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CHECK report for vulcan on tokay2

This page was generated on 2019-10-16 12:39:31 -0400 (Wed, 16 Oct 2019).

Package 1718/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
vulcan 1.6.0
Federico M. Giorgi
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/vulcan
Branch: RELEASE_3_9
Last Commit: 989fc10
Last Changed Date: 2019-05-02 11:54:09 -0400 (Thu, 02 May 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: vulcan
Version: 1.6.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:vulcan.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings vulcan_1.6.0.tar.gz
StartedAt: 2019-10-16 07:50:30 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 08:00:03 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 573.1 seconds
RetCode: 0
Status:  OK  
CheckDir: vulcan.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:vulcan.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings vulcan_1.6.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/vulcan.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 'vulcan/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'vulcan' version '1.6.0'
* 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 8.29   0.75   22.51
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
average_fragment_length 7.94    0.5    9.25
* 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-3.9-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/3.9/bioc/src/contrib/vulcan_1.6.0.tar.gz && rm -rf vulcan.buildbin-libdir && mkdir vulcan.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=vulcan.buildbin-libdir vulcan_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL vulcan_1.6.0.zip && rm vulcan_1.6.0.tar.gz vulcan_1.6.0.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  1945k      0 --:--:-- --:--:-- --:--:-- 2122k

install for i386

* installing *source* package 'vulcan' ...
** using staged installation
** 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 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 'vulcan' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'vulcan' as vulcan_1.6.0.zip
* DONE (vulcan)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'vulcan' successfully unpacked and MD5 sums checked

Tests output


Example timings

vulcan.Rcheck/examples_i386/vulcan-Ex.timings

nameusersystemelapsed
average_fragment_length 8.29 0.7522.51
corr2p0.020.000.02
densityauc0.030.010.05
dpareto0.020.000.02
fisherp000
gsea0.230.280.51
kmgformat0.020.000.02
null_gsea0.030.000.03
p2corr000
p2z000
pareto.fit000
plot_gsea0.030.000.03
ppareto0.020.000.02
rea000
slice000
stouffer000
textplot20.170.020.18
val2col000
vulcan2.840.203.25
vulcan.annotate1.220.081.30
vulcan.import0.000.020.01
vulcan.normalize000
vulcan.pathways1.540.001.55
wstouffer000
z2p000

vulcan.Rcheck/examples_x64/vulcan-Ex.timings

nameusersystemelapsed
average_fragment_length7.940.509.25
corr2p1.080.011.09
densityauc0.030.000.03
dpareto0.010.000.02
fisherp000
gsea0.160.030.18
kmgformat0.010.000.02
null_gsea0.040.000.03
p2corr000
p2z000
pareto.fit000
plot_gsea0.060.000.06
ppareto000
rea000
slice000
stouffer000
textplot20.170.000.18
val2col000
vulcan3.110.073.17
vulcan.annotate2.330.012.34
vulcan.import0.010.020.03
vulcan.normalize000
vulcan.pathways1.460.001.46
wstouffer000
z2p000