Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-21 13:06:49 -0500 (Fri, 21 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" 4079
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4140
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 PCAN on tokay2


To the developers/maintainers of the PCAN package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/PCAN.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 1385/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PCAN 1.22.0  (landing page)
Matthew Page and Patrice Godard
Snapshot Date: 2022-01-20 01:55:04 -0500 (Thu, 20 Jan 2022)
git_url: https://git.bioconductor.org/packages/PCAN
git_branch: RELEASE_3_14
git_last_commit: 102b5fb
git_last_commit_date: 2021-10-26 12:26:11 -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: PCAN
Version: 1.22.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PCAN.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings PCAN_1.22.0.tar.gz
StartedAt: 2022-01-21 00:23:20 -0500 (Fri, 21 Jan 2022)
EndedAt: 2022-01-21 00:30:30 -0500 (Fri, 21 Jan 2022)
EllapsedTime: 429.2 seconds
RetCode: 0
Status:   OK  
CheckDir: PCAN.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PCAN.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings PCAN_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/PCAN.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 'PCAN/DESCRIPTION' ... OK
* this is package 'PCAN' version '1.22.0'
* 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 'PCAN' 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 (user + system) or elapsed time > 5s
                user system elapsed
hpGeneListComp 51.93   0.16   52.08
compareHPSets  51.51   0.14   51.65
hpGeneHeatmap  50.48   0.23   50.73
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
hpGeneHeatmap  60.61   0.16   60.80
hpGeneListComp 57.23   0.20   57.50
compareHPSets  56.34   0.14   56.49
* 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

PCAN.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/PCAN_1.22.0.tar.gz && rm -rf PCAN.buildbin-libdir && mkdir PCAN.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=PCAN.buildbin-libdir PCAN_1.22.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL PCAN_1.22.0.zip && rm PCAN_1.22.0.tar.gz PCAN_1.22.0.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
 26 1862k   26  495k    0     0  1494k      0  0:00:01 --:--:--  0:00:01 1493k
100 1862k  100 1862k    0     0  2824k      0 --:--:-- --:--:-- --:--:-- 2825k

install for i386

* installing *source* package 'PCAN' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'PCAN'
    finding HTML links ... done
    calcHpSim                               html  
    compareHPSets                           html  
    finding level-2 HTML links ... done

    computeHpIC                             html  
    geneByHp                                html  
    geneByTrait                             html  
    geneDef                                 html  
    hpByTrait                               html  
    hpDef                                   html  
    hpGeneHeatmap                           html  
    hpGeneListComp                          html  
    hpSetCompBestMatch                      html  
    hpSetCompSummary                        html  
    hp_ancestors                            html  
    hp_class                                html  
    hp_descendants                          html  
    hqStrNw                                 html  
    hsEntrezByRPath                         html  
    rPath                                   html  
    traitDef                                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 'PCAN' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'PCAN' as PCAN_1.22.0.zip
* DONE (PCAN)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'PCAN' successfully unpacked and MD5 sums checked

Tests output


Example timings

PCAN.Rcheck/examples_i386/PCAN-Ex.timings

nameusersystemelapsed
calcHpSim1.920.112.04
compareHPSets51.51 0.1451.65
computeHpIC1.840.081.92
geneByHp1.710.011.72
geneByTrait0.030.030.06
geneDef2.250.032.28
hpByTrait2.120.052.17
hpDef1.520.021.54
hpGeneHeatmap50.48 0.2350.73
hpGeneListComp51.93 0.1652.08
hpSetCompBestMatch2.530.062.59
hpSetCompSummary2.480.062.55
hp_ancestors1.690.051.73
hp_class0.050.000.05
hp_descendants1.500.031.53
hqStrNw000
hsEntrezByRPath000
rPath000
traitDef2.620.082.70

PCAN.Rcheck/examples_x64/PCAN-Ex.timings

nameusersystemelapsed
calcHpSim1.750.131.87
compareHPSets56.34 0.1456.49
computeHpIC1.570.031.60
geneByHp1.620.021.64
geneByTrait0.050.000.04
geneDef2.580.072.66
hpByTrait2.650.082.75
hpDef1.660.061.72
hpGeneHeatmap60.61 0.1660.80
hpGeneListComp57.23 0.2057.50
hpSetCompBestMatch2.600.042.62
hpSetCompSummary2.200.062.27
hp_ancestors1.640.031.67
hp_class0.050.000.05
hp_descendants1.540.031.57
hqStrNw000
hsEntrezByRPath000
rPath000
traitDef2.440.062.50