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CHECK report for SEPA on tokay1

This page was generated on 2019-04-13 11:25:35 -0400 (Sat, 13 Apr 2019).

Package 1413/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SEPA 1.12.0
Zhicheng Ji
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/SEPA
Branch: RELEASE_3_8
Last Commit: 0b21a28
Last Changed Date: 2018-10-30 11:41:58 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  NA 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: SEPA
Version: 1.12.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SEPA.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings SEPA_1.12.0.tar.gz
StartedAt: 2019-04-13 05:24:00 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 05:39:13 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 912.9 seconds
RetCode: 0
Status:  OK  
CheckDir: SEPA.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SEPA.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings SEPA_1.12.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/SEPA.Rcheck'
* using R version 3.5.3 (2019-03-11)
* 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 '1.12.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
windowGOanalysis    89.50   0.39   89.89
windowGOvisualize   76.49   0.30   76.78
pseudotimepattern   70.39   0.55   70.94
pseudotimevisualize 65.56   0.00   65.56
patternGOanalysis   50.18   0.97   51.20
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
windowGOanalysis    98.69   0.32   99.02
windowGOvisualize   89.21   0.24   89.45
pseudotimepattern   70.11   0.26   70.38
pseudotimevisualize 65.93   0.02   65.94
patternGOanalysis   53.86   0.70   54.57
* 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 NOTE
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/SEPA.Rcheck/00check.log'
for details.



Installation output

SEPA.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/SEPA_1.12.0.tar.gz && rm -rf SEPA.buildbin-libdir && mkdir SEPA.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SEPA.buildbin-libdir SEPA_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL SEPA_1.12.0.zip && rm SEPA_1.12.0.tar.gz SEPA_1.12.0.zip
###
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  % 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  16.0M      0 --:--:-- --:--:-- --:--:-- 17.8M

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
In R CMD INSTALL

install for x64

* installing *source* package 'SEPA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SEPA' as SEPA_1.12.0.zip
* DONE (SEPA)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'SEPA' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

SEPA.Rcheck/examples_i386/SEPA-Ex.timings

nameusersystemelapsed
SEPAui000
patternGOanalysis50.18 0.9751.20
patternsummary101
pseudotimepattern70.39 0.5570.94
pseudotimevisualize65.56 0.0065.56
truetimepattern101
truetimevisualize0.280.000.29
windowGOanalysis89.50 0.3989.89
windowGOvisualize76.49 0.3076.78

SEPA.Rcheck/examples_x64/SEPA-Ex.timings

nameusersystemelapsed
SEPAui000
patternGOanalysis53.86 0.7054.57
patternsummary1.010.021.03
pseudotimepattern70.11 0.2670.38
pseudotimevisualize65.93 0.0265.94
truetimepattern1.020.001.02
truetimevisualize0.280.020.29
windowGOanalysis98.69 0.3299.02
windowGOvisualize89.21 0.2489.45