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CHECK report for FANTOM3and4CAGE on riesling1

This page was generated on 2021-01-21 16:01:28 -0500 (Thu, 21 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE FANTOM3and4CAGE PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 117/386HostnameOS / ArchINSTALLBUILDCHECK
FANTOM3and4CAGE 1.27.0
Vanja Haberle
Snapshot Date: 2021-01-21 09:00:14 -0500 (Thu, 21 Jan 2021)
URL: https://git.bioconductor.org/packages/FANTOM3and4CAGE
Branch: master
Last Commit: 7a1076a
Last Changed Date: 2020-10-27 10:00:55 -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: FANTOM3and4CAGE
Version: 1.27.0
Command: D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:FANTOM3and4CAGE.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings FANTOM3and4CAGE_1.27.0.tar.gz
StartedAt: 2021-01-21 11:22:23 -0500 (Thu, 21 Jan 2021)
EndedAt: 2021-01-21 11:23:25 -0500 (Thu, 21 Jan 2021)
EllapsedTime: 62.3 seconds
RetCode: 0
Status:  OK  
CheckDir: FANTOM3and4CAGE.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:FANTOM3and4CAGE.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings FANTOM3and4CAGE_1.27.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.13-data-experiment/meat/FANTOM3and4CAGE.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 'FANTOM3and4CAGE/DESCRIPTION' ... OK
* this is package 'FANTOM3and4CAGE' version '1.27.0'
* 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 'FANTOM3and4CAGE' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 34.4Mb
  sub-directories of 1Mb or more:
    data  34.3Mb
* 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
* 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 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
FANTOMtissueCAGEhuman 6.67   0.15    6.83
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
FANTOMtissueCAGEhuman 5.15   0.22    5.38
* 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 NOTE
See
  'D:/biocbuild/bbs-3.13-data-experiment/meat/FANTOM3and4CAGE.Rcheck/00check.log'
for details.



Installation output

FANTOM3and4CAGE.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/FANTOM3and4CAGE_1.27.0.tar.gz && rm -rf FANTOM3and4CAGE.buildbin-libdir && mkdir FANTOM3and4CAGE.buildbin-libdir && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=FANTOM3and4CAGE.buildbin-libdir FANTOM3and4CAGE_1.27.0.tar.gz && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL FANTOM3and4CAGE_1.27.0.zip && rm FANTOM3and4CAGE_1.27.0.tar.gz FANTOM3and4CAGE_1.27.0.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
  6 34.5M    6 2330k    0     0  2688k      0  0:00:13 --:--:--  0:00:13 2685k
 10 34.5M   10 3816k    0     0  2058k      0  0:00:17  0:00:01  0:00:16 2057k
 16 34.5M   16 6006k    0     0  1927k      0  0:00:18  0:00:03  0:00:15 1927k
 88 34.5M   88 30.4M    0     0  7445k      0  0:00:04  0:00:04 --:--:-- 7445k
 92 34.5M   92 31.8M    0     0  6725k      0  0:00:05  0:00:04  0:00:01 6723k
100 34.5M  100 34.5M    0     0  7261k      0  0:00:04  0:00:04 --:--:-- 8252k

install for i386

* installing *source* package 'FANTOM3and4CAGE' ...
** using staged installation
** data
** help
*** installing help indices
  converting help for package 'FANTOM3and4CAGE'
    finding HTML links ... done
    FANTOMhumanSamples                      html  
REDIRECT:topic	 FANTOMhumanSamples -> FANTOMhumanSamples.html [ SUCCESS ]
    FANTOMmouseSamples                      html  
REDIRECT:topic	 FANTOMmouseSamples -> FANTOMmouseSamples.html [ SUCCESS ]
    FANTOMtimecourseCAGEhuman               html  
REDIRECT:topic	 FANTOMtimecourseCAGEhuman -> FANTOMtimecourseCAGEhuman.html [ SUCCESS ]
    FANTOMtimecourseCAGEmouse               html  
REDIRECT:topic	 FANTOMtimecourseCAGEmouse -> FANTOMtimecourseCAGEmouse.html [ SUCCESS ]
    FANTOMtissueCAGEhuman                   html  
REDIRECT:topic	 FANTOMtissueCAGEhuman -> FANTOMtissueCAGEhuman.html [ SUCCESS ]
    FANTOMtissueCAGEmouse                   html  
REDIRECT:topic	 FANTOMtissueCAGEmouse -> FANTOMtissueCAGEmouse.html [ SUCCESS ]
** 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 'FANTOM3and4CAGE' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'FANTOM3and4CAGE' as FANTOM3and4CAGE_1.27.0.zip
* DONE (FANTOM3and4CAGE)
* installing to library 'D:/biocbuild/bbs-3.13-bioc/R/library'
package 'FANTOM3and4CAGE' successfully unpacked and MD5 sums checked

Tests output


Example timings

FANTOM3and4CAGE.Rcheck/examples_i386/FANTOM3and4CAGE-Ex.timings

nameusersystemelapsed
FANTOMhumanSamples0.000.020.01
FANTOMmouseSamples000
FANTOMtimecourseCAGEhuman2.910.093.00
FANTOMtimecourseCAGEmouse0.200.050.25
FANTOMtissueCAGEhuman6.670.156.83
FANTOMtissueCAGEmouse2.600.212.79

FANTOM3and4CAGE.Rcheck/examples_x64/FANTOM3and4CAGE-Ex.timings

nameusersystemelapsed
FANTOMhumanSamples0.020.000.02
FANTOMmouseSamples000
FANTOMtimecourseCAGEhuman2.370.062.44
FANTOMtimecourseCAGEmouse0.180.020.19
FANTOMtissueCAGEhuman5.150.225.38
FANTOMtissueCAGEmouse2.050.152.20