Package: SEPA

Version: 1.13.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SEPA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SEPA_1.13.0.tar.gz

StartedAt: 2019-03-18 04:56:02 -0400 (Mon, 18 Mar 2019)

EndedAt: 2019-03-18 05:03:39 -0400 (Mon, 18 Mar 2019)

EllapsedTime: 456.7 seconds

RetCode: 1

Status:  ERROR

CheckDir: SEPA.Rcheck

Warnings: NA

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SEPA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SEPA_1.13.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/SEPA.Rcheck’
* using R Under development (unstable) (2019-01-22 r76000)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SEPA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SEPA’ version ‘1.13.0’
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘SEPA’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 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 ... NOTE
patternGOanalysis: no visible global function definition for ‘new’
pseudotimepattern : <anonymous>: no visible global function definition
  for ‘lm’
pseudotimepattern: no visible global function definition for ‘p.adjust’
pseudotimepattern: no visible global function definition for ‘lm’
pseudotimepattern: no visible global function definition for ‘lines’
pseudotimepattern: no visible global function definition for ‘confint’
pseudotimepattern: no visible global function definition for ‘fitted’
pseudotimepattern : <anonymous>: no visible global function definition
  for ‘fitted’
pseudotimevisualize: no visible binding for global variable
  ‘pseudotime’
pseudotimevisualize: no visible binding for global variable ‘Var2’
pseudotimevisualize: no visible binding for global variable ‘Var1’
pseudotimevisualize: no visible binding for global variable ‘value’
pseudotimevisualize: no visible binding for global variable ‘xend’
pseudotimevisualize: no visible binding for global variable ‘yend’
truetimepattern : <anonymous> : <anonymous>: no visible global function
  definition for ‘t.test’
truetimepattern : <anonymous>: no visible global function definition
  for ‘p.adjust’
truetimevisualize : <anonymous> : <anonymous>: no visible global
  function definition for ‘median’
truetimevisualize: no visible binding for global variable ‘time’
truetimevisualize: no visible binding for global variable ‘expmean’
truetimevisualize: no visible binding for global variable ‘Gene’
windowGOanalysis: no visible global function definition for ‘new’
windowGOvisualize: no visible binding for global variable ‘Var1’
windowGOvisualize: no visible binding for global variable ‘value’
Undefined global functions or variables:
  Gene Var1 Var2 confint expmean fitted lines lm median new p.adjust
  pseudotime t.test time value xend yend
Consider adding
  importFrom("graphics", "lines")
  importFrom("methods", "new")
  importFrom("stats", "confint", "fitted", "lm", "median", "p.adjust",
             "t.test", "time")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘SEPA-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: truetimevisualize
> ### Title: truetimevisualize
> ### Aliases: truetimevisualize
> 
> ### ** Examples
> 
> data(HSMMdata)
> truetimevisualize(HSMMdata,truetime,c("ENSG00000122180.4","ENSG00000125968.7"))
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
SEPA
 --- call from context --- 
FUN(X[[i]], ...)
 --- call from argument --- 
if (mode == "mean") {
    mean(e[truetime == levels(truetime)[i]])
} else {
    median(e[truetime == levels(truetime)[i]])
}
 --- R stacktrace ---
where 1: FUN(X[[i]], ...)
where 2: lapply(X = X, FUN = FUN, ...)
where 3: sapply(1:length(levels(truetime)), function(i) {
    if (mode == "mean") {
        mean(e[truetime == levels(truetime)[i]])
    }
    else {
        median(e[truetime == levels(truetime)[i]])
    }
})
where 4: FUN(X[[i]], ...)
where 5: lapply(X = X, FUN = FUN, ...)
where 6: sapply(gene, function(singlegene) {
    e <- expr[singlegene, names(truetime)]
    sapply(1:length(levels(truetime)), function(i) {
        if (mode == "mean") {
            mean(e[truetime == levels(truetime)[i]])
        }
        else {
            median(e[truetime == levels(truetime)[i]])
        }
    })
})
where 7: as.vector(sapply(gene, function(singlegene) {
    e <- expr[singlegene, names(truetime)]
    sapply(1:length(levels(truetime)), function(i) {
        if (mode == "mean") {
            mean(e[truetime == levels(truetime)[i]])
        }
        else {
            median(e[truetime == levels(truetime)[i]])
        }
    })
}))
where 8: truetimevisualize(HSMMdata, truetime, c("ENSG00000122180.4", 
    "ENSG00000125968.7"))

 --- value of length: 2 type: logical ---
[1]  TRUE FALSE
 --- function from context --- 
function (i) 
{
    if (mode == "mean") {
        mean(e[truetime == levels(truetime)[i]])
    }
    else {
        median(e[truetime == levels(truetime)[i]])
    }
}
<bytecode: 0x7fad82ee3470>
<environment: 0x7fad82f415c0>
 --- function search by body ---
 ----------- END OF FAILURE REPORT -------------- 
Fatal error: the condition has length > 1
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/SEPA.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL SEPA
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘SEPA’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (SEPA)

name	user	system	elapsed
SEPAui	0.000	0.000	0.001
patternGOanalysis	91.848	3.262	95.184
patternsummary	1.700	0.019	1.719
pseudotimepattern	98.579	5.156	103.784
pseudotimevisualize	99.558	3.089	102.720
truetimepattern	1.871	0.039	1.911