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CHECK report for vulcan on tokay2

This page was generated on 2018-10-17 08:44:39 -0400 (Wed, 17 Oct 2018).

Package 1541/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
vulcan 1.2.0
Federico M. Giorgi
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/vulcan
Branch: RELEASE_3_7
Last Commit: 0357cea
Last Changed Date: 2018-04-30 10:35:48 -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: vulcan
Version: 1.2.0
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:vulcan.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings vulcan_1.2.0.tar.gz
StartedAt: 2018-10-17 05:24:15 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 05:33:22 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 547.6 seconds
RetCode: 0
Status:  OK  
CheckDir: vulcan.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:vulcan.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings vulcan_1.2.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/vulcan.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 'vulcan/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'vulcan' version '1.2.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'ChIPpeakAnno' 'TxDb.Hsapiens.UCSC.hg19.knownGene' 'zoo'
  'GenomicRanges' 'S4Vectors' 'viper' 'DiffBind' 'locfit'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'vulcan' 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
average_fragment_length 9.34   1.09    19.3
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
average_fragment_length 6.59   0.34    6.99
* 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/vulcan.Rcheck/00check.log'
for details.



Installation output

vulcan.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/vulcan_1.2.0.tar.gz && rm -rf vulcan.buildbin-libdir && mkdir vulcan.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=vulcan.buildbin-libdir vulcan_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL vulcan_1.2.0.zip && rm vulcan_1.2.0.tar.gz vulcan_1.2.0.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  144k  100  144k    0     0  1888k      0 --:--:-- --:--:-- --:--:-- 2122k

install for i386

* installing *source* package 'vulcan' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'vulcan'
    finding HTML links ... done
    average_fragment_length                 html  
    corr2p                                  html  
    densityauc                              html  
    dpareto                                 html  
    fisherp                                 html  
    gsea                                    html  
    kmgformat                               html  
    null_gsea                               html  
    p2corr                                  html  
    p2z                                     html  
    pareto.fit                              html  
    plot_gsea                               html  
    ppareto                                 html  
    rea                                     html  
    slice                                   html  
    stouffer                                html  
    textplot2                               html  
    val2col                                 html  
    vulcan                                  html  
    vulcan.annotate                         html  
    vulcan.import                           html  
    vulcan.normalize                        html  
    vulcan.pathways                         html  
    wstouffer                               html  
    z2p                                     html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'vulcan' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'vulcan' as vulcan_1.2.0.zip
* DONE (vulcan)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'vulcan' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

vulcan.Rcheck/examples_i386/vulcan-Ex.timings

nameusersystemelapsed
average_fragment_length 9.34 1.0919.30
corr2p000
densityauc0.030.000.03
dpareto000
fisherp000
gsea0.200.080.29
kmgformat0.010.000.02
null_gsea0.020.000.01
p2corr000
p2z000
pareto.fit0.000.020.02
plot_gsea0.030.000.03
ppareto000
rea000
slice0.020.000.02
stouffer000
textplot20.150.000.15
val2col000
vulcan3.270.093.53
vulcan.annotate1.760.021.78
vulcan.import0.020.000.02
vulcan.normalize000
vulcan.pathways1.800.041.84
wstouffer000
z2p000

vulcan.Rcheck/examples_x64/vulcan-Ex.timings

nameusersystemelapsed
average_fragment_length6.590.346.99
corr2p000
densityauc0.020.000.02
dpareto0.010.000.01
fisherp000
gsea0.180.020.19
kmgformat0.010.000.01
null_gsea0.020.000.02
p2corr000
p2z000
pareto.fit0.010.000.02
plot_gsea0.020.000.01
ppareto000
rea000
slice000
stouffer000
textplot20.190.000.18
val2col000
vulcan3.190.123.32
vulcan.annotate1.610.021.62
vulcan.import0.010.000.02
vulcan.normalize000
vulcan.pathways1.750.001.75
wstouffer000
z2p000