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CHECK report for goseq on tokay2

This page was generated on 2019-10-16 12:23:41 -0400 (Wed, 16 Oct 2019).

Package 698/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
goseq 1.36.0
Matthew Young , Nadia Davidson
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/goseq
Branch: RELEASE_3_9
Last Commit: 26c9f7d
Last Changed Date: 2019-05-02 11:53:14 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 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
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: goseq
Version: 1.36.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:goseq.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings goseq_1.36.0.tar.gz
StartedAt: 2019-10-16 04:09:19 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 04:16:48 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 449.0 seconds
RetCode: 0
Status:  OK  
CheckDir: goseq.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:goseq.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings goseq_1.36.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/goseq.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'goseq/DESCRIPTION' ... OK
* this is package 'goseq' version '1.36.0'
* 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 '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
* 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
'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
.onAttach: no visible global function definition for 'winMenuAddItem'
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 winMenuAddItem
Consider adding
  importFrom("methods", "show")
  importFrom("utils", "installed.packages", "tail", "winMenuAddItem")
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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
goseq              31.79   2.00   33.83
getgo              10.83   0.87   11.71
nullp               7.90   1.44    9.35
plotPWF             6.88   1.35    8.23
getlength           5.32   2.48    7.89
supportedOrganisms  0.40   0.01    5.42
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
goseq              33.08   1.65   34.72
getgo              14.14   0.98   15.13
nullp               9.43   1.29   10.73
plotPWF             5.87   1.21    9.83
getlength           5.71   1.23    6.94
supportedOrganisms  0.44   0.01    5.72
* 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
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/goseq.Rcheck/00check.log'
for details.



Installation output

goseq.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/goseq_1.36.0.tar.gz && rm -rf goseq.buildbin-libdir && mkdir goseq.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=goseq.buildbin-libdir goseq_1.36.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL goseq_1.36.0.zip && rm goseq_1.36.0.tar.gz goseq_1.36.0.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
100  466k  100  466k    0     0  7061k      0 --:--:-- --:--:-- --:--:-- 7909k

install for i386

* installing *source* package 'goseq' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'goseq'
    finding HTML links ... done
    genes                                   html  
    getgo                                   html  
    finding level-2 HTML links ... done

    getlength                               html  
    goseq                                   html  
    makespline                              html  
    nullp                                   html  
    plotPWF                                 html  
    supportedOrganisms                      html  
** 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 'goseq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'goseq' as goseq_1.36.0.zip
* DONE (goseq)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'goseq' successfully unpacked and MD5 sums checked

Tests output


Example timings

goseq.Rcheck/examples_i386/goseq-Ex.timings

nameusersystemelapsed
genes0.050.000.04
getgo10.83 0.8711.71
getlength5.322.487.89
goseq31.79 2.0033.83
makespline0.070.000.06
nullp7.901.449.35
plotPWF6.881.358.23
supportedOrganisms0.400.015.42

goseq.Rcheck/examples_x64/goseq-Ex.timings

nameusersystemelapsed
genes0.030.000.03
getgo14.14 0.9815.13
getlength5.711.236.94
goseq33.08 1.6534.72
makespline0.090.000.09
nullp 9.43 1.2910.73
plotPWF5.871.219.83
supportedOrganisms0.440.015.72