- using R Under development (unstable) (2019-12-11 r77556)
- using platform: x86_64-pc-linux-gnu (64-bit)
- using session charset: ISO8859-15
- checking for file 'AMAP.Seq/DESCRIPTION' ... OK
- checking extension type ... Package
- this is package 'AMAP.Seq' version '1.0'
- checking package namespace information ... OK
- checking package dependencies ... OK
- checking if this is a source package ... OK
- checking if there is a namespace ... OK
- checking for executable files ... OK
- checking for hidden files and directories ... OK
- checking for portable file names ... OK
- checking for sufficient/correct file permissions ... OK
- checking serialization versions ... OK
- checking whether package 'AMAP.Seq' can be installed ... OK
- checking package directory ... OK
- checking for future file timestamps ... OK
- checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
- checking top-level files ... OK
- checking for left-over files ... OK
- checking index information ... OK
- checking package subdirectories ... OK
- checking R files for non-ASCII characters ... OK
- checking R files for syntax errors ... OK
- checking whether the package can be loaded ... OK
- checking whether the package can be loaded with stated dependencies ... OK
- checking whether the package can be unloaded cleanly ... OK
- checking whether the namespace can be loaded with stated dependencies ... OK
- checking whether the namespace can be unloaded cleanly ... OK
- checking loading without being on the library search path ... OK
- checking use of S3 registration ... OK
- checking dependencies in R code ... OK
- checking S3 generic/method consistency ... OK
- checking replacement functions ... OK
- checking foreign function calls ... OK
- checking R code for possible problems ... [8s/9s] NOTE
EXP.step: no visible global function definition for 'rgamma'
EXP.step: no visible global function definition for 'rnorm'
MAX.step: no visible global function definition for 'uniroot'
Norm.GMedian: no visible binding for global variable 'median'
RNASeq.Data.Gene: no visible binding for global variable 'quantile'
decom.initial: no visible global function definition for 'kmeans'
decom.initial: no visible global function definition for 'quantile'
decom.initial: no visible global function definition for 'var'
dispersion.nb.QL: no visible binding for global variable 'quantile'
est.mu.nb.mle: no visible global function definition for 'runif'
est.v.nb.QL: no visible global function definition for 'runif'
pdf2grid: no visible global function definition for 'dnorm'
pdf2grid: no visible global function definition for 'dgamma'
prior.grid: no visible global function definition for 'sd'
prior.grid: no visible global function definition for 'dnorm'
test.AMAP: no visible global function definition for 'rgamma'
test.AMAP: no visible global function definition for 'rnorm'
test.AMAP: no visible global function definition for 'quantile'
Undefined global functions or variables:
dgamma dnorm kmeans median quantile rgamma rnorm runif sd uniroot var
Consider adding
importFrom("stats", "dgamma", "dnorm", "kmeans", "median", "quantile",
"rgamma", "rnorm", "runif", "sd", "uniroot", "var")
to your NAMESPACE file.
- checking Rd files ... OK
- checking Rd metadata ... OK
- checking Rd line widths ... NOTE
Rd file 'MGN.EM.Rd':
\usage lines wider than 90 characters:
MGN.EM(data, nK, p0 = NULL, d0 = 0, nK0 = 0, iter.max = 10, print.steps = FALSE, MGN0 = NULL, model = NULL, nMC = 10000)
Rd file 'test.AMAP.Rd':
\usage lines wider than 90 characters:
test.AMAP(data, MGN, del.lim = NULL, FC = NULL, print.steps = FALSE, Integration = "MC",nMC=NULL)
\examples lines wider than 100 characters:
data("SimuHapMap") # a matrix 'counts' storing simulated data with 10000 genes, two treatments, of which each has 5 replicates
These lines will be truncated in the PDF manual.
- checking Rd cross-references ... OK
- checking for missing documentation entries ... OK
- checking for code/documentation mismatches ... OK
- checking Rd \usage sections ... OK
- checking Rd contents ... OK
- checking for unstated dependencies in examples ... OK
- checking contents of 'data' directory ... OK
- checking data for non-ASCII characters ... OK
- checking data for ASCII and uncompressed saves ... OK
- checking examples ... [4s/5s] OK
- checking PDF version of manual ... OK
- checking for non-standard things in the check directory ... OK
- DONE
Status: 3 NOTEs