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CHECK report for TFutils on tokay2

This page was generated on 2018-10-17 08:45:39 -0400 (Wed, 17 Oct 2018).

Package 1479/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TFutils 1.0.0
Shweta Gopaulakrishnan
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/TFutils
Branch: RELEASE_3_7
Last Commit: 2f08b9b
Last Changed Date: 2018-04-30 10:35:50 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: TFutils
Version: 1.0.0
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TFutils.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings TFutils_1.0.0.tar.gz
StartedAt: 2018-10-17 05:10:51 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 05:18:20 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 448.9 seconds
RetCode: 0
Status:  OK  
CheckDir: TFutils.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TFutils.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings TFutils_1.0.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/TFutils.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'TFutils/DESCRIPTION' ... OK
* this is package 'TFutils' version '1.0.0'
* 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 'TFutils' 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 ... OK
* 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 ... NOTE
  Note: found 62 marked UTF-8 strings
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
genemodForGviz    5   0.11    5.11
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 OK
* 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-3.7-bioc/meat/TFutils.Rcheck/00check.log'
for details.



Installation output

TFutils.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/TFutils_1.0.0.tar.gz && rm -rf TFutils.buildbin-libdir && mkdir TFutils.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=TFutils.buildbin-libdir TFutils_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL TFutils_1.0.0.zip && rm TFutils_1.0.0.tar.gz TFutils_1.0.0.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 2045k  100 2045k    0     0  25.3M      0 --:--:-- --:--:-- --:--:-- 27.7M

install for i386

* installing *source* package 'TFutils' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'TFutils'
    finding HTML links ... done
    HGNCmap                                 html  
    TFCatalog-class                         html  
    TFCatalog                               html  
    TFtargs                                 html  
    URL_s3_tf                               html  
    cisbpTFcat                              html  
    fimo16                                  html  
    fimoMap                                 html  
    genemodForGviz                          html  
    genemodelDF                             html  
    grabTab                                 html  
    gwascat_hg19_chr17                      html  
    hocomoco.mono                           html  
    importFIMO                              html  
    importFIMO_local_split                  html  
    metadata_tf                             html  
    named_tf                                html  
    show-TFCatalog-method                   html  
    tfhash                                  html  
    tftColl                                 html  
    tftCollMap                              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'TFutils' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'TFutils' as TFutils_1.0.0.zip
* DONE (TFutils)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'TFutils' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

TFutils.Rcheck/tests_i386/testthat.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(TFutils)
> 
> test_check("TFutils")
== testthat results  ===========================================================
OK: 5 SKIPPED: 0 FAILED: 0
> 
> 
> proc.time()
   user  system elapsed 
  15.46    1.28   16.78 

TFutils.Rcheck/tests_x64/testthat.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(TFutils)
> 
> test_check("TFutils")
== testthat results  ===========================================================
OK: 5 SKIPPED: 0 FAILED: 0
> 
> 
> proc.time()
   user  system elapsed 
   24.4     1.0    26.7 

Example timings

TFutils.Rcheck/examples_i386/TFutils-Ex.timings

nameusersystemelapsed
HGNCmap000
TFCatalog0.070.000.07
TFtargs000
URL_s3_tf000
cisbpTFcat0.110.000.11
fimo160.010.000.01
fimoMap0.020.000.02
genemodForGviz3.970.504.48
genemodelDF0.100.030.12
grabTab0.250.170.43
gwascat_hg19_chr170.060.010.08
hocomoco.mono000
importFIMO0.040.040.06
importFIMO_local_split0.030.000.17
metadata_tf0.010.000.02
named_tf0.020.000.01
tfhash1.220.101.33
tftColl0.230.000.24
tftCollMap000

TFutils.Rcheck/examples_x64/TFutils-Ex.timings

nameusersystemelapsed
HGNCmap000
TFCatalog0.070.010.08
TFtargs000
URL_s3_tf000
cisbpTFcat0.030.010.04
fimo160.030.000.03
fimoMap000
genemodForGviz5.000.115.11
genemodelDF0.110.000.11
grabTab0.280.080.36
gwascat_hg19_chr170.060.000.06
hocomoco.mono0.020.000.02
importFIMO0.050.000.05
importFIMO_local_split0.010.000.01
metadata_tf000
named_tf0.020.000.02
tfhash0.790.170.97
tftColl0.300.000.29
tftCollMap000