Last updated on 2019-12-04 10:47:31 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 5.1.1 | 20.44 | 146.27 | 166.71 | NOTE | |
| r-devel-linux-x86_64-debian-gcc | 5.1.1 | 17.53 | 112.79 | 130.32 | NOTE | |
| r-devel-linux-x86_64-fedora-clang | 5.1.1 | 184.00 | NOTE | |||
| r-devel-linux-x86_64-fedora-gcc | 5.1.1 | 184.52 | NOTE | |||
| r-devel-windows-ix86+x86_64 | 5.1.1 | 55.00 | 214.00 | 269.00 | NOTE | |
| r-devel-windows-ix86+x86_64-gcc8 | 5.1.1 | 54.00 | 221.00 | 275.00 | NOTE | |
| r-patched-linux-x86_64 | 5.1.1 | 18.12 | 139.10 | 157.22 | NOTE | |
| r-patched-solaris-x86 | 5.1.1 | 287.60 | NOTE | |||
| r-release-linux-x86_64 | 5.1.1 | 17.04 | 139.70 | 156.74 | NOTE | |
| r-release-windows-ix86+x86_64 | 5.1.1 | 52.00 | 315.00 | 367.00 | NOTE | |
| r-release-osx-x86_64 | 5.1.1 | NOTE | ||||
| r-oldrel-windows-ix86+x86_64 | 5.1.1 | 41.00 | 264.00 | 305.00 | NOTE | |
| r-oldrel-osx-x86_64 | 5.1.1 | NOTE |
Version: 5.1.1
Check: package dependencies
Result: NOTE
Depends: includes the non-default packages:
'seqinr', 'pcaMethods', 'Matrix', 'ROCR', 'Hmisc', 'KernSmooth',
'seqLogo'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
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-devel-windows-ix86+x86_64-gcc8, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-windows-ix86+x86_64, r-release-osx-x86_64
Version: 5.1.1
Check: dependencies in R code
Result: NOTE
'library' or 'require' calls to packages already attached by Depends:
'Hmisc' 'KernSmooth' 'Matrix' 'ROCR' 'methods' 'pcaMethods' 'seqLogo'
'seqinr'
Please remove these calls from your code.
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-devel-windows-ix86+x86_64-gcc8, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64
Version: 5.1.1
Check: R code for possible problems
Result: NOTE
DivergenceDROSOPHILA: no visible global function definition for 'data'
DivergenceHOMO: no visible global function definition for 'data'
DivergenceMUS: no visible global function definition for 'data'
DivergenceRATTUS: no visible global function definition for 'data'
EntropyDROSOPHILA: no visible global function definition for 'data'
EntropyHOMO: no visible global function definition for 'data'
EntropyMUS: no visible global function definition for 'data'
EntropyRATTUS: no visible global function definition for 'data'
JacksonParameters: no visible global function definition for 'prcomp'
MEET: no visible global function definition for 'write.table'
MEET: no visible global function definition for 'read.table'
MEET: no visible global function definition for 'data'
PCanalysis: no visible global function definition for 'residuals'
PredictPCA: no visible global function definition for 'residuals'
QresidualsDROSOPHILA: no visible global function definition for 'data'
QresidualsHOMO: no visible global function definition for 'data'
QresidualsMUS: no visible global function definition for 'data'
QresidualsRATTUS: no visible global function definition for 'data'
QtoJackson: no visible global function definition for 'pnorm'
Read.aligned: no visible global function definition for 'read.table'
chooseModel : <anonymous>: no visible global function definition for
'sd'
pvalue: no visible global function definition for 'sd'
pvalue: no visible global function definition for 'extendrange'
writeMEME: no visible global function definition for 'write.table'
writeResultsHTML: no visible global function definition for 'data'
writeResultsHTML: no visible binding for global variable
'RattusEntropy'
writeResultsHTML: no visible binding for global variable
'RattusDivergence'
writeResultsHTML: no visible binding for global variable
'RattusQresiduals'
writeResultsHTML: no visible binding for global variable 'MusEntropy'
writeResultsHTML: no visible binding for global variable
'MusDivergence'
writeResultsHTML: no visible binding for global variable
'MusQresiduals'
writeResultsHTML: no visible binding for global variable
'DrosophilaEntropy'
writeResultsHTML: no visible binding for global variable
'DrosophilaDivergence'
writeResultsHTML: no visible binding for global variable
'DrosophilaQresiduals'
writeResultsHTML: no visible binding for global variable 'HomoEntropy'
writeResultsHTML: no visible binding for global variable
'HomoDivergence'
writeResultsHTML: no visible binding for global variable
'HomoQresiduals'
writeResultsHTML: no visible global function definition for 'png'
writeResultsHTML: no visible global function definition for 'dev.off'
Undefined global functions or variables:
DrosophilaDivergence DrosophilaEntropy DrosophilaQresiduals
HomoDivergence HomoEntropy HomoQresiduals MusDivergence MusEntropy
MusQresiduals RattusDivergence RattusEntropy RattusQresiduals data
dev.off extendrange png pnorm prcomp read.table residuals sd
write.table
Consider adding
importFrom("grDevices", "dev.off", "extendrange", "png")
importFrom("stats", "pnorm", "prcomp", "residuals", "sd")
importFrom("utils", "data", "read.table", "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-devel-windows-ix86+x86_64-gcc8, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64
Version: 5.1.1
Check: Rd line widths
Result: NOTE
Rd file 'MEET.Rd':
\usage lines wider than 90 characters:
MEET(TF,nameTF, seqin, alg, method, mode, org, vector, num_motif, len_motif, direction, threshold, order, model,position, mv, gapopen, ... [TRUNCATED]
Rd file 'MIread.Rd':
\examples lines wider than 100 characters:
test<-MIread(training.set=iicc[["a1"]]$Transcriptionfactor, val.set=iicc[["a1"]]$Transcriptionfactor[1,],iicc=model)
Rd file 'align.muscle.Rd':
\usage lines wider than 90 characters:
align.muscle(filein , fileout = "Sq.fa", gapopen = gapopen, maxiters = maxiters, gapextend = gapextend, call)
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: 5.1.1
Check: for non-standard things in the check directory
Result: NOTE
Found the following files/directories:
'background.fa' 'motif.dat'
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
Version: 5.1.1
Check: compiled code
Result: NOTE
File ‘MEET/libs/MEET.so’:
Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’
It is good practice to register native routines and to disable symbol
search.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 5.1.1
Check: package dependencies
Result: NOTE
Depends: includes the non-default packages:
'seqinr' 'pcaMethods' 'Matrix' 'ROCR' 'Hmisc' 'KernSmooth' 'seqLogo'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Flavors: r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64