global
function definition for ‘packageVersion’
writeGenotypeCallsToFile,missing-genotypeCall: no visible global
function definition for ‘write.table’
Undefined global functions or variables:
abline as.SeqFastadna as.alignment as.matrix.alignment barplot c2s
con consensus dev.off getName getSequence hist legend na.omit name
new packageVersion par pdf plot plot.new read.alignment read.delim
read.fasta s2c title write.fasta write.table
Consider adding
importFrom("grDevices", "dev.off", "pdf")
importFrom("graphics", "abline", "barplot", "hist", "legend", "par",
"plot", "plot.new", "title")
importFrom("methods", "new")
importFrom("stats", "na.omit")
importFrom("utils", "packageVersion", "read.delim", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Flavors: r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64
Current CRAN status:
Version: 0.01
Check: R code for possible problems
Result: NOTE
listGenoToTable: no visible binding for global variable 'dummy'
Undefined global functions or variables:
dummy
Found the following assignments to the global environment:
File 'mlPhaser/R/mlPhaser.R':
assign("validHaploGroups", c(get("validHaploGroups", globalenv()),
groupStoreList), globalenv())
assign("validHaploGroups", list(), globalenv())
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-patched-linux-x86_64, r-release-linux-x86_64
Version: 0.01
Check: Rd line widths
Result: NOTE
Rd file 'phaseReport.Rd':
\examples lines wider than 100 characters:
phaseReport(my.genotypes,haplotypes, haploFreqs, outFormat="all") # outFormat="all" is the default
These lines will be truncated in the PDF manual.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-linux-x86_64, r-release-linux-x86_64
Version: 0.01
Check: R code for possible problems
Result: NOTE
listGenoToTable: no visible binding for global variable ‘dummy’
Undefined global functions or variables:
dummy
Flavors: r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-patched-solaris-x86, r-release-macos-x86_64, r-release-windows-ix86+x86_64, r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64