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CHECK report for TFARM on tokay1

This page was generated on 2019-04-13 11:28:16 -0400 (Sat, 13 Apr 2019).

Package 1554/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TFARM 1.4.0
Liuba Nausicaa Martino
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/TFARM
Branch: RELEASE_3_8
Last Commit: ac05e23
Last Changed Date: 2018-10-30 11:42:06 -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: TFARM
Version: 1.4.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TFARM.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings TFARM_1.4.0.tar.gz
StartedAt: 2019-04-13 05:53:54 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 05:57:29 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 215.0 seconds
RetCode: 0
Status:  OK  
CheckDir: TFARM.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:TFARM.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings TFARM_1.4.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/TFARM.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 'TFARM/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'TFARM' version '1.4.0'
* 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 'TFARM' 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 ... 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
rulesTF0  6.1   0.19     6.3
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
         user system elapsed
rulesTF0 5.72   0.04    5.75
* 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: OK


Installation output

TFARM.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/TFARM_1.4.0.tar.gz && rm -rf TFARM.buildbin-libdir && mkdir TFARM.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=TFARM.buildbin-libdir TFARM_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL TFARM_1.4.0.zip && rm TFARM_1.4.0.tar.gz TFARM_1.4.0.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 69720  100 69720    0     0  1589k      0 --:--:-- --:--:-- --:--:-- 1745k

install for i386

* installing *source* package 'TFARM' ...
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'TFARM'
    finding HTML links ... done
    DELTA                                   html  
    IComp                                   html  
    IMP                                     html  
    IMP_Z                                   html  
    IPCA                                    html  
    I_c_2                                   html  
    MCF7_chr1                               html  
    TF_Imp                                  html  
    distribViz                              html  
    heatI                                   html  
    imp_FOSL2                               html  
    items                                   html  
    itemset                                 html  
    p_TFs                                   html  
    presAbs                                 html  
    r_FOSL2                                 html  
    r_TEAD4                                 html  
    r_noFOSL2                               html  
    rulesGen                                html  
    rulesTF                                 html  
    rulesTF0                                html  
    search_rule                             html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'TFARM' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'TFARM' as TFARM_1.4.0.zip
* DONE (TFARM)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'TFARM' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

TFARM.Rcheck/examples_i386/TFARM-Ex.timings

nameusersystemelapsed
DELTA000
IComp0.020.010.03
IMP000
IMP_Z000
IPCA0.020.000.02
I_c_2000
MCF7_chr10.140.000.14
TF_Imp0.010.000.01
distribViz0.020.000.02
heatI0.020.000.02
imp_FOSL2000
items000
itemset000
p_TFs0.000.020.01
presAbs0.040.030.08
r_FOSL20.000.010.02
r_TEAD4000
r_noFOSL2000
rulesGen0.690.020.71
rulesTF0.110.000.11
rulesTF06.100.196.30

TFARM.Rcheck/examples_x64/TFARM-Ex.timings

nameusersystemelapsed
DELTA000
IComp0.030.000.03
IMP000
IMP_Z000
IPCA0.010.000.01
I_c_2000
MCF7_chr10.170.020.19
TF_Imp000
distribViz0.020.000.01
heatI0.010.000.02
imp_FOSL20.020.000.01
items000
itemset000
p_TFs000
presAbs0.090.040.14
r_FOSL2000
r_TEAD4000
r_noFOSL2000
rulesGen0.920.000.92
rulesTF0.110.030.14
rulesTF05.720.045.75