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CHECK report for SpikeInSubset on malbec2

This page was generated on 2021-01-21 16:01:22 -0500 (Thu, 21 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE SpikeInSubset PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 344/386HostnameOS / ArchINSTALLBUILDCHECK
SpikeInSubset 1.31.0
Rafael A. Irizarry
Snapshot Date: 2021-01-21 09:00:14 -0500 (Thu, 21 Jan 2021)
URL: https://git.bioconductor.org/packages/SpikeInSubset
Branch: master
Last Commit: a23e23d
Last Changed Date: 2020-10-27 09:47:05 -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: SpikeInSubset
Version: 1.31.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:SpikeInSubset.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings SpikeInSubset_1.31.0.tar.gz
StartedAt: 2021-01-21 12:50:21 -0500 (Thu, 21 Jan 2021)
EndedAt: 2021-01-21 12:51:58 -0500 (Thu, 21 Jan 2021)
EllapsedTime: 96.9 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: SpikeInSubset.Rcheck
Warnings: 3

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:SpikeInSubset.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings SpikeInSubset_1.31.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-data-experiment/meat/SpikeInSubset.Rcheck’
* using R Under development (unstable) (2021-01-05 r79797)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SpikeInSubset/DESCRIPTION’ ... OK
* this is package ‘SpikeInSubset’ version ‘1.31.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘SpikeInSubset’ can be installed ... WARNING
Found the following significant warnings:
  Warning: /home/biocbuild/bbs-3.13-data-experiment/meat/SpikeInSubset/man/xhyb.Rd: docType ‘instance’ is unrecognized
See ‘/home/biocbuild/bbs-3.13-data-experiment/meat/SpikeInSubset.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is 20.5Mb
  sub-directories of 1Mb or more:
    data  20.4Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
* 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
Packages in Depends field not imported from:
  ‘Biobase’ ‘affy’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* 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 ... WARNING
prepare_Rd: xhyb.Rd: docType ‘instance’ is unrecognized
* 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 ... WARNING
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                           old_size new_size compress
  hgu133a.spikein.xhyb.rda     12Kb      2Kb     gzip
  mas133.rda                  2.2Mb    992Kb       xz
  mas95.rda                   1.3Mb    573Kb       xz
  rma133.rda                  2.2Mb    899Kb       xz
  rma95.rda                   1.3Mb    522Kb       xz
  spikein133.rda              7.3Mb    4.3Mb       xz
  spikein95.rda               6.1Mb    3.6Mb       xz
* checking examples ... NONE
* checking PDF version of manual ... OK
* DONE

Status: 3 WARNINGs, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.13-data-experiment/meat/SpikeInSubset.Rcheck/00check.log’
for details.



Installation output

SpikeInSubset.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL SpikeInSubset
###
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* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘SpikeInSubset’ ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
Warning: /home/biocbuild/bbs-3.13-data-experiment/meat/SpikeInSubset/man/xhyb.Rd: docType ‘instance’ is unrecognized
*** installing help indices
** 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
* DONE (SpikeInSubset)

Tests output


Example timings