Last updated on 2020-08-07 01:50:20 CEST.
| Package | WARN | NOTE |
|---|---|---|
| metaMA | 12 | |
| metaRNASeq | 2 | 10 |
| SMVar | 12 |
Current CRAN status: NOTE: 12
Version: 3.1.2
Check: DESCRIPTION meta-information
Result: NOTE
Malformed Description field: should contain one or more complete sentences.
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-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: 3.1.2
Check: R code for possible problems
Result: NOTE
EScombination: no visible global function definition for 'model.matrix'
EScombination: no visible global function definition for 'p.adjust'
EScombination: no visible global function definition for 'pt'
EScombination.paired: no visible global function definition for
'p.adjust'
EScombination.paired: no visible global function definition for 'pt'
calcfit2Diffrep: no visible global function definition for
'model.matrix'
directEScombi: no visible global function definition for 'pnorm'
directEScombi: no visible global function definition for 'p.adjust'
directpvalcombi : fstatmeta: no visible global function definition for
'qnorm'
directpvalcombi: no visible global function definition for 'pnorm'
directpvalcombi: no visible global function definition for 'p.adjust'
pvalcombination: no visible global function definition for
'model.matrix'
pvalcombination: no visible global function definition for 'p.adjust'
pvalcombination: no visible global function definition for 'pt'
pvalcombination.paired: no visible global function definition for
'p.adjust'
pvalcombination.paired: no visible global function definition for 'pt'
Undefined global functions or variables:
model.matrix p.adjust pnorm pt qnorm
Consider adding
importFrom("stats", "model.matrix", "p.adjust", "pnorm", "pt", "qnorm")
to your NAMESPACE file.
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-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: 3.1.2
Check: installed package size
Result: NOTE
installed size is 9.5Mb
sub-directories of 1Mb or more:
data 9.1Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-ix86+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: 3.1.2
Flags: --no-vignettes
Check: installed package size
Result: NOTE
installed size is 9.5Mb
sub-directories of 1Mb or more:
data 9.1Mb
Flavor: r-patched-solaris-x86
Version: 3.1.2
Flags: --no-vignettes
Check: DESCRIPTION meta-information
Result: NOTE
Malformed Description field: should contain one or more complete sentences.
Flavor: r-patched-solaris-x86
Version: 3.1.2
Flags: --no-vignettes
Check: R code for possible problems
Result: NOTE
EScombination: no visible global function definition for ‘model.matrix’
EScombination: no visible global function definition for ‘p.adjust’
EScombination: no visible global function definition for ‘pt’
EScombination.paired: no visible global function definition for
‘p.adjust’
EScombination.paired: no visible global function definition for ‘pt’
calcfit2Diffrep: no visible global function definition for
‘model.matrix’
directEScombi: no visible global function definition for ‘pnorm’
directEScombi: no visible global function definition for ‘p.adjust’
directpvalcombi : fstatmeta: no visible global function definition for
‘qnorm’
directpvalcombi: no visible global function definition for ‘pnorm’
directpvalcombi: no visible global function definition for ‘p.adjust’
pvalcombination: no visible global function definition for
‘model.matrix’
pvalcombination: no visible global function definition for ‘p.adjust’
pvalcombination: no visible global function definition for ‘pt’
pvalcombination.paired: no visible global function definition for
‘p.adjust’
pvalcombination.paired: no visible global function definition for ‘pt’
Undefined global functions or variables:
model.matrix p.adjust pnorm pt qnorm
Consider adding
importFrom("stats", "model.matrix", "p.adjust", "pnorm", "pt", "qnorm")
to your NAMESPACE file.
Flavor: r-patched-solaris-x86
Version: 3.1.2
Check: package dependencies
Result: NOTE
Packages suggested but not available for checking:
'annaffy', 'hgu133plus2.db', 'hgu95av2.db'
Flavor: r-release-macos-x86_64
Version: 3.1.2
Check: package dependencies
Result: NOTE
Packages suggested but not available for checking:
'org.Hs.eg.db', 'annaffy', 'hgu133plus2.db', 'hgu133a.db',
'hgu95av2.db'
Flavor: r-oldrel-macos-x86_64
Current CRAN status: WARN: 2, NOTE: 10
Version: 1.0.2
Check: R code for possible problems
Result: NOTE
fishercomb: no visible global function definition for 'pchisq'
fishercomb: no visible global function definition for 'p.adjust'
invnorm : <anonymous>: no visible global function definition for
'qnorm'
invnorm: no visible global function definition for 'pnorm'
invnorm: no visible global function definition for 'p.adjust'
sim.function : <anonymous>: no visible global function definition for
'rnorm'
sim.function : <anonymous>: no visible global function definition for
'rnbinom'
Undefined global functions or variables:
p.adjust pchisq pnorm qnorm rnbinom rnorm
Consider adding
importFrom("stats", "p.adjust", "pchisq", "pnorm", "qnorm", "rnbinom",
"rnorm")
to your NAMESPACE file.
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, r-release-macos-x86_64, r-oldrel-macos-x86_64
Version: 1.0.2
Flags: --no-vignettes
Check: R code for possible problems
Result: NOTE
fishercomb: no visible global function definition for 'pchisq'
fishercomb: no visible global function definition for 'p.adjust'
invnorm : <anonymous>: no visible global function definition for
'qnorm'
invnorm: no visible global function definition for 'pnorm'
invnorm: no visible global function definition for 'p.adjust'
sim.function : <anonymous>: no visible global function definition for
'rnorm'
sim.function : <anonymous>: no visible global function definition for
'rnbinom'
Undefined global functions or variables:
p.adjust pchisq pnorm qnorm rnbinom rnorm
Consider adding
importFrom("stats", "p.adjust", "pchisq", "pnorm", "qnorm", "rnbinom",
"rnorm")
to your NAMESPACE file.
Flavors: r-devel-windows-ix86+x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64
Version: 1.0.2
Flags: --no-build-vignettes
Check: R code for possible problems
Result: NOTE
fishercomb: no visible global function definition for ‘pchisq’
fishercomb: no visible global function definition for ‘p.adjust’
invnorm : <anonymous>: no visible global function definition for
‘qnorm’
invnorm: no visible global function definition for ‘pnorm’
invnorm: no visible global function definition for ‘p.adjust’
sim.function : <anonymous>: no visible global function definition for
‘rnorm’
sim.function : <anonymous>: no visible global function definition for
‘rnbinom’
Undefined global functions or variables:
p.adjust pchisq pnorm qnorm rnbinom rnorm
Consider adding
importFrom("stats", "p.adjust", "pchisq", "pnorm", "qnorm", "rnbinom",
"rnorm")
to your NAMESPACE file.
Flavor: r-patched-solaris-x86
Version: 1.0.2
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: ‘HTSFilter’
Flavor: r-release-macos-x86_64
Version: 1.0.2
Check: running R code from vignettes
Result: WARN
Errors in running code in vignettes:
when running code in ‘metaRNASeq.Rnw’
...
estimateSizeFactorsForMatrix,
getVarianceStabilizedData,
varianceStabilizingTransformation
> library(HTSFilter)
When sourcing ‘metaRNASeq.R’:
Error: there is no package called ‘HTSFilter’
Execution halted
‘metaRNASeq.Rnw’... failed
Flavor: r-release-macos-x86_64
Version: 1.0.2
Check: re-building of vignette outputs
Result: NOTE
Error(s) in re-building vignettes:
--- re-building ‘metaRNASeq.Rnw’ using Sweave
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:parallel’:
clusterApply, clusterApplyLB, clusterCall,
clusterEvalQ, clusterExport, clusterMap,
parApply, parCapply, parLapply, parLapplyLB,
parRapply, parSapply, parSapplyLB
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
Filter, Find, Map, Position, Reduce,
anyDuplicated, append, as.data.frame, basename,
cbind, colnames, dirname, do.call, duplicated,
eval, evalq, get, grep, grepl, intersect,
is.unsorted, lapply, mapply, match, mget, order,
paste, pmax, pmax.int, pmin, pmin.int, rank,
rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which, which.max,
which.min
Attaching package: ‘S4Vectors’
The following object is masked from ‘package:base’:
expand.grid
Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view
with 'browseVignettes()'. To cite Bioconductor,
see 'citation("Biobase")', and for packages
'citation("pkgname")'.
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: ‘matrixStats’
The following objects are masked from ‘package:Biobase’:
anyMissing, rowMedians
Attaching package: ‘DelayedArray’
The following objects are masked from ‘package:matrixStats’:
colMaxs, colMins, colRanges, rowMaxs, rowMins,
rowRanges
The following objects are masked from ‘package:base’:
aperm, apply, rowsum
converting counts to integer mode
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
converting counts to integer mode
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
Loading required package: locfit
locfit 1.5-9.4 2020-03-24
Loading required package: lattice
Welcome to 'DESeq'. For improved performance,
usability and functionality, please consider
migrating to 'DESeq2'.
Attaching package: ‘DESeq’
The following objects are masked from ‘package:DESeq2’:
estimateSizeFactorsForMatrix,
getVarianceStabilizedData,
varianceStabilizingTransformation
Error: processing vignette 'metaRNASeq.Rnw' failed with diagnostics:
chunk 9 (label = DESeq1study)
Error in library(HTSFilter) : there is no package called ‘HTSFilter’
--- failed re-building ‘metaRNASeq.Rnw’
SUMMARY: processing the following file failed:
‘metaRNASeq.Rnw’
Error: Vignette re-building failed.
Execution halted
Flavor: r-release-macos-x86_64
Version: 1.0.2
Check: package dependencies
Result: NOTE
Packages suggested but not available for checking:
'HTSFilter', 'DESeq', 'DESeq2'
Flavor: r-oldrel-macos-x86_64
Version: 1.0.2
Check: running R code from vignettes
Result: WARN
Errors in running code in vignettes:
when running code in ‘metaRNASeq.Rnw’
...
> options(width = 60)
> library(metaRNASeq)
> library(DESeq2)
When sourcing ‘metaRNASeq.R’:
Error: there is no package called ‘DESeq2’
Execution halted
Flavor: r-oldrel-macos-x86_64
Version: 1.0.2
Check: re-building of vignette outputs
Result: NOTE
Error(s) in re-building vignettes:
...
--- re-building ‘metaRNASeq.Rnw’ using Sweave
Error: processing vignette 'metaRNASeq.Rnw' failed with diagnostics:
chunk 2 (label = loadparameters)
Error in library(DESeq2) : there is no package called ‘DESeq2’
--- failed re-building ‘metaRNASeq.Rnw’
SUMMARY: processing the following file failed:
‘metaRNASeq.Rnw’
Error: Vignette re-building failed.
Execution halted
Flavor: r-oldrel-macos-x86_64
Current CRAN status: NOTE: 12
Version: 1.3.3
Check: DESCRIPTION meta-information
Result: NOTE
Malformed Description field: should contain one or more complete sentences.
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: 1.3.3
Check: R code for possible problems
Result: NOTE
SMVar.paired : <anonymous>: no visible global function definition for
'var'
SMVar.paired: no visible global function definition for 'var'
SMVar.paired: no visible global function definition for 'pt'
SMVar.paired: no visible global function definition for 'p.adjust'
SMVar.paired: no visible global function definition for 'write.table'
SMVar.unpaired : <anonymous>: no visible global function definition for
'var'
SMVar.unpaired: no visible global function definition for 'var'
SMVar.unpaired: no visible global function definition for 'pt'
SMVar.unpaired: no visible global function definition for 'p.adjust'
SMVar.unpaired: no visible global function definition for 'write.table'
Undefined global functions or variables:
p.adjust pt var write.table
Consider adding
importFrom("stats", "p.adjust", "pt", "var")
importFrom("utils", "write.table")
to your NAMESPACE file.
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: 1.3.3
Check: Rd line widths
Result: NOTE
Rd file 'SMVar.paired.Rd':
\usage lines wider than 90 characters:
SMVar.paired(geneNumbers, logratio, fileexport = NULL, minrep = 2, method = "BH", threshold = 0.05)
Rd file 'SMVar.unpaired.Rd':
\usage lines wider than 90 characters:
SMVar.unpaired(geneNumbers, listcond, fileexport = NULL, minrep = 2, method = "BH", threshold = 0.05)
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