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CHECK report for KEGGdzPathwaysGEO on riesling1

This page was generated on 2021-01-14 15:59:08 -0500 (Thu, 14 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE KEGGdzPathwaysGEO PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 192/385HostnameOS / ArchINSTALLBUILDCHECK
KEGGdzPathwaysGEO 1.29.0
Gaurav Bhatti
Snapshot Date: 2021-01-14 09:00:13 -0500 (Thu, 14 Jan 2021)
URL: https://git.bioconductor.org/packages/KEGGdzPathwaysGEO
Branch: master
Last Commit: 71b93f9
Last Changed Date: 2020-10-27 09:56:50 -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: KEGGdzPathwaysGEO
Version: 1.29.0
Command: D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:KEGGdzPathwaysGEO.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings KEGGdzPathwaysGEO_1.29.0.tar.gz
StartedAt: 2021-01-14 11:24:58 -0500 (Thu, 14 Jan 2021)
EndedAt: 2021-01-14 11:29:04 -0500 (Thu, 14 Jan 2021)
EllapsedTime: 246.0 seconds
RetCode: 0
Status:  OK  
CheckDir: KEGGdzPathwaysGEO.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:KEGGdzPathwaysGEO.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings KEGGdzPathwaysGEO_1.29.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.13-data-experiment/meat/KEGGdzPathwaysGEO.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 'KEGGdzPathwaysGEO/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'KEGGdzPathwaysGEO' 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 'KEGGdzPathwaysGEO' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 300.9Mb
  sub-directories of 1Mb or more:
    data  300.6Mb
* 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 ... NOTE
Namespaces in Imports field not imported from:
  'Biobase' 'BiocGenerics'
  All declared Imports should be used.
* 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: 2 NOTEs
See
  'D:/biocbuild/bbs-3.13-data-experiment/meat/KEGGdzPathwaysGEO.Rcheck/00check.log'
for details.



Installation output

KEGGdzPathwaysGEO.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/KEGGdzPathwaysGEO_1.29.0.tar.gz && rm -rf KEGGdzPathwaysGEO.buildbin-libdir && mkdir KEGGdzPathwaysGEO.buildbin-libdir && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=KEGGdzPathwaysGEO.buildbin-libdir KEGGdzPathwaysGEO_1.29.0.tar.gz && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL KEGGdzPathwaysGEO_1.29.0.zip && rm KEGGdzPathwaysGEO_1.29.0.tar.gz KEGGdzPathwaysGEO_1.29.0.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
  1  300M    1 4777k    0     0  76.4M      0  0:00:03 --:--:--  0:00:03 76.4M
 39  300M   39  117M    0     0   111M      0  0:00:02  0:00:01  0:00:01  111M
 70  300M   70  212M    0     0   102M      0  0:00:02  0:00:02 --:--:--  102M
 83  300M   83  251M    0     0  82.2M      0  0:00:03  0:00:03 --:--:-- 82.2M
100  300M  100  300M    0     0  81.9M      0  0:00:03  0:00:03 --:--:-- 81.9M

install for i386

* installing *source* package 'KEGGdzPathwaysGEO' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'KEGGdzPathwaysGEO'
    finding HTML links ... done
    GSE1297                                 html  
REDIRECT:topic	 GSE1297 -> GSE1297.html [ SUCCESS ]
    GSE14762                                html  
REDIRECT:topic	 GSE14762 -> GSE14762.html [ SUCCESS ]
    GSE15471                                html  
REDIRECT:topic	 GSE15471 -> GSE15471.html [ SUCCESS ]
    GSE16515                                html  
REDIRECT:topic	 GSE16515 -> GSE16515.html [ SUCCESS ]
    GSE18842                                html  
REDIRECT:topic	 GSE18842 -> GSE18842.html [ SUCCESS ]
    GSE19188                                html  
REDIRECT:topic	 GSE19188 -> GSE19188.html [ SUCCESS ]
    GSE19728                                html  
REDIRECT:topic	 GSE19728 -> GSE19728.html [ SUCCESS ]
    GSE20153                                html  
REDIRECT:topic	 GSE20153 -> GSE20153.html [ SUCCESS ]
    GSE20291                                html  
REDIRECT:topic	 GSE20291 -> GSE20291.html [ SUCCESS ]
    GSE21354                                html  
REDIRECT:topic	 GSE21354 -> GSE21354.html [ SUCCESS ]
    GSE3467                                 html  
REDIRECT:topic	 GSE3467 -> GSE3467.html [ SUCCESS ]
    GSE3585                                 html  
REDIRECT:topic	 GSE3585 -> GSE3585.html [ SUCCESS ]
    GSE3678                                 html  
REDIRECT:topic	 GSE3678 -> GSE3678.html [ SUCCESS ]
    GSE4107                                 html  
REDIRECT:topic	 GSE4107 -> GSE4107.html [ SUCCESS ]
    GSE5281_EC                              html  
REDIRECT:topic	 GSE5281_EC -> GSE5281_EC.html [ SUCCESS ]
    GSE5281_HIP                             html  
REDIRECT:topic	 GSE5281_HIP -> GSE5281_HIP.html [ SUCCESS ]
    GSE5281_VCX                             html  
REDIRECT:topic	 GSE5281_VCX -> GSE5281_VCX.html [ SUCCESS ]
    GSE6956AA                               html  
REDIRECT:topic	 GSE6956AA -> GSE6956AA.html [ SUCCESS ]
    GSE6956C                                html  
REDIRECT:topic	 GSE6956C -> GSE6956C.html [ SUCCESS ]
    GSE781                                  html  
REDIRECT:topic	 GSE781 -> GSE781.html [ SUCCESS ]
    GSE8671                                 html  
REDIRECT:topic	 GSE8671 -> GSE8671.html [ SUCCESS ]
    GSE8762                                 html  
REDIRECT:topic	 GSE8762 -> GSE8762.html [ SUCCESS ]
    GSE9348                                 html  
REDIRECT:topic	 GSE9348 -> GSE9348.html [ SUCCESS ]
    GSE9476                                 html  
REDIRECT:topic	 GSE9476 -> GSE9476.html [ SUCCESS ]
    KEGGdzPathwaysGEO-package               html  
REDIRECT:topic	 KEGGdzPathwaysGEO-package -> KEGGdzPathwaysGEO-package.html [ SUCCESS ]
REDIRECT:topic	 KEGGdzPathwaysGEO -> KEGGdzPathwaysGEO-package.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 'KEGGdzPathwaysGEO' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'KEGGdzPathwaysGEO' as KEGGdzPathwaysGEO_1.29.0.zip
* DONE (KEGGdzPathwaysGEO)
* installing to library 'D:/biocbuild/bbs-3.13-bioc/R/library'
package 'KEGGdzPathwaysGEO' successfully unpacked and MD5 sums checked

Tests output


Example timings

KEGGdzPathwaysGEO.Rcheck/examples_i386/KEGGdzPathwaysGEO-Ex.timings

nameusersystemelapsed
GSE12970.040.000.05
GSE147620.110.000.10
GSE154710.220.020.24
GSE165150.110.010.13
GSE188420.270.030.30
GSE191880.480.040.51
GSE197280.10.00.1
GSE201530.070.000.08
GSE202910.070.000.06
GSE213540.090.000.10
GSE34670.090.000.09
GSE35850.030.000.03
GSE36780.070.000.06
GSE41070.110.000.11
GSE5281_EC0.090.000.10
GSE5281_HIP0.110.000.11
GSE5281_VCX0.110.000.11
GSE6956AA0.040.000.03
GSE6956C0.060.000.06
GSE7810.030.000.03
GSE86710.220.000.22
GSE87620.110.000.11
GSE93480.280.000.28
GSE94760.090.000.09
KEGGdzPathwaysGEO-package0.250.020.27

KEGGdzPathwaysGEO.Rcheck/examples_x64/KEGGdzPathwaysGEO-Ex.timings

nameusersystemelapsed
GSE12970.050.000.05
GSE147620.080.020.09
GSE154710.190.010.20
GSE165150.110.000.11
GSE188420.250.020.26
GSE191880.410.060.47
GSE197280.070.000.08
GSE201530.070.000.06
GSE202910.030.020.05
GSE213540.090.000.09
GSE34670.080.000.08
GSE35850.030.000.03
GSE36780.060.010.08
GSE41070.100.000.09
GSE5281_EC0.070.000.08
GSE5281_HIP0.110.000.10
GSE5281_VCX0.100.020.11
GSE6956AA0.020.000.02
GSE6956C0.060.000.06
GSE7810.030.000.03
GSE86710.190.000.19
GSE87620.070.010.10
GSE93480.220.040.25
GSE94760.080.000.08
KEGGdzPathwaysGEO-package0.200.030.24