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CHECK report for miRNApath on tokay1

This page was generated on 2019-04-13 11:20:44 -0400 (Sat, 13 Apr 2019).

Package 972/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
miRNApath 1.42.0
James M. Ward
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/miRNApath
Branch: RELEASE_3_8
Last Commit: 717b31d
Last Changed Date: 2018-10-30 11:41:44 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
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: miRNApath
Version: 1.42.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:miRNApath.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings miRNApath_1.42.0.tar.gz
StartedAt: 2019-04-13 03:53:08 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 03:56:01 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 173.3 seconds
RetCode: 0
Status:  OK  
CheckDir: miRNApath.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:miRNApath.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings miRNApath_1.42.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/miRNApath.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 'miRNApath/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'miRNApath' version '1.42.0'
* 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 'miRNApath' 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 ... NOTE
Warning: no function found corresponding to methods exports from 'miRNApath' for: 'show'

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
** 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 ... NOTE
Warning: no function found corresponding to methods exports from 'miRNApath' for: 'show'

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Package in Depends field not imported from: 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
loadmirnapath: no visible global function definition for 'read.table'
loadmirnapath: no visible global function definition for 'new'
loadmirnapathways: no visible global function definition for
  'read.table'
loadmirnatogene: no visible global function definition for 'read.table'
mirnaTable: no visible global function definition for 'reshape'
runEnrichment : <anonymous> : <anonymous>: no visible global function
  definition for 'phyper'
runEnrichment: no visible global function definition for 'slotNames'
Undefined global functions or variables:
  new phyper read.table reshape slotNames
Consider adding
  importFrom("methods", "new", "slotNames")
  importFrom("stats", "phyper", "reshape")
  importFrom("utils", "read.table")
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
mirnaTable 53.69   0.01   53.71
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
mirnaTable 32.42   0.02   32.44
* 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: 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/miRNApath.Rcheck/00check.log'
for details.



Installation output

miRNApath.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/miRNApath_1.42.0.tar.gz && rm -rf miRNApath.buildbin-libdir && mkdir miRNApath.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=miRNApath.buildbin-libdir miRNApath_1.42.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL miRNApath_1.42.0.zip && rm miRNApath_1.42.0.tar.gz miRNApath_1.42.0.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  439k  100  439k    0     0  7375k      0 --:--:-- --:--:-- --:--:-- 7849k

install for i386

* installing *source* package 'miRNApath' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'miRNApath'
    finding HTML links ... done
    checkColumns                            html  
    convertFoldChange                       html  
    filtermirnapath                         html  
    loadmirnapath                           html  
    loadmirnapathways                       html  
    loadmirnatogene                         html  
    miRNApath-package                       html  
    mirnaTable                              html  
    mirnaobj                                html  
    mirnapath-class                         html  
    runEnrichment                           html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'miRNApath' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'miRNApath' as miRNApath_1.42.0.zip
* DONE (miRNApath)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'miRNApath' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

miRNApath.Rcheck/examples_i386/miRNApath-Ex.timings

nameusersystemelapsed
checkColumns000
convertFoldChange000
filtermirnapath0.050.000.05
loadmirnapath0.080.000.59
loadmirnapathways0.200.000.21
loadmirnatogene0.140.020.15
miRNApath-package000
mirnaTable53.69 0.0153.71
mirnaobj0.030.000.03
mirnapath-class0.020.000.01
runEnrichment000

miRNApath.Rcheck/examples_x64/miRNApath-Ex.timings

nameusersystemelapsed
checkColumns000
convertFoldChange000
filtermirnapath0.030.000.03
loadmirnapath0.060.010.11
loadmirnapathways0.110.000.11
loadmirnatogene0.140.000.14
miRNApath-package000
mirnaTable32.42 0.0232.44
mirnaobj0.020.000.02
mirnapath-class0.030.000.03
runEnrichment000