Back to Multiple platform build/check report for BioC 3.13
ABCDEFGHIJK[L]MNOPQRSTUVWXYZ

This page was generated on 2021-10-15 15:06:09 -0400 (Fri, 15 Oct 2021).

CHECK results for loci2path on tokay2

To the developers/maintainers of the loci2path package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/loci2path.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 996/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
loci2path 1.12.0  (landing page)
Tianlei Xu
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/loci2path
git_branch: RELEASE_3_13
git_last_commit: fd21ec3
git_last_commit_date: 2021-05-19 12:32:10 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 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: loci2path
Version: 1.12.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:loci2path.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings loci2path_1.12.0.tar.gz
StartedAt: 2021-10-15 01:11:20 -0400 (Fri, 15 Oct 2021)
EndedAt: 2021-10-15 01:13:21 -0400 (Fri, 15 Oct 2021)
EllapsedTime: 120.8 seconds
RetCode: 0
Status:   OK  
CheckDir: loci2path.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:loci2path.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings loci2path_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/loci2path.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 'loci2path/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'loci2path' version '1.12.0'
* package encoding: UTF-8
* 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 'loci2path' 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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: OK


Installation output

loci2path.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/loci2path_1.12.0.tar.gz && rm -rf loci2path.buildbin-libdir && mkdir loci2path.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=loci2path.buildbin-libdir loci2path_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL loci2path_1.12.0.zip && rm loci2path_1.12.0.tar.gz loci2path_1.12.0.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
  4  318k    4 16227    0     0   136k      0  0:00:02 --:--:--  0:00:02  136k
100  318k  100  318k    0     0   831k      0 --:--:-- --:--:-- --:--:--  830k

install for i386

* installing *source* package 'loci2path' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'loci2path'
    finding HTML links ... done
    biocarta                                html  
    check.geneid                            html  
    eqtlSet-class                           html  
    eset.list                               html  
    geneSet-class                           html  
    getHeatmap-methods                      html  
    getMat-methods                          html  
    getPathDescription-methods              html  
    getPval-methods                         html  
    getTissueDegree-methods                 html  
    getWordcloud-methods                    html  
    loci2pathResult-class                   html  
    query-methods                           html  
    query.gr                                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 'loci2path' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'loci2path' as loci2path_1.12.0.zip
* DONE (loci2path)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'loci2path' successfully unpacked and MD5 sums checked

Tests output


Example timings

loci2path.Rcheck/examples_i386/loci2path-Ex.timings

nameusersystemelapsed
biocarta000
check.geneid0.000.010.02
eqtlSet-class0.300.050.37
eset.list000
geneSet-class0.010.000.04
getHeatmap-methods0.600.200.78
getMat-methods0.290.030.33
getPathDescription-methods0.300.020.30
getPval-methods0.170.000.19
getTissueDegree-methods0.280.000.29
getWordcloud-methods0.320.010.35
loci2pathResult-class0.260.020.28
query-methods0.450.000.48
query.gr000

loci2path.Rcheck/examples_x64/loci2path-Ex.timings

nameusersystemelapsed
biocarta000
check.geneid0.020.000.01
eqtlSet-class0.170.010.19
eset.list0.000.020.02
geneSet-class000
getHeatmap-methods0.590.030.62
getMat-methods0.290.000.30
getPathDescription-methods0.260.020.30
getPval-methods0.300.010.31
getTissueDegree-methods0.260.000.26
getWordcloud-methods0.250.000.25
loci2pathResult-class0.200.020.22
query-methods0.360.000.36
query.gr000