Multiple platform build/check report for BioC 3.9 - CHECK report for SEPA on tokay2

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SEPA.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings SEPA_1.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/SEPA.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... 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: 0x072837b8>
<environment: 0x071df5a0>
 --- function search by body ---
 ----------- END OF FAILURE REPORT -------------- 
Fatal error: the condition has length > 1

** running examples for arch 'x64' ... 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: 0x000000001055d698>
<environment: 0x00000000104875a0>
 --- 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: 2 ERRORs, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/SEPA.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/SEPA_1.13.0.tar.gz && rm -rf SEPA.buildbin-libdir && mkdir SEPA.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SEPA.buildbin-libdir SEPA_1.13.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL SEPA_1.13.0.zip && rm SEPA_1.13.0.tar.gz SEPA_1.13.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  696k  100  696k    0     0  4979k      0 --:--:-- --:--:-- --:--:-- 5160k

install for i386

* installing *source* package 'SEPA' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'SEPA'
    finding HTML links ... done
    HSMMdata                                html  
    SEPA                                    html  
    SEPAui                                  html  
    patternGOanalysis                       html  
    patternsummary                          html  
    pseudotime                              html  
    pseudotimepattern                       html  
    pseudotimevisualize                     html  
    truetime                                html  
    truetimepattern                         html  
    truetimevisualize                       html  
    windowGOanalysis                        html  
    windowGOvisualize                       html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'SEPA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SEPA' as SEPA_1.13.0.zip
* DONE (SEPA)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'SEPA' successfully unpacked and MD5 sums checked

CHECK report for SEPA on tokay2

Summary

Command output

Installation output

Tests output

Example timings