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CHECK report for goseq on malbec2

This page was generated on 2020-10-17 11:54:53 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE goseq PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 755/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
goseq 1.40.0
Matthew Young , Nadia Davidson
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/goseq
Branch: RELEASE_3_11
Last Commit: 55b1180
Last Changed Date: 2020-04-27 14:21:52 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: goseq
Version: 1.40.0
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:goseq.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings goseq_1.40.0.tar.gz
StartedAt: 2020-10-17 01:54:07 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 02:00:46 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 399.2 seconds
RetCode: 0
Status:  OK 
CheckDir: goseq.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:goseq.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings goseq_1.40.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/goseq.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘goseq/DESCRIPTION’ ... OK
* this is package ‘goseq’ version ‘1.40.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘goseq’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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
'library' or 'require' call to ‘rtracklayer’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
getlength: no visible global function definition for
  ‘installed.packages’
getlength: no visible global function definition for ‘tail’
getlength: no visible global function definition for
  ‘transcriptLengths’
getlength: no visible global function definition for ‘browserSession’
getlength: no visible global function definition for ‘genome<-’
getlength: no visible global function definition for ‘ucscTableQuery’
getlength: no visible global function definition for ‘getTable’
makespline: no visible global function definition for ‘show’
supportedOrganisms: no visible global function definition for
  ‘ucscGenomes’
Undefined global functions or variables:
  browserSession genome<- getTable installed.packages show tail
  transcriptLengths ucscGenomes ucscTableQuery
Consider adding
  importFrom("methods", "show")
  importFrom("utils", "installed.packages", "tail")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
goseq     32.620  0.372  33.254
getgo     12.167  0.450  12.739
getlength  9.018  0.563  45.672
nullp      8.121  0.184   8.307
plotPWF    5.537  0.136   5.676
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.11-bioc/meat/goseq.Rcheck/00check.log’
for details.



Installation output

goseq.Rcheck/00install.out

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### Running command:
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###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL goseq
###
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘goseq’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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
* DONE (goseq)

Tests output


Example timings

goseq.Rcheck/goseq-Ex.timings

nameusersystemelapsed
genes0.0310.0000.030
getgo12.167 0.45012.739
getlength 9.018 0.56345.672
goseq32.620 0.37233.254
makespline0.0930.0000.092
nullp8.1210.1848.307
plotPWF5.5370.1365.676
supportedOrganisms0.5200.0004.637