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

CHECK results for GMRP on tokay2

To the developers/maintainers of the GMRP package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GMRP.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 783/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GMRP 1.20.0  (landing page)
Yuan-De Tan
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/GMRP
git_branch: RELEASE_3_13
git_last_commit: bfb1e34
git_last_commit_date: 2021-05-19 12:36:23 -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: GMRP
Version: 1.20.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GMRP.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings GMRP_1.20.0.tar.gz
StartedAt: 2021-10-14 23:55:37 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 23:57:23 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 105.2 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: GMRP.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GMRP.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings GMRP_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/GMRP.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 'GMRP/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GMRP' version '1.20.0'
* 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 'GMRP' can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'GMRP' is deprecated and will be removed from Bioconductor
  Warning: replacing previous import 'grDevices::windows' by 'GenomicRanges::windows' when loading 'GMRP'
See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/GMRP.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 ... 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 installed files from 'inst/doc' ... 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: 1 WARNING
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/GMRP.Rcheck/00check.log'
for details.



Installation output

GMRP.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/GMRP_1.20.0.tar.gz && rm -rf GMRP.buildbin-libdir && mkdir GMRP.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GMRP.buildbin-libdir GMRP_1.20.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL GMRP_1.20.0.zip && rm GMRP_1.20.0.tar.gz GMRP_1.20.0.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
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  375k  100  375k    0     0  1414k      0 --:--:-- --:--:-- --:--:-- 1416k

install for i386

* installing *source* package 'GMRP' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'grDevices::windows' by 'GenomicRanges::windows' when loading 'GMRP'
** help
*** installing help indices
  converting help for package 'GMRP'
    finding HTML links ... done
    GMRP-package                            html  
    SNP358.data                             html  
    SNP368annot.data                        html  
    beta.data                               html  
    cad.data                                html  
    chrp                                    html  
    fmerge                                  html  
    lpd.data                                html  
    mktable                                 html  
    path                                    html  
    pathdiagram                             html  
    pathdiagram2                            html  
    snpPositAnnot                           html  
    ucscannot                               html  
** building package indices
** installing vignettes
   'GMRP.Rnw' 
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'grDevices::windows' by 'GenomicRanges::windows' when loading 'GMRP'
Warning: Package 'GMRP' is deprecated and will be removed from Bioconductor
  version 3.7
** testing if installed package can be loaded from final location
Warning: replacing previous import 'grDevices::windows' by 'GenomicRanges::windows' when loading 'GMRP'
Warning: Package 'GMRP' is deprecated and will be removed from Bioconductor
  version 3.7
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'GMRP' ...
** testing if installed package can be loaded
Warning: replacing previous import 'grDevices::windows' by 'GenomicRanges::windows' when loading 'GMRP'
Warning: Package 'GMRP' is deprecated and will be removed from Bioconductor
  version 3.7
* MD5 sums
packaged installation of 'GMRP' as GMRP_1.20.0.zip
* DONE (GMRP)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'GMRP' successfully unpacked and MD5 sums checked

Tests output


Example timings

GMRP.Rcheck/examples_i386/GMRP-Ex.timings

nameusersystemelapsed
GMRP-package0.240.080.31
SNP358.data0.000.010.02
SNP368annot.data0.020.000.01
beta.data000
cad.data0.010.020.03
chrp0.050.010.06
fmerge0.000.020.02
lpd.data0.050.000.05
mktable0.090.030.12
path0.000.020.02
pathdiagram0.060.010.08
pathdiagram20.100.030.12
snpPositAnnot0.060.000.06
ucscannot0.030.020.05

GMRP.Rcheck/examples_x64/GMRP-Ex.timings

nameusersystemelapsed
GMRP-package0.170.010.19
SNP358.data000
SNP368annot.data0.010.000.02
beta.data000
cad.data0.020.000.01
chrp0.030.000.04
fmerge0.010.000.01
lpd.data0.020.000.02
mktable0.050.030.07
path000
pathdiagram0.060.000.06
pathdiagram20.060.000.06
snpPositAnnot0.030.010.05
ucscannot0.020.020.03