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CHECK report for seqc on riesling1

This page was generated on 2021-01-18 15:58:51 -0500 (Mon, 18 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE seqc PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 326/385HostnameOS / ArchINSTALLBUILDCHECK
seqc 1.25.0
Yang Liao and Wei Shi
Snapshot Date: 2021-01-18 09:00:15 -0500 (Mon, 18 Jan 2021)
URL: https://git.bioconductor.org/packages/seqc
Branch: master
Last Commit: 4c8ffe8
Last Changed Date: 2020-10-27 10:10:46 -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 [ WARNINGS ]

Summary

Package: seqc
Version: 1.25.0
Command: D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:seqc.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings seqc_1.25.0.tar.gz
StartedAt: 2021-01-18 11:44:46 -0500 (Mon, 18 Jan 2021)
EndedAt: 2021-01-18 11:46:07 -0500 (Mon, 18 Jan 2021)
EllapsedTime: 81.7 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: seqc.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:seqc.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings seqc_1.25.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.13-data-experiment/meat/seqc.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 'seqc/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'seqc' version '1.25.0'
* 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 'seqc' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: Previous alias or file overwritten by alias: seqc-package
  Rd warning: Previous alias or file overwritten by alias: seqc
See 'D:/biocbuild/bbs-3.13-data-experiment/meat/seqc.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is 306.8Mb
  sub-directories of 1Mb or more:
    data  306.6Mb
* 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 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/seqc.Rcheck/00check.log'
for details.



Installation output

seqc.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/seqc_1.25.0.tar.gz && rm -rf seqc.buildbin-libdir && mkdir seqc.buildbin-libdir && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=seqc.buildbin-libdir seqc_1.25.0.tar.gz && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL seqc_1.25.0.zip && rm seqc_1.25.0.tar.gz seqc_1.25.0.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
  5  178M    5 10.1M    0     0  79.7M      0  0:00:02 --:--:--  0:00:02 79.0M
 66  178M   66  118M    0     0   104M      0  0:00:01  0:00:01 --:--:--  104M
100  178M  100  178M    0     0   105M      0  0:00:01  0:00:01 --:--:--  105M

install for i386

* installing *source* package 'seqc' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'seqc'
    finding HTML links ... done
    FCData                                  html  
REDIRECT:topic	 ILM_aceview_gene_AGR -> FCData.html [ SUCCESS ]
REDIRECT:topic	 ILM_aceview_gene_BGI -> FCData.html [ SUCCESS ]
REDIRECT:topic	 ILM_aceview_gene_CNL -> FCData.html [ SUCCESS ]
REDIRECT:topic	 ILM_aceview_gene_COH -> FCData.html [ SUCCESS ]
REDIRECT:topic	 ILM_aceview_gene_MAY -> FCData.html [ SUCCESS ]
REDIRECT:topic	 ILM_aceview_gene_NVS -> FCData.html [ SUCCESS ]
REDIRECT:topic	 ILM_refseq_gene_AGR -> FCData.html [ SUCCESS ]
REDIRECT:topic	 ILM_refseq_gene_BGI -> FCData.html [ SUCCESS ]
REDIRECT:topic	 ILM_refseq_gene_CNL -> FCData.html [ SUCCESS ]
REDIRECT:topic	 ILM_refseq_gene_COH -> FCData.html [ SUCCESS ]
REDIRECT:topic	 ILM_refseq_gene_MAY -> FCData.html [ SUCCESS ]
REDIRECT:topic	 ILM_refseq_gene_NVS -> FCData.html [ SUCCESS ]
REDIRECT:topic	 LIF_aceview_gene_LIV -> FCData.html [ SUCCESS ]
REDIRECT:topic	 LIF_aceview_gene_NWU -> FCData.html [ SUCCESS ]
REDIRECT:topic	 LIF_aceview_gene_PSU -> FCData.html [ SUCCESS ]
REDIRECT:topic	 LIF_aceview_gene_SQW -> FCData.html [ SUCCESS ]
REDIRECT:topic	 LIF_refseq_gene_LIV -> FCData.html [ SUCCESS ]
REDIRECT:topic	 LIF_refseq_gene_NWU -> FCData.html [ SUCCESS ]
REDIRECT:topic	 LIF_refseq_gene_PSU -> FCData.html [ SUCCESS ]
REDIRECT:topic	 LIF_refseq_gene_SQW -> FCData.html [ SUCCESS ]
REDIRECT:topic	 ROC_aceview_gene_MGP -> FCData.html [ SUCCESS ]
REDIRECT:topic	 ROC_aceview_gene_NYU -> FCData.html [ SUCCESS ]
REDIRECT:topic	 ROC_aceview_gene_SQW -> FCData.html [ SUCCESS ]
REDIRECT:topic	 ROC_refseq_gene_MGP -> FCData.html [ SUCCESS ]
REDIRECT:topic	 ROC_refseq_gene_NYU -> FCData.html [ SUCCESS ]
REDIRECT:topic	 ROC_refseq_gene_SQW -> FCData.html [ SUCCESS ]
REDIRECT:file	 FCData.html -> FCData.html [ SUCCESS ]
    FCJunctions                             html  
REDIRECT:topic	 ILM_junction_AGR_A -> FCJunctions.html [ SUCCESS ]
REDIRECT:topic	 ILM_junction_AGR_B -> FCJunctions.html [ SUCCESS ]
REDIRECT:topic	 ILM_junction_AGR_C -> FCJunctions.html [ SUCCESS ]
REDIRECT:topic	 ILM_junction_AGR_D -> FCJunctions.html [ SUCCESS ]
REDIRECT:topic	 ILM_junction_BGI_A -> FCJunctions.html [ SUCCESS ]
REDIRECT:topic	 ILM_junction_BGI_B -> FCJunctions.html [ SUCCESS ]
REDIRECT:topic	 ILM_junction_BGI_C -> FCJunctions.html [ SUCCESS ]
REDIRECT:topic	 ILM_junction_BGI_D -> FCJunctions.html [ SUCCESS ]
REDIRECT:topic	 ILM_junction_CNL_A -> FCJunctions.html [ SUCCESS ]
REDIRECT:topic	 ILM_junction_CNL_B -> FCJunctions.html [ SUCCESS ]
REDIRECT:topic	 ILM_junction_CNL_C -> FCJunctions.html [ SUCCESS ]
REDIRECT:topic	 ILM_junction_CNL_D -> FCJunctions.html [ SUCCESS ]
REDIRECT:topic	 ILM_junction_COH_A -> FCJunctions.html [ SUCCESS ]
REDIRECT:topic	 ILM_junction_COH_B -> FCJunctions.html [ SUCCESS ]
REDIRECT:topic	 ILM_junction_COH_C -> FCJunctions.html [ SUCCESS ]
REDIRECT:topic	 ILM_junction_COH_D -> FCJunctions.html [ SUCCESS ]
REDIRECT:topic	 ILM_junction_MAY_A -> FCJunctions.html [ SUCCESS ]
REDIRECT:topic	 ILM_junction_MAY_B -> FCJunctions.html [ SUCCESS ]
REDIRECT:topic	 ILM_junction_MAY_C -> FCJunctions.html [ SUCCESS ]
REDIRECT:topic	 ILM_junction_MAY_D -> FCJunctions.html [ SUCCESS ]
REDIRECT:topic	 ILM_junction_NVS_A -> FCJunctions.html [ SUCCESS ]
REDIRECT:topic	 ILM_junction_NVS_B -> FCJunctions.html [ SUCCESS ]
REDIRECT:topic	 ILM_junction_NVS_C -> FCJunctions.html [ SUCCESS ]
REDIRECT:topic	 ILM_junction_NVS_D -> FCJunctions.html [ SUCCESS ]
REDIRECT:topic	 LIF_junction_LIV_A -> FCJunctions.html [ SUCCESS ]
REDIRECT:topic	 LIF_junction_LIV_B -> FCJunctions.html [ SUCCESS ]
REDIRECT:topic	 LIF_junction_LIV_C -> FCJunctions.html [ SUCCESS ]
REDIRECT:topic	 LIF_junction_LIV_D -> FCJunctions.html [ SUCCESS ]
REDIRECT:topic	 LIF_junction_NWU_A -> FCJunctions.html [ SUCCESS ]
REDIRECT:topic	 LIF_junction_NWU_B -> FCJunctions.html [ SUCCESS ]
REDIRECT:topic	 LIF_junction_NWU_C -> FCJunctions.html [ SUCCESS ]
REDIRECT:topic	 LIF_junction_NWU_D -> FCJunctions.html [ SUCCESS ]
REDIRECT:topic	 LIF_junction_PSU_A -> FCJunctions.html [ SUCCESS ]
REDIRECT:topic	 LIF_junction_PSU_B -> FCJunctions.html [ SUCCESS ]
REDIRECT:topic	 LIF_junction_PSU_C -> FCJunctions.html [ SUCCESS ]
REDIRECT:topic	 LIF_junction_PSU_D -> FCJunctions.html [ SUCCESS ]
REDIRECT:topic	 LIF_junction_SQW_A -> FCJunctions.html [ SUCCESS ]
REDIRECT:topic	 LIF_junction_SQW_B -> FCJunctions.html [ SUCCESS ]
REDIRECT:topic	 LIF_junction_SQW_C -> FCJunctions.html [ SUCCESS ]
REDIRECT:topic	 LIF_junction_SQW_D -> FCJunctions.html [ SUCCESS ]
REDIRECT:topic	 ROC_junction_MGP_A -> FCJunctions.html [ SUCCESS ]
REDIRECT:topic	 ROC_junction_MGP_B -> FCJunctions.html [ SUCCESS ]
REDIRECT:topic	 ROC_junction_NYU_A -> FCJunctions.html [ SUCCESS ]
REDIRECT:topic	 ROC_junction_NYU_B -> FCJunctions.html [ SUCCESS ]
REDIRECT:topic	 ROC_junction_SQW_A -> FCJunctions.html [ SUCCESS ]
REDIRECT:topic	 ROC_junction_SQW_B -> FCJunctions.html [ SUCCESS ]
REDIRECT:file	 FCJunctions.html -> FCJunctions.html [ SUCCESS ]
    SEQC-package                            html  
REDIRECT:topic	 SEQC-package -> SEQC-package.html [ SUCCESS ]
REDIRECT:topic	 seqc-package -> SEQC-package.html [ SUCCESS ]
REDIRECT:topic	 SEQC -> SEQC-package.html [ SUCCESS ]
REDIRECT:topic	 seqc -> SEQC-package.html [ SUCCESS ]
Rd warning: Previous alias or file overwritten by alias: seqc-package
Rd warning: Previous alias or file overwritten by alias: seqc
    seqc.eSet                               html  
REDIRECT:topic	 seqc.eSet -> seqc.eSet.html [ SUCCESS ]
    seqc.samples                            html  
REDIRECT:topic	 seqc.samples -> seqc.samples.html [ SUCCESS ]
    taqman                                  html  
REDIRECT:topic	 taqman -> taqman.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 'seqc' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'seqc' as seqc_1.25.0.zip
* DONE (seqc)
* installing to library 'D:/biocbuild/bbs-3.13-bioc/R/library'
package 'seqc' successfully unpacked and MD5 sums checked

Tests output


Example timings

seqc.Rcheck/examples_i386/seqc-Ex.timings

nameusersystemelapsed
FCData0.390.050.43
FCJunctions000
SEQC-package000
taqman0.020.000.01

seqc.Rcheck/examples_x64/seqc-Ex.timings

nameusersystemelapsed
FCData0.350.080.44
FCJunctions000
SEQC-package0.020.000.02
taqman000