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This page was generated on 2022-01-24 13:06:20 -0500 (Mon, 24 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4080
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4141
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for goseq on tokay2


To the developers/maintainers of the goseq package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/goseq.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 803/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
goseq 1.46.0  (landing page)
Matthew Young , Nadia Davidson
Snapshot Date: 2022-01-23 01:55:04 -0500 (Sun, 23 Jan 2022)
git_url: https://git.bioconductor.org/packages/goseq
git_branch: RELEASE_3_14
git_last_commit: 1fb5626
git_last_commit_date: 2021-10-26 11:55:51 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: goseq
Version: 1.46.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:goseq.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings goseq_1.46.0.tar.gz
StartedAt: 2022-01-23 20:18:17 -0500 (Sun, 23 Jan 2022)
EndedAt: 2022-01-23 20:25:19 -0500 (Sun, 23 Jan 2022)
EllapsedTime: 422.3 seconds
RetCode: 0
Status:   OK  
CheckDir: goseq.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:goseq.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings goseq_1.46.0.tar.gz
###
##############################################################################
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/goseq.Rcheck'
* using R version 4.1.2 (2021-11-01)
* 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 '1.46.0'
* 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 (user + system) or elapsed time > 5s
           user system elapsed
goseq     27.93   2.64   30.61
nullp      9.89   1.45   11.35
getgo      9.87   0.53   10.41
getlength  7.34   2.16   12.52
plotPWF    6.89   1.39    8.28
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
goseq     23.10   1.60   24.73
getgo     10.97   0.77   11.73
nullp      6.06   1.12    7.19
plotPWF    5.83   0.86    6.68
getlength  5.25   1.09    6.34
* 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-3.14-bioc/meat/goseq.Rcheck/00check.log'
for details.



Installation output

goseq.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/goseq_1.46.0.tar.gz && rm -rf goseq.buildbin-libdir && mkdir goseq.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=goseq.buildbin-libdir goseq_1.46.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL goseq_1.46.0.zip && rm goseq_1.46.0.tar.gz goseq_1.46.0.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
100  465k  100  465k    0     0  1269k      0 --:--:-- --:--:-- --:--:-- 1272k

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_1.46.0.zip
* DONE (goseq)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'goseq' successfully unpacked and MD5 sums checked

Tests output


Example timings

goseq.Rcheck/examples_i386/goseq-Ex.timings

nameusersystemelapsed
genes0.020.000.01
getgo 9.87 0.5310.41
getlength 7.34 2.1612.52
goseq27.93 2.6430.61
makespline0.090.000.09
nullp 9.89 1.4511.35
plotPWF6.891.398.28
supportedOrganisms0.560.003.56

goseq.Rcheck/examples_x64/goseq-Ex.timings

nameusersystemelapsed
genes0.010.000.02
getgo10.97 0.7711.73
getlength5.251.096.34
goseq23.10 1.6024.73
makespline0.110.000.11
nullp6.061.127.19
plotPWF5.830.866.68
supportedOrganisms0.570.023.29