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CHECK report for TFEA.ChIP on tokay2

This page was generated on 2019-10-16 12:40:13 -0400 (Wed, 16 Oct 2019).

Package 1641/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TFEA.ChIP 1.4.2
Laura Puente SantamarĂ­a
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/TFEA.ChIP
Branch: RELEASE_3_9
Last Commit: 679bcf9
Last Changed Date: 2019-07-18 02:34:02 -0400 (Thu, 18 Jul 2019)
malbec2 Linux (Ubuntu 18.04.2 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
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: TFEA.ChIP
Version: 1.4.2
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TFEA.ChIP.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings TFEA.ChIP_1.4.2.tar.gz
StartedAt: 2019-10-16 07:32:04 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 07:40:47 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 523.8 seconds
RetCode: 0
Status:  OK  
CheckDir: TFEA.ChIP.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TFEA.ChIP.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings TFEA.ChIP_1.4.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/TFEA.ChIP.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'TFEA.ChIP/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'TFEA.ChIP' version '1.4.2'
* package encoding: UTF-8
* 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 'TFEA.ChIP' 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
contingency_matrix 9.78   0.58   10.36
GSEA_run           8.39   0.34    8.73
set_user_data      6.71   0.16    6.85
GeneID2entrez      1.46   0.09   10.30
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
contingency_matrix 8.61   0.26    8.88
GSEA_run           7.93   0.22    8.14
set_user_data      6.33   0.13    6.46
GeneID2entrez      1.46   0.08   11.22
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.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: OK


Installation output

TFEA.ChIP.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/TFEA.ChIP_1.4.2.tar.gz && rm -rf TFEA.ChIP.buildbin-libdir && mkdir TFEA.ChIP.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=TFEA.ChIP.buildbin-libdir TFEA.ChIP_1.4.2.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL TFEA.ChIP_1.4.2.zip && rm TFEA.ChIP_1.4.2.tar.gz TFEA.ChIP_1.4.2.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 3908k  100 3908k    0     0  42.2M      0 --:--:-- --:--:-- --:--:-- 45.9M

install for i386

* installing *source* package 'TFEA.ChIP' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'TFEA.ChIP'
    finding HTML links ... done
    ARNT.metadata                           html  
    ARNT.peaks.bed                          html  
    CM_list                                 html  
    DnaseHS_db                              html  
    Entrez.gene.IDs                         html  
    GR2tfbs_db                              html  
    GSEA.result                             html  
    GSEA_ESpermutations                     html  
    GSEA_EnrichmentScore                    html  
    GSEA_run                                html  
    GeneID2entrez                           html  
    Genes.Upreg                             html  
    Mat01                                   html  
    MetaData                                html  
    Select_genes                            html  
    contingency_matrix                      html  
    getCMstats                              html  
    get_LFC_bar                             html  
    get_chip_index                          html  
    gr.list                                 html  
    highlight_TF                            html  
    hypoxia                                 html  
    hypoxia_DESeq                           html  
    log2.FC                                 html  
    makeTFBSmatrix                          html  
    plot_CM                                 html  
    plot_ES                                 html  
    plot_RES                                html  
    preprocessInputData                     html  
    rankTFs                                 html  
    set_user_data                           html  
    stat_mat                                html  
    tfbs.database                           html  
    txt2GR                                  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 'TFEA.ChIP' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'TFEA.ChIP' as TFEA.ChIP_1.4.2.zip
* DONE (TFEA.ChIP)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'TFEA.ChIP' successfully unpacked and MD5 sums checked

Tests output

TFEA.ChIP.Rcheck/tests_i386/runTests.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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.

> BiocGenerics:::testPackage(pkgname = "TFEA.ChIP")

Because of space limitations, TFEA.ChIPs internal database only includes ChIP-seq experiments from the ENCODE project. 
To download the full ReMap database, as well as other ready-to-use databases, visit https://github.com/LauraPS1/TFEA.ChIP_downloads

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  |======================================================================| 100%

  |                                                                            
  |                                                                      |   0%
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  |===================================                                   |  50%
  |                                                                            
  |======================================================================| 100%
Done! 2 genes of 2 successfully converted.

Done! 1 genes of 1 successfully converted.

Done! 1 genes of 1 successfully converted.

Done! 2 genes of 2 successfully converted.

Done! 16909 genes of 17527 successfully converted.

Couldn't find Entrez IDs for 618 genes.

Loading required package: DESeq2
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min


Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from 'package:base':

    aperm, apply, rowsum

Done! 10612 genes of 11667 successfully converted.

Couldn't find Entrez IDs for 1055 genes.

Done! 16909 genes of 17527 successfully converted.

Couldn't find Entrez IDs for 618 genes.

Done! 10612 genes of 11667 successfully converted.

Couldn't find Entrez IDs for 1055 genes.



RUNIT TEST PROTOCOL -- Wed Oct 16 07:39:56 2019 
*********************************************** 
Number of test functions: 11 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
TFEA.ChIP RUnit Tests - 11 test functions, 0 errors, 0 failures
Number of test functions: 11 
Number of errors: 0 
Number of failures: 0 
Warning message:
Some genes returned 1:many mapping to ENTREZ ID. Genes were assigned the first ENTREZ ID match found.
 
> 
> proc.time()
   user  system elapsed 
  48.73    2.06   50.87 

TFEA.ChIP.Rcheck/tests_x64/runTests.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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.

> BiocGenerics:::testPackage(pkgname = "TFEA.ChIP")

Because of space limitations, TFEA.ChIPs internal database only includes ChIP-seq experiments from the ENCODE project. 
To download the full ReMap database, as well as other ready-to-use databases, visit https://github.com/LauraPS1/TFEA.ChIP_downloads

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |======================================================================| 100%
Done! 2 genes of 2 successfully converted.

Done! 1 genes of 1 successfully converted.

Done! 1 genes of 1 successfully converted.

Done! 2 genes of 2 successfully converted.

Done! 16909 genes of 17527 successfully converted.

Couldn't find Entrez IDs for 618 genes.

Loading required package: DESeq2
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min


Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from 'package:base':

    aperm, apply, rowsum

Done! 10612 genes of 11667 successfully converted.

Couldn't find Entrez IDs for 1055 genes.

Done! 16909 genes of 17527 successfully converted.

Couldn't find Entrez IDs for 618 genes.

Done! 10612 genes of 11667 successfully converted.

Couldn't find Entrez IDs for 1055 genes.



RUNIT TEST PROTOCOL -- Wed Oct 16 07:40:42 2019 
*********************************************** 
Number of test functions: 11 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
TFEA.ChIP RUnit Tests - 11 test functions, 0 errors, 0 failures
Number of test functions: 11 
Number of errors: 0 
Number of failures: 0 
Warning message:
Some genes returned 1:many mapping to ENTREZ ID. Genes were assigned the first ENTREZ ID match found.
 
> 
> proc.time()
   user  system elapsed 
  44.71    1.53   46.23 

Example timings

TFEA.ChIP.Rcheck/examples_i386/TFEA.ChIP-Ex.timings

nameusersystemelapsed
GR2tfbs_db0.860.080.94
GSEA_EnrichmentScore000
GSEA_run8.390.348.73
GeneID2entrez 1.46 0.0910.30
Select_genes0.170.080.25
contingency_matrix 9.78 0.5810.36
getCMstats0.110.050.16
get_chip_index0.050.040.09
makeTFBSmatrix0.060.040.09
plot_CM0.590.120.72
plot_ES1.580.021.60
plot_RES1.610.071.68
preprocessInputData2.00.32.3
rankTFs0.010.000.02
set_user_data6.710.166.85
txt2GR0.040.000.05

TFEA.ChIP.Rcheck/examples_x64/TFEA.ChIP-Ex.timings

nameusersystemelapsed
GR2tfbs_db0.630.080.71
GSEA_EnrichmentScore000
GSEA_run7.930.228.14
GeneID2entrez 1.46 0.0811.22
Select_genes0.210.050.25
contingency_matrix8.610.268.88
getCMstats0.080.030.11
get_chip_index0.040.030.07
makeTFBSmatrix0.060.020.08
plot_CM0.550.080.63
plot_ES1.270.111.67
plot_RES1.780.092.22
preprocessInputData2.060.252.31
rankTFs0.010.000.01
set_user_data6.330.136.46
txt2GR0.050.000.04