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CHECK report for seq2pathway.data on riesling1

This page was generated on 2021-01-21 16:01:38 -0500 (Thu, 21 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE seq2pathway.data PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 326/386HostnameOS / ArchINSTALLBUILDCHECK
seq2pathway.data 1.23.0
Xinan Holly Yang
Snapshot Date: 2021-01-21 09:00:14 -0500 (Thu, 21 Jan 2021)
URL: https://git.bioconductor.org/packages/seq2pathway.data
Branch: master
Last Commit: 88fe5e9
Last Changed Date: 2020-10-27 10:11:18 -0500 (Tue, 27 Oct 2020)
malbec2 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK [ WARNINGS ]

Summary

Package: seq2pathway.data
Version: 1.23.0
Command: D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:seq2pathway.data.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings seq2pathway.data_1.23.0.tar.gz
StartedAt: 2021-01-21 11:46:40 -0500 (Thu, 21 Jan 2021)
EndedAt: 2021-01-21 11:47:11 -0500 (Thu, 21 Jan 2021)
EllapsedTime: 31.2 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: seq2pathway.data.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:seq2pathway.data.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings seq2pathway.data_1.23.0.tar.gz
###
##############################################################################
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* using log directory 'D:/biocbuild/bbs-3.13-data-experiment/meat/seq2pathway.data.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 'seq2pathway.data/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'seq2pathway.data' version '1.23.0'
* 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 'seq2pathway.data' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 226.0Mb
  sub-directories of 1Mb or more:
    data       4.3Mb
    extdata  221.4Mb
* 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 ... WARNING
File 'data/datalist' contains malformed line(s):
  '' ''
* 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
** 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, 1 NOTE
See
  'D:/biocbuild/bbs-3.13-data-experiment/meat/seq2pathway.data.Rcheck/00check.log'
for details.



Installation output

seq2pathway.data.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/seq2pathway.data_1.23.0.tar.gz && rm -rf seq2pathway.data.buildbin-libdir && mkdir seq2pathway.data.buildbin-libdir && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=seq2pathway.data.buildbin-libdir seq2pathway.data_1.23.0.tar.gz && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL seq2pathway.data_1.23.0.zip && rm seq2pathway.data_1.23.0.tar.gz seq2pathway.data_1.23.0.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
  3 49.5M    3 1659k    0     0  1817k      0  0:00:27 --:--:--  0:00:27 1815k
  6 49.5M    6 3239k    0     0  1651k      0  0:00:30  0:00:01  0:00:29 1650k
  9 49.5M    9 4999k    0     0  1679k      0  0:00:30  0:00:02  0:00:28 1679k
 14 49.5M   14 7559k    0     0  1878k      0  0:00:26  0:00:04  0:00:22 1878k
 18 49.5M   18 9365k    0     0  1845k      0  0:00:27  0:00:05  0:00:22 1845k
 24 49.5M   24 12.1M    0     0  1914k      0  0:00:26  0:00:06  0:00:20 1930k
 26 49.5M   26 12.8M    0     0  1905k      0  0:00:26  0:00:06  0:00:20 2005k
 60 49.5M   60 29.9M    0     0  3871k      0  0:00:13  0:00:07  0:00:06 5192k
 92 49.5M   92 46.0M    0     0  5191k      0  0:00:09  0:00:09 --:--:-- 7829k
100 49.5M  100 49.5M    0     0  5524k      0  0:00:09  0:00:09 --:--:--  9.8M

install for i386

* installing *source* package 'seq2pathway.data' ...
** using staged installation
** data
** inst
** help
*** installing help indices
  converting help for package 'seq2pathway.data'
    finding HTML links ... done
    Des_BP_list                             html  
REDIRECT:topic	 Des_BP_list -> Des_BP_list.html [ SUCCESS ]
    Des_CC_list                             html  
REDIRECT:topic	 Des_CC_list -> Des_CC_list.html [ SUCCESS ]
    Des_MF_list                             html  
REDIRECT:topic	 Des_MF_list -> Des_MF_list.html [ SUCCESS ]
    GO_BP_list                              html  
REDIRECT:topic	 GO_BP_list -> GO_BP_list.html [ SUCCESS ]
    GO_CC_list                              html  
REDIRECT:topic	 GO_CC_list -> GO_CC_list.html [ SUCCESS ]
    GO_GENCODE_df_hg_v19                    html  
REDIRECT:topic	 GO_GENCODE_df_hg_v19 -> GO_GENCODE_df_hg_v19.html [ SUCCESS ]
    GO_GENCODE_df_hg_v20                    html  
REDIRECT:topic	 GO_GENCODE_df_hg_v20 -> GO_GENCODE_df_hg_v20.html [ SUCCESS ]
    GO_GENCODE_df_mm_vM1                    html  
REDIRECT:topic	 GO_GENCODE_df_mm_vM1 -> GO_GENCODE_df_mm_vM1.html [ SUCCESS ]
    GO_GENCODE_df_mm_vM3                    html  
REDIRECT:topic	 GO_GENCODE_df_mm_vM3 -> GO_GENCODE_df_mm_vM3.html [ SUCCESS ]
    GO_GENCODE_df_mm_vM4                    html  
REDIRECT:topic	 GO_GENCODE_df_mm_vM4 -> GO_GENCODE_df_mm_vM4.html [ SUCCESS ]
    GO_MF_list                              html  
REDIRECT:topic	 GO_MF_list -> GO_MF_list.html [ SUCCESS ]
    MsigDB_C5                               html  
REDIRECT:topic	 MsigDB_C5 -> MsigDB_C5.html [ SUCCESS ]
    Msig_GENCODE_df_hg_v19                  html  
REDIRECT:topic	 Msig_GENCODE_df_hg_v19 -> Msig_GENCODE_df_hg_v19.html [ SUCCESS ]
    Msig_GENCODE_df_hg_v20                  html  
REDIRECT:topic	 Msig_GENCODE_df_hg_v20 -> Msig_GENCODE_df_hg_v20.html [ SUCCESS ]
    Msig_GENCODE_df_mm_vM1                  html  
REDIRECT:topic	 Msig_GENCODE_df_mm_vM1 -> Msig_GENCODE_df_mm_vM1.html [ SUCCESS ]
    Msig_GENCODE_df_mm_vM3                  html  
REDIRECT:topic	 Msig_GENCODE_df_mm_vM3 -> Msig_GENCODE_df_mm_vM3.html [ SUCCESS ]
    Msig_GENCODE_df_mm_vM4                  html  
REDIRECT:topic	 Msig_GENCODE_df_mm_vM4 -> Msig_GENCODE_df_mm_vM4.html [ SUCCESS ]
    dat_gene2path_RNA                       html  
REDIRECT:topic	 dat_gene2path_RNA -> dat_gene2path_RNA.html [ SUCCESS ]
    dat_gene2path_chip                      html  
REDIRECT:topic	 dat_gene2path_chip -> dat_gene2path_chip.html [ SUCCESS ]
    dat_seq2pathway_GOterms                 html  
REDIRECT:topic	 dat_seq2pathway_GOterms -> dat_seq2pathway_GOterms.html [ SUCCESS ]
    dat_seq2pathway_Msig                    html  
REDIRECT:topic	 dat_seq2pathway_Msig -> dat_seq2pathway_Msig.html [ SUCCESS ]
    gencode_coding                          html  
REDIRECT:topic	 gencode_coding -> gencode_coding.html [ SUCCESS ]
    gene_description                        html  
REDIRECT:topic	 gene_description -> gene_description.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 'seq2pathway.data' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'seq2pathway.data' as seq2pathway.data_1.23.0.zip
* DONE (seq2pathway.data)
* installing to library 'D:/biocbuild/bbs-3.13-bioc/R/library'
package 'seq2pathway.data' successfully unpacked and MD5 sums checked

Tests output


Example timings

seq2pathway.data.Rcheck/examples_i386/seq2pathway.data-Ex.timings

nameusersystemelapsed
Des_BP_list0.050.000.05
Des_CC_list0.020.000.02
Des_MF_list0.050.020.06
GO_BP_list0.060.010.08
GO_CC_list0.060.160.22
GO_GENCODE_df_hg_v190.020.000.02
GO_GENCODE_df_hg_v200.010.000.02
GO_GENCODE_df_mm_vM10.020.000.01
GO_GENCODE_df_mm_vM30.000.010.02
GO_GENCODE_df_mm_vM4000
GO_MF_list0.030.000.03
Msig_GENCODE_df_hg_v190.020.020.03
Msig_GENCODE_df_hg_v200.010.010.03
Msig_GENCODE_df_mm_vM10.020.000.02
Msig_GENCODE_df_mm_vM30.000.020.02
Msig_GENCODE_df_mm_vM4000
gencode_coding0.080.000.08

seq2pathway.data.Rcheck/examples_x64/seq2pathway.data-Ex.timings

nameusersystemelapsed
Des_BP_list0.030.000.03
Des_CC_list0.020.010.03
Des_MF_list0.020.030.04
GO_BP_list0.040.020.07
GO_CC_list0.100.090.18
GO_GENCODE_df_hg_v190.030.000.03
GO_GENCODE_df_hg_v200.010.000.02
GO_GENCODE_df_mm_vM10.020.000.02
GO_GENCODE_df_mm_vM30.000.020.01
GO_GENCODE_df_mm_vM40.010.000.02
GO_MF_list0.020.010.03
Msig_GENCODE_df_hg_v190.020.020.03
Msig_GENCODE_df_hg_v200.010.000.02
Msig_GENCODE_df_mm_vM10.000.020.02
Msig_GENCODE_df_mm_vM30.020.000.01
Msig_GENCODE_df_mm_vM40.010.000.02
gencode_coding0.080.000.08