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CHECK report for synapterdata on riesling1

This page was generated on 2021-01-14 15:59:12 -0500 (Thu, 14 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE synapterdata PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 348/385HostnameOS / ArchINSTALLBUILDCHECK
synapterdata 1.29.0
Laurent Gatto
Snapshot Date: 2021-01-14 09:00:13 -0500 (Thu, 14 Jan 2021)
URL: https://git.bioconductor.org/packages/synapterdata
Branch: master
Last Commit: 8b5d800
Last Changed Date: 2020-10-27 09:55:57 -0500 (Tue, 27 Oct 2020)
malbec2 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK [ OK ]

Summary

Package: synapterdata
Version: 1.29.0
Command: D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:synapterdata.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings synapterdata_1.29.0.tar.gz
StartedAt: 2021-01-14 11:43:33 -0500 (Thu, 14 Jan 2021)
EndedAt: 2021-01-14 11:46:58 -0500 (Thu, 14 Jan 2021)
EllapsedTime: 205.7 seconds
RetCode: 0
Status:  OK  
CheckDir: synapterdata.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:synapterdata.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings synapterdata_1.29.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.13-data-experiment/meat/synapterdata.Rcheck'
* using R Under development (unstable) (2020-12-30 r79736)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'synapterdata/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'synapterdata' version '1.29.0'
* 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 'synapterdata' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 422.5Mb
  sub-directories of 1Mb or more:
    data      28.0Mb
    extdata  394.4Mb
* checking package 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 examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  'D:/biocbuild/bbs-3.13-data-experiment/meat/synapterdata.Rcheck/00check.log'
for details.



Installation output

synapterdata.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.4/BBS/3.13/data-experiment/src/contrib/synapterdata_1.29.0.tar.gz && rm -rf synapterdata.buildbin-libdir && mkdir synapterdata.buildbin-libdir && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=synapterdata.buildbin-libdir synapterdata_1.29.0.tar.gz && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL synapterdata_1.29.0.zip && rm synapterdata_1.29.0.tar.gz synapterdata_1.29.0.zip
###
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##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  8  418M    8 33.4M    0     0  58.9M      0  0:00:07 --:--:--  0:00:07 58.8M
 35  418M   35  146M    0     0  93.5M      0  0:00:04  0:00:01  0:00:03 93.4M
 56  418M   56  238M    0     0  92.8M      0  0:00:04  0:00:02  0:00:02 92.8M
 75  418M   75  314M    0     0  88.0M      0  0:00:04  0:00:03  0:00:01 88.0M
100  418M  100  418M    0     0  92.1M      0  0:00:04  0:00:04 --:--:-- 92.1M

install for i386

* installing *source* package 'synapterdata' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'synapterdata'
    finding HTML links ... done
    getHDMSeFinalPeptide                    html  
REDIRECT:topic	 getHDMSeFinalPeptide -> getHDMSeFinalPeptide.html [ SUCCESS ]
REDIRECT:topic	 getMSeFinalPeptide -> getHDMSeFinalPeptide.html [ SUCCESS ]
REDIRECT:topic	 getMSePep3D -> getHDMSeFinalPeptide.html [ SUCCESS ]
REDIRECT:topic	 getFasta -> getHDMSeFinalPeptide.html [ SUCCESS ]
    getMasterRds                            html  
REDIRECT:topic	 getMaster -> getMasterRds.html [ SUCCESS ]
REDIRECT:topic	 loadMaster -> getMasterRds.html [ SUCCESS ]
REDIRECT:file	 getMasterRds.html -> getMasterRds.html [ SUCCESS ]
    synapterdata-package                    html  
REDIRECT:topic	 synapterdata-package -> synapterdata-package.html [ SUCCESS ]
REDIRECT:topic	 synapterdata -> synapterdata-package.html [ SUCCESS ]
    synobj2                                 html  
REDIRECT:topic	 synobj2 -> synobj2.html [ SUCCESS ]
REDIRECT:topic	 synobj2RData -> synobj2.html [ SUCCESS ]
    ups25a                                  html  
REDIRECT:topic	 ups25a -> ups25a.html [ SUCCESS ]
REDIRECT:topic	 ups25b -> ups25a.html [ SUCCESS ]
REDIRECT:topic	 ups25c -> ups25a.html [ SUCCESS ]
REDIRECT:topic	 ups50a -> ups25a.html [ SUCCESS ]
REDIRECT:topic	 ups50b -> ups25a.html [ SUCCESS ]
REDIRECT:topic	 ups50c -> ups25a.html [ SUCCESS ]
** building package indices
** 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 'synapterdata' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'synapterdata' as synapterdata_1.29.0.zip
* DONE (synapterdata)
* installing to library 'D:/biocbuild/bbs-3.13-bioc/R/library'
package 'synapterdata' successfully unpacked and MD5 sums checked

Tests output


Example timings

synapterdata.Rcheck/examples_i386/synapterdata-Ex.timings

nameusersystemelapsed
getHDMSeFinalPeptide000
getMasterRds0.110.000.11
synobj21.890.021.91
ups25a1.030.041.07

synapterdata.Rcheck/examples_x64/synapterdata-Ex.timings

nameusersystemelapsed
getHDMSeFinalPeptide000
getMasterRds0.060.000.07
synobj21.820.031.86
ups25a0.440.030.47