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This page was generated on 2022-01-24 13:07:12 -0500 (Mon, 24 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4080
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4141
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for vulcan on tokay2


To the developers/maintainers of the vulcan package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/vulcan.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 2057/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
vulcan 1.16.0  (landing page)
Federico M. Giorgi
Snapshot Date: 2022-01-23 01:55:04 -0500 (Sun, 23 Jan 2022)
git_url: https://git.bioconductor.org/packages/vulcan
git_branch: RELEASE_3_14
git_last_commit: b25ca79
git_last_commit_date: 2021-10-26 12:38:33 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: vulcan
Version: 1.16.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:vulcan.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings vulcan_1.16.0.tar.gz
StartedAt: 2022-01-24 04:12:58 -0500 (Mon, 24 Jan 2022)
EndedAt: 2022-01-24 04:22:00 -0500 (Mon, 24 Jan 2022)
EllapsedTime: 542.3 seconds
RetCode: 0
Status:   OK  
CheckDir: vulcan.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:vulcan.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings vulcan_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/vulcan.Rcheck'
* using R version 4.1.2 (2021-11-01)
* 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 '1.16.0'
* 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 ... NOTE
vulcan.normalize: no visible global function definition for 'assay'
Undefined global functions or variables:
  assay
* 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 (user + system) or elapsed time > 5s
                        user system elapsed
vulcan                  7.63   1.28    8.95
average_fragment_length 7.52   1.24   11.33
vulcan.pathways         5.71   0.09    5.81
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
vulcan                  7.02   0.03    7.05
average_fragment_length 4.83   0.38    5.50
* 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/vulcan.Rcheck/00check.log'
for details.



Installation output

vulcan.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/vulcan_1.16.0.tar.gz && rm -rf vulcan.buildbin-libdir && mkdir vulcan.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=vulcan.buildbin-libdir vulcan_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL vulcan_1.16.0.zip && rm vulcan_1.16.0.tar.gz vulcan_1.16.0.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
 10  143k   10 16077    0     0   136k      0  0:00:01 --:--:--  0:00:01  136k
100  143k  100  143k    0     0   759k      0 --:--:-- --:--:-- --:--:--  761k

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_1.16.0.zip
* DONE (vulcan)
* installing to library 'C:/Users/biocbuild/bbs-3.14-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 7.52 1.2411.33
corr2p000
densityauc0.050.000.04
dpareto0.010.000.02
fisherp000
gsea0.280.000.28
kmgformat0.130.000.13
null_gsea0.030.000.03
p2corr000
p2z000
pareto.fit0.030.000.03
plot_gsea0.060.000.07
ppareto000
rea000
slice0.020.000.01
stouffer000
textplot20.310.000.31
val2col0.040.000.05
vulcan7.631.288.95
vulcan.annotate2.730.172.91
vulcan.import0.020.020.03
vulcan.normalize000
vulcan.pathways5.710.095.81
wstouffer000
z2p000

vulcan.Rcheck/examples_x64/vulcan-Ex.timings

nameusersystemelapsed
average_fragment_length4.830.385.50
corr2p000
densityauc0.030.000.04
dpareto000
fisherp000
gsea0.190.010.20
kmgformat0.090.000.10
null_gsea0.050.000.04
p2corr000
p2z000
pareto.fit0.050.000.05
plot_gsea0.040.000.05
ppareto000
rea000
slice000
stouffer000
textplot20.220.000.22
val2col0.030.000.03
vulcan7.020.037.05
vulcan.annotate2.140.042.19
vulcan.import0.030.000.03
vulcan.normalize000
vulcan.pathways4.360.074.42
wstouffer000
z2p000