Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-10-15 15:06:17 -0400 (Fri, 15 Oct 2021).

CHECK results for PSICQUIC on tokay2

To the developers/maintainers of the PSICQUIC package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/PSICQUIC.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 1455/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PSICQUIC 1.30.0  (landing page)
Paul Shannon
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/PSICQUIC
git_branch: RELEASE_3_13
git_last_commit: 3d77738
git_last_commit_date: 2021-05-19 12:01:47 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: PSICQUIC
Version: 1.30.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PSICQUIC.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings PSICQUIC_1.30.0.tar.gz
StartedAt: 2021-10-15 03:50:55 -0400 (Fri, 15 Oct 2021)
EndedAt: 2021-10-15 03:58:58 -0400 (Fri, 15 Oct 2021)
EllapsedTime: 483.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: PSICQUIC.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PSICQUIC.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings PSICQUIC_1.30.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/PSICQUIC.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'PSICQUIC/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'PSICQUIC' version '1.30.0'
* 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 'PSICQUIC' can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import 'IRanges::desc' by 'plyr::desc' when loading 'PSICQUIC'
See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/PSICQUIC.Rcheck/00install.out' for details.
* 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
.loadRegistry: no visible global function definition for 'DataFrame'
Undefined global functions or variables:
  DataFrame
* 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
PSICQUIC-class 16.85   0.67   80.06
IDMapper-class 11.46   0.14   37.12
interactions    2.64   0.36   25.25
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
PSICQUIC-class 14.08   0.42   79.89
IDMapper-class  8.03   0.09   43.58
interactions    2.97   0.16   59.09
* 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: 1 WARNING, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/PSICQUIC.Rcheck/00check.log'
for details.



Installation output

PSICQUIC.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/PSICQUIC_1.30.0.tar.gz && rm -rf PSICQUIC.buildbin-libdir && mkdir PSICQUIC.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=PSICQUIC.buildbin-libdir PSICQUIC_1.30.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL PSICQUIC_1.30.0.zip && rm PSICQUIC_1.30.0.tar.gz PSICQUIC_1.30.0.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
100 65448  100 65448    0     0   322k      0 --:--:-- --:--:-- --:--:--  324k

install for i386

* installing *source* package 'PSICQUIC' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'IRanges::desc' by 'plyr::desc' when loading 'PSICQUIC'
Creating a new generic function for 'count' in package 'PSICQUIC'
** help
*** installing help indices
  converting help for package 'PSICQUIC'
    finding HTML links ... done
    IDMapper-class                          html  
    PSICQUIC-class                          html  
    PSICQUIC-package                        html  
    interactions                            html  
    providers                               html  
    rawQuery                                html  
    webBrowser-functions                    html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'IRanges::desc' by 'plyr::desc' when loading 'PSICQUIC'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'IRanges::desc' by 'plyr::desc' when loading 'PSICQUIC'
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'PSICQUIC' ...
** testing if installed package can be loaded
Warning: replacing previous import 'IRanges::desc' by 'plyr::desc' when loading 'PSICQUIC'
* MD5 sums
packaged installation of 'PSICQUIC' as PSICQUIC_1.30.0.zip
* DONE (PSICQUIC)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'PSICQUIC' successfully unpacked and MD5 sums checked

Tests output

PSICQUIC.Rcheck/tests_i386/runTests.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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("PSICQUIC")
> 
> proc.time()
   user  system elapsed 
   0.29    0.03    0.31 

PSICQUIC.Rcheck/tests_x64/runTests.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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("PSICQUIC")
> 
> proc.time()
   user  system elapsed 
   0.26    0.03    0.28 

Example timings

PSICQUIC.Rcheck/examples_i386/PSICQUIC-Ex.timings

nameusersystemelapsed
IDMapper-class11.46 0.1437.12
PSICQUIC-class16.85 0.6780.06
interactions 2.64 0.3625.25
providers0.070.000.93
rawQuery0.140.001.78
webBrowser-functions000

PSICQUIC.Rcheck/examples_x64/PSICQUIC-Ex.timings

nameusersystemelapsed
IDMapper-class 8.03 0.0943.58
PSICQUIC-class14.08 0.4279.89
interactions 2.97 0.1659.09
providers0.060.000.94
rawQuery0.160.001.95
webBrowser-functions000